From dfce093301f0da2ef39fc41975ca24288e5e8625 Mon Sep 17 00:00:00 2001 From: admin Date: Wed, 30 Oct 2024 06:45:28 +0000 Subject: [PATCH] Jenkins update build 216. --- automated_tool_installation_log.tsv | 17 + staging.gvl.org.au/annotation.yml | 140 ++++---- staging.gvl.org.au/assembly.yml | 255 +++++++-------- staging.gvl.org.au/bacterial_typing.yml | 8 +- staging.gvl.org.au/bb_tools.yml | 8 +- staging.gvl.org.au/bed.yml | 14 +- staging.gvl.org.au/blast.yml | 18 +- staging.gvl.org.au/chemicaltoolbox.yml | 66 ++-- staging.gvl.org.au/chip_seq.yml | 16 +- staging.gvl.org.au/collection_operations.yml | 14 +- staging.gvl.org.au/convert_formats.yml | 52 +-- staging.gvl.org.au/deeptools.yml | 112 +++---- staging.gvl.org.au/dna_metabarcoding.yml | 8 +- staging.gvl.org.au/emboss.yml | 6 +- staging.gvl.org.au/epigenetics.yml | 6 +- staging.gvl.org.au/fastafastq.yml | 122 +++---- staging.gvl.org.au/fastq_quality_control.yml | 38 +-- staging.gvl.org.au/filter_and_sort.yml | 2 +- staging.gvl.org.au/gemini_tools.yml | 36 +-- staging.gvl.org.au/genome_editing.yml | 8 +- staging.gvl.org.au/get_data.yml | 48 +-- staging.gvl.org.au/graphdisplay_data.yml | 74 ++--- staging.gvl.org.au/hca_single_cell.yml | 32 +- staging.gvl.org.au/hicexplorer.yml | 22 +- staging.gvl.org.au/imaging.yml | 74 ++--- staging.gvl.org.au/ivar.yml | 74 ++--- .../join_subtract_and_group.yml | 6 +- staging.gvl.org.au/machine_learning.yml | 40 +-- staging.gvl.org.au/mapping.yml | 60 ++-- staging.gvl.org.au/metabolomics.yml | 34 +- staging.gvl.org.au/metagenomic_analysis.yml | 166 +++++----- staging.gvl.org.au/mothur.yml | 2 +- staging.gvl.org.au/multiple_alignments.yml | 60 ++-- staging.gvl.org.au/nanopore.yml | 52 +-- staging.gvl.org.au/none.yml | 58 ++-- staging.gvl.org.au/phylogenetics.yml | 94 +++--- staging.gvl.org.au/picard.yml | 8 +- staging.gvl.org.au/proteomic_ai.yml | 16 +- staging.gvl.org.au/proteomics.yml | 218 ++++++------- staging.gvl.org.au/rad_seq.yml | 74 ++--- staging.gvl.org.au/rna_seq.yml | 190 +++++------ staging.gvl.org.au/rseqc.yml | 4 +- staging.gvl.org.au/sambam.yml | 74 ++--- staging.gvl.org.au/send_data.yml | 8 +- staging.gvl.org.au/single_cell.yml | 197 ++++++------ staging.gvl.org.au/statistics.yml | 26 +- staging.gvl.org.au/text_manipulation.yml | 50 +-- staging.gvl.org.au/variant_calling.yml | 50 +-- staging.gvl.org.au/vcfbcf.yml | 288 ++++++++--------- staging.gvl.org.au/viral_tools.yml | 2 +- usegalaxy.org.au/annotation.yml | 130 ++++---- usegalaxy.org.au/assembly.yml | 246 +++++++-------- usegalaxy.org.au/bacterial_typing.yml | 8 +- usegalaxy.org.au/bb_tools.yml | 6 +- usegalaxy.org.au/bed.yml | 14 +- usegalaxy.org.au/blast.yml | 14 +- usegalaxy.org.au/chemicaltoolbox.yml | 50 +-- usegalaxy.org.au/chip_seq.yml | 10 +- usegalaxy.org.au/collection_operations.yml | 10 +- usegalaxy.org.au/convert_formats.yml | 54 ++-- usegalaxy.org.au/deeptools.yml | 126 ++++---- usegalaxy.org.au/dna_metabarcoding.yml | 14 +- usegalaxy.org.au/emboss.yml | 2 +- usegalaxy.org.au/epigenetics.yml | 8 +- usegalaxy.org.au/fastafastq.yml | 108 +++---- usegalaxy.org.au/fastq_quality_control.yml | 36 +-- .../fetch_alignmentssequences.yml | 2 +- usegalaxy.org.au/gemini_tools.yml | 22 +- usegalaxy.org.au/genome_editing.yml | 6 +- usegalaxy.org.au/get_data.yml | 46 +-- usegalaxy.org.au/graphdisplay_data.yml | 64 ++-- usegalaxy.org.au/hca_single_cell.yml | 38 +-- usegalaxy.org.au/hicexplorer.yml | 18 +- usegalaxy.org.au/imaging.yml | 66 ++-- usegalaxy.org.au/ivar.yml | 72 ++--- usegalaxy.org.au/join_subtract_and_group.yml | 6 +- usegalaxy.org.au/machine_learning.yml | 36 +-- usegalaxy.org.au/mapping.yml | 56 ++-- usegalaxy.org.au/metabolomics.yml | 30 +- usegalaxy.org.au/metagenomic_analysis.yml | 188 +++++------ usegalaxy.org.au/mothur.yml | 6 +- usegalaxy.org.au/multiple_alignments.yml | 58 ++-- usegalaxy.org.au/nanopore.yml | 48 +-- usegalaxy.org.au/none.yml | 54 ++-- usegalaxy.org.au/phylogenetics.yml | 88 +++--- usegalaxy.org.au/picard.yml | 10 +- usegalaxy.org.au/proteomic_ai.yml | 16 +- usegalaxy.org.au/proteomics.yml | 212 ++++++------- usegalaxy.org.au/rad_seq.yml | 70 ++-- usegalaxy.org.au/rna_seq.yml | 168 +++++----- usegalaxy.org.au/rseqc.yml | 2 +- usegalaxy.org.au/sambam.yml | 82 ++--- usegalaxy.org.au/send_data.yml | 8 +- usegalaxy.org.au/single_cell.yml | 203 ++++++------ usegalaxy.org.au/statistics.yml | 34 +- usegalaxy.org.au/text_manipulation.yml | 44 +-- usegalaxy.org.au/variant_calling.yml | 38 +-- usegalaxy.org.au/vcfbcf.yml | 298 +++++++++--------- usegalaxy.org.au/viral_tools.yml | 2 +- 99 files changed, 2997 insertions(+), 2977 deletions(-) diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index d09ba08d1..877648185 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -7981,3 +7981,20 @@ Update 215 23/10/24 07:35:35 snpeff False Installed iuc ca2b512e8d7c ca2b512e8d7 Install 1685 24/10/24 05:15:33 aarnet_filesender True Installed galaxy-australia 8a4b0f14aa4e latest 2/2 Send Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1685/install_log.txt Install 1687 29/10/24 00:49:41 cemitool True Installed iuc 9d93999d9028 9d93999d9028 3/3 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1687/install_log.txt Install 1689 29/10/24 02:51:46 alphafold2 False Installed galaxy-australia e7f1b552a695 latest Proteomic AI toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1689/install_log.txt +Update 216 30/10/24 01:36:47 agat False Tests failed bgruening d6ede73082da d6ede73082da Staging Testing 15/16 Convert Formats toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 01:37:32 alevin False Installed bgruening b0fe3e482cb7 b0fe3e482cb7 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:41:38 busco False Tests failed iuc e5c372c91e46 e5c372c91e46 Staging Testing 0/8 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:42:04 cuffmerge False Errored devteam 04adc9db1581 04adc9db1581 Staging Installation RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:42:20 cutesv False Errored iuc cb441f258c37 cb441f258c37 Staging Installation Variant Calling toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:42:35 dorado False Errored galaxy-australia c2a23340f233 c2a23340f233 Staging Installation Nanopore toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:42:52 featurecounts False Errored iuc 1b851f87fbe0 1b851f87fbe0 Staging Installation RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:43:07 freebayes False Errored devteam 3e954e7125bf 3e954e7125bf Staging Installation Variant Calling toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:43:24 hifiasm False Errored bgruening 5161f204ba63 5161f204ba63 Staging Installation Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:43:35 music_compare False Errored bgruening 7009462b958f 7009462b958f Staging Installation Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:43:48 music_construct_eset False Errored bgruening 7022ce682d2f 7022ce682d2f Staging Installation Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:44:00 music_deconvolution False Errored bgruening e7b79fd6b595 e7b79fd6b595 Staging Installation Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:44:12 music_inspect_eset False Errored bgruening 94c0b3baf8fd 94c0b3baf8fd Staging Installation Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:44:24 music_manipulate_eset False Errored bgruening 192355cd1641 192355cd1641 Staging Installation Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:44:39 pretext_snapshot False Errored iuc 326098bc19cc 326098bc19cc Staging Installation Graph/Display Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:44:51 scanpy_remove_confounders False Errored iuc c5541bfb8feb c5541bfb8feb Staging Installation Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt +Update 216 30/10/24 06:45:07 ucsc_twobittofa False Errored iuc e9bbe2f71784 e9bbe2f71784 Staging Installation Convert Formats toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index 4443c214a..d6a7fddca 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 4efdca267d51 - - 6e9aea89e388 - - 3f3e247c053d - - 78c75f134c16 - c2ef298da409 + - 78c75f134c16 + - 3f3e247c053d + - 6e9aea89e388 + - 4efdca267d51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -19,8 +19,8 @@ tools: - name: aegean_gaeval owner: iuc revisions: - - 1dd7adc21b6d - 8dc7512c9dc9 + - 1dd7adc21b6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_locuspocus @@ -33,23 +33,23 @@ tools: - name: aegean_parseval owner: iuc revisions: - - 1b52f0c8ad7f - d6c074a93c51 + - 1b52f0c8ad7f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: + - 1aae04680c4b + - 44018dd6b447 - fe3ca740a485 - - cd2480f35935 - - 3e1f6f6d557e - - f29602ae449e - - b5d8e5475247 - 133f36c29579 - - 44018dd6b447 - - 4f2967b27e67 - - 1aae04680c4b + - f29602ae449e - a79ee60b6926 + - 4f2967b27e67 + - b5d8e5475247 + - cd2480f35935 + - 3e1f6f6d557e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -62,36 +62,36 @@ tools: - name: augustus_training owner: bgruening revisions: - - 6519ebe25019 - - dc027fa56d55 - - 7be22100e5e1 - f1e653756174 + - 7be22100e5e1 + - dc027fa56d55 + - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: + - 09855551d713 - 28433faa6e42 - ca6d970d931c - - 09855551d713 - bd0e53f3a891 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - d77802fe76f7 - da5f1924bb2e - - 728dacaf08a9 - 92eee5f31117 + - d77802fe76f7 + - 728dacaf08a9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - 7355bbf5e05f - - fe48aa4ccd5e - 8fd427007e93 + - fe48aa4ccd5e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -103,8 +103,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 8bd92f2404dd - 1b9a9409831d + - 8bd92f2404dd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -116,17 +116,17 @@ tools: - name: cpat owner: bgruening revisions: - - 7ccc6234b54e - 8e9e228c54c4 - 1ac12c0cc7a0 + - 7ccc6234b54e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - - 9d1fbff733cf - d9c3016f7283 - 63662ae295d6 + - 9d1fbff733cf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -150,61 +150,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: + - b6b5cd37f2a2 - 9c15ca7e764e - - 582fd74dc2a1 - 756376aeb1ae - - b6b5cd37f2a2 - - 3bbe70fef6df - - 14f588312c56 - 9f2455341fac + - 582fd74dc2a1 + - 14f588312c56 + - 3bbe70fef6df tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 8e1ace8f77c6 - - 0ffe5be70caf - - a230ea445788 - - 30fb23d4c31c - 73428a792541 - 989f7c061f35 + - 30fb23d4c31c - 1691af4a0d17 + - 0ffe5be70caf + - 8e1ace8f77c6 + - a230ea445788 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 494f0bb4a993 - - 563a19373357 - - 5a5ae61da69c - - e94187d661df - 30f08d74024f + - e94187d661df + - 563a19373357 - 0418d28136de + - 494f0bb4a993 + - 5a5ae61da69c - 57c6718cbfcc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 7abc5f6dd595 - - 4b96ced19f75 - - 2bba2ff070d9 - - d6c7106b7b2e - 1bc5a03faf2e + - d6c7106b7b2e + - 2bba2ff070d9 - f77d7b685bb3 + - 7abc5f6dd595 + - 4b96ced19f75 - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: + - 520e30695ec3 + - 52af33194019 + - d3af38b9c7e1 - 54961e026fe4 + - d77fdcca400e - fed64e676186 - - d3af38b9c7e1 - - 52af33194019 - b3cf4684e9c7 - - 520e30695ec3 - - d77fdcca400e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -217,8 +217,8 @@ tools: owner: iuc revisions: - 79261884facd - - 2aea122fbd25 - 07d7991bf205 + - 2aea122fbd25 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -230,10 +230,10 @@ tools: - name: goseq owner: iuc revisions: - - ef2ad746b589 - - 8b3e3657034e - 43798b4caee0 + - 8b3e3657034e - 602de62d995b + - ef2ad746b589 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -257,8 +257,8 @@ tools: - name: infernal owner: bgruening revisions: - - 477d829d3250 - c9e29ac5d099 + - 477d829d3250 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan @@ -284,26 +284,26 @@ tools: - name: maker_map_ids owner: iuc revisions: - - 326f9c294b09 - e906fa778440 + - 326f9c294b09 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: + - d46d803ca6cc - 3c1a01127868 - 370c210d9541 - - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: + - e95d52d295d7 + - 033755194fe9 - 624606f7c996 - b815ec682418 - - 033755194fe9 - c8ac28e8ac44 - - e95d52d295d7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -345,11 +345,11 @@ tools: - name: prokka owner: crs4 revisions: - - 8a22554cdde2 - - bf68eb663bc3 - d643e3b03500 - - a17498c603ec + - bf68eb663bc3 - eaee459f3d69 + - 8a22554cdde2 + - a17498c603ec tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -361,15 +361,15 @@ tools: - name: repeat_masker owner: bgruening revisions: - - 3f987772e283 - ba6d2c32f797 + - 3f987772e283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler owner: csbl revisions: - - 41bfbaf3c959 - 8661b2607b7e + - 41bfbaf3c959 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -394,22 +394,22 @@ tools: owner: iuc revisions: - 5c7b70713fb5 - - 68693743661e - 5a29ab10dba6 - - 268d162b9c49 - - 8f92c2b26e6d - - 6322be79bd8e - 5b80f544c67f - - cfcf33df7fc0 + - 268d162b9c49 - ca2b512e8d7c + - cfcf33df7fc0 + - 68693743661e + - 6322be79bd8e + - 8f92c2b26e6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: + - 09d6806c609e - 2b3e65a4252f - 5fab4f81391d - - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -421,8 +421,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -434,17 +434,17 @@ tools: - name: tbprofiler owner: iuc revisions: - - 809dfc93d593 + - 037a11682176 + - 51dd22484644 + - 45083d070fb8 + - 200c378d85f3 + - d03af1c7002c + - e1a9d6fd258d - 4839e590cb26 - 37213cf56392 - - 45083d070fb8 - ba6f87115e13 - - e1a9d6fd258d - - d03af1c7002c - - 200c378d85f3 - - 037a11682176 + - 809dfc93d593 - ac8250086ac3 - - 51dd22484644 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index fcf60deee..da90f98cf 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,80 +2,81 @@ tools: - name: abyss owner: iuc revisions: - - 890b794c997d - - fa5259cc561b - - 0e93176640ac - - 553bfe8bd0b5 - - a929ce596a34 - d6d5ccc2c581 - - 841084c5fc46 - 0124fce4654a - - 8f1b150a2487 + - a929ce596a34 + - 553bfe8bd0b5 + - 841084c5fc46 + - 0e93176640ac - 7547fcab5d19 + - fa5259cc561b + - 890b794c997d + - 8f1b150a2487 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 21e491ad532a - 067592b6b312 + - 21e491ad532a - 94fe43e75ddc + - b9e31c5c01c7 - ddddce450736 - b2860df42e16 - - b9e31c5c01c7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 25ca5d73aedf - 321347bd0494 + - 25ca5d73aedf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - faee8629b460 - - 3371c5bdc17a + - 22286dab5aa1 - 5258e18bbe23 - a7f16f24e9a1 - - 22286dab5aa1 + - faee8629b460 + - 3371c5bdc17a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - 53dd00a4ab68 - 8c2167481e72 + - 53dd00a4ab68 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - 94170eee0ad8 + - e5c372c91e46 - 1e62c28ba91d - - 5ecdeca79a0d - - 41030a6c03b7 - - 2babe6d5c561 - - 0d243f458b53 - cf13a1e03e5b - - 4048d82f0c88 + - 0d243f458b53 + - 5ecdeca79a0d + - 602fb8e63aa7 - 1440ae06552f - bb935709506a - 46ae58b1d792 - - 2dd755c1c6ff + - 41030a6c03b7 + - e4bd1e99bacf + - 94170eee0ad8 + - 2babe6d5c561 + - 4048d82f0c88 - f18f0b887c31 - - ea8146ee148f - e824f5d958d0 - - 602fb8e63aa7 - - e4bd1e99bacf + - ea8146ee148f + - 2dd755c1c6ff tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 5732f959936a - 86f150c8019d + - 5732f959936a - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -88,32 +89,32 @@ tools: - name: flye owner: bgruening revisions: - - cb8dfd28c16f - - 3ee0ef312022 + - e27815e82dd4 - 8d4f03b5fe9d - - 3e4f8642c77e - 276f5d8712d5 + - cb8dfd28c16f + - 3e4f8642c77e + - 3ee0ef312022 + - 291923e6f276 - 1ce9b1d72ec3 - - e27815e82dd4 - 1f0769f0b56b - - 291923e6f276 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 3169a38c2656 - 460fad600dce - 01210c4e9144 - b2f674562a18 + - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 06bcf65179fb - - ba88bc5a6446 - 7348b69e5109 + - ba88bc5a6446 + - 06bcf65179fb - 8b330a577046 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -121,9 +122,9 @@ tools: owner: bgruening revisions: - 3fba9c77550a - - 690c2caa367e - 6ec1b853c8fd - 5127a713de83 + - 690c2caa367e - 3ef480892a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -136,23 +137,23 @@ tools: - name: hifiasm owner: bgruening revisions: + - 9ef6920c3089 + - 0ee0c3089254 - 284a1cb82b61 - - da9d8bf98802 - df25d4fb79b7 - - 6505bd37670d - - 60024a528cbd - - 3f7be05a1597 - - 9ef6920c3089 + - da9d8bf98802 - 2061fb3b81b4 + - 6505bd37670d + - 045c7c3d8e59 - f3c89da3af16 - - 71740308d412 - - ec9e21e9c71b - 5f625c63b8bc - - 045c7c3d8e59 + - 3f7be05a1597 + - 71740308d412 + - 5bec28269d95 - 366a11d316a7 - 41cea2aa2dce - - 0ee0c3089254 - - 5bec28269d95 + - ec9e21e9c71b + - 60024a528cbd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -170,28 +171,28 @@ tools: - name: megahit owner: iuc revisions: - - a96f3ad4e0d8 - de387b2b2803 - - 14ddfc8ffb93 - 7518ee87b53d + - 14ddfc8ffb93 + - a96f3ad4e0d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: + - 39edec572bae + - d7edbc9c3a07 - 09c589057ee8 + - f8113c25bc6b - 9d79beb19ac3 - eb7b00ec347d - - f8113c25bc6b - - d7edbc9c3a07 - - 39edec572bae tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - eadfd71dde37 - 29dabd8db6f2 + - eadfd71dde37 - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -199,14 +200,14 @@ tools: owner: nml revisions: - 99ecfdafc64f + - e731ea24e48d + - eb7a370f6588 - 2ecf5a570907 + - f338e9942b27 - 606b09cc9860 - - e731ea24e48d - fd128c111ab0 - 3ca2d2a9068c - f369ef5f210b - - f338e9942b27 - - eb7a370f6588 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -219,10 +220,10 @@ tools: owner: iuc revisions: - 8b6d0d85252b - - b799a615995d - 8dee0218ac7d - - a7b889b90140 - 73a3846701e1 + - b799a615995d + - a7b889b90140 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -254,46 +255,46 @@ tools: - name: pretext_map owner: iuc revisions: - - 2b16ba799da9 - bbe19ef04a74 + - 79b48f02db49 - d256a51a656b - - 8fef980d48b5 - dfb8a4497339 - 02831bf9e95f - - 79b48f02db49 + - 8fef980d48b5 + - 2b16ba799da9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - 76d4cbefff85 - - e9bd16ba5ebd - a315c25dc813 + - e9bd16ba5ebd + - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 342a1d1fed7b - 875d0f36d66f - 6fcbee531de6 - - 72472698a2df - - 3061c8b029e5 - - 59db8ea8c845 + - 7594365c546b - 675488238c96 + - 59db8ea8c845 + - 3061c8b029e5 + - 72472698a2df - ebb0dcdb621a - - 7594365c546b + - 342a1d1fed7b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - a199cd7ac344 - - d865b62f501c - cd06929b224b - - 78c533842eeb - aa39b19ca11e + - d865b62f501c - 39bed8de8017 + - 78c533842eeb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -311,12 +312,12 @@ tools: - name: raven owner: iuc revisions: - - 33b7d8481a76 + - 3edba9afc9bc - 2b2a352488fa - 5c55448d0f33 - - 3edba9afc9bc - - f8564b2d7f63 + - 33b7d8481a76 - f11b994b7eb2 + - f8564b2d7f63 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast @@ -329,13 +330,13 @@ tools: - name: rnaspades owner: iuc revisions: - - 5fc94b3a4704 + - 28189050e437 + - e122f9101584 + - 378e55aeeb25 - 1d06c8b38e77 + - 5fc94b3a4704 - ef69617ecb42 - - 378e55aeeb25 - 53c2bc8c2ae3 - - e122f9101584 - - 28189050e437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -347,191 +348,191 @@ tools: - name: shovill owner: iuc revisions: + - 865119fcb694 + - 83ead2be47b2 - f698c7604b3b - ad80238462c1 - - 196a599ec43d - - 865119fcb694 - d9f6a00b6db7 - - 83ead2be47b2 - ee17a294d3a3 + - 196a599ec43d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 015283de3004 - - 5e0825476fb7 - 24e471d13fe9 + - 5e0825476fb7 + - 015283de3004 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 604782a8a53a - - c33a476f4001 - - 7490b213baa9 - 904bf932cf78 - - 051fd2db8a27 + - 7490b213baa9 - 1bb12736175c - 1fc82fe7ebef + - c33a476f4001 + - 051fd2db8a27 + - 604782a8a53a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 9678993ca5bd - - d6e617c4e338 + - 655fa188c3cc - 34305b013402 + - ad8b536d1caa - 808b3a0a6716 + - 9678993ca5bd - fee85957cebe - - 655fa188c3cc - - ad8b536d1caa + - d6e617c4e338 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: + - 6b5a5842531e - 21da31ed41a1 - b8002c3f7141 - - 037f9927c4ff - - 8d4b90bf9caf - - e5a3b75a271f - 7e27faaad80e - - 6b5a5842531e + - e5a3b75a271f + - 8d4b90bf9caf + - 037f9927c4ff tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 5b26685e5d3b - - 328aa71f0f3c - - 2a10645aeadd - - f1532cb33c75 - 86f66ab58e14 + - f1532cb33c75 - 9de69775f512 + - 2a10645aeadd - 7922870efcca + - 328aa71f0f3c + - 5b26685e5d3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 1708851f8804 + - 85fb02c43042 - 340bc17f49cf - 6aad515a5270 - e41dcb0e913b - 8cc856b935ee - - 85fb02c43042 + - 1708851f8804 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: + - b3490b036c5a - d159735a6a9f - - b65a43f70b99 - 6357b127161e - - b3490b036c5a - 249f6a28c751 - - de1260f8a300 + - b65a43f70b99 - d5fb354f745d + - de1260f8a300 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - dd7ad84f3943 + - d5887ace0dd4 - 9006e5836729 + - 7897763d14ec - a90db5dbaaf3 + - dd7ad84f3943 - d2d1df21dfb9 - - 7897763d14ec - 33368fec3b70 - b7829778729f - - d5887ace0dd4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 8f631679571f - - 189e837009c9 - - 505a9833ab5d - ed2425b9fd27 - - ced385aa976d - 6f4c8ad6ea01 + - 189e837009c9 + - ced385aa976d + - 505a9833ab5d + - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - f31d376ce725 - - e59bee4565b3 - - 356afed970b4 - - 9ded6109434a - d40ed4eb0c0e - 19bdfd1e6fe3 + - e59bee4565b3 + - 9ded6109434a + - f31d376ce725 + - 356afed970b4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 4688ae3b49b5 - b23249f81bc4 - - af40e971a8cc - - 6dd935e4984b + - 4688ae3b49b5 - ebd801e712bc + - af40e971a8cc - 80a17897564d + - 6dd935e4984b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - 59bd28f6265d - cb1e3db43020 - - b5e35a2ca4f3 - - b64696992ee9 - 937ea677d437 + - 59bd28f6265d + - b64696992ee9 + - b5e35a2ca4f3 - bb11fefb23a3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: + - 6015aa0303f2 - 05bd7504fdb2 - - 383bb5ad32e2 - - 2628f6790eda - 6bfab4a4a988 + - 383bb5ad32e2 - cb4768eeca3b - - 6015aa0303f2 + - 2628f6790eda tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: + - e022dff952df + - e92675014ac9 + - 0a3a602cd1e3 - 8f9f06995f98 - - 3e44ef016b45 - 9e3e80cc4ad4 - - e022dff952df - 6e26c9afd301 - - 0a3a602cd1e3 - - e92675014ac9 + - 3e44ef016b45 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: + - 8d09f8be269e - 5da9a0e2fb2d - 920677cd220f - - 8d09f8be269e - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 82398ba86ba7 - 37d88f41c810 - - d81360ea69d8 + - 82398ba86ba7 - 0e2b4e3f9ca1 - 4a53b89fa703 + - d81360ea69d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index 882e2f10a..70d1d2558 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,10 +2,10 @@ tools: - name: integron_finder owner: iuc revisions: - - bfd290fe1588 + - 392f100eebcd - 1ae00120dd24 + - bfd290fe1588 - 4768f7f8e93f - - 392f100eebcd tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -17,17 +17,17 @@ tools: - name: mlst owner: iuc revisions: - - 1f5641a52664 - 8e8dc9a1e3e5 - ded48b36f3b7 - 31812e7a1315 + - 1f5641a52664 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 5c8ff92e38a9 - 17fcac7ddf54 + - 5c8ff92e38a9 - 24a7a95867b0 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bb_tools.yml b/staging.gvl.org.au/bb_tools.yml index 2618cb260..eedea7738 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,13 +2,13 @@ tools: - name: bbtools_bbduk owner: iuc revisions: + - 159b04e36791 - d1f62024a08b + - a9c9d768b751 - 204a131e47db - - 7beb76ffbc0f - - 1c427e24fb79 - 0840ba83860c - - a9c9d768b751 - - 159b04e36791 + - 1c427e24fb79 + - 7beb76ffbc0f tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index fff88f581..1e8c52133 100644 --- a/staging.gvl.org.au/bed.yml +++ b/staging.gvl.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - 64e2edfe7a2c - - dde39ba9c031 - e19bebe96cd2 - - 0a5c785ac6db - - a1a923cd89e8 - a8eabd2838f6 - - b28e0cfa7ba1 + - 07e8b80f278c + - 589e7e57fd6d - 87ee588b3d45 + - 64e2edfe7a2c - ce3c7f062223 - - 07e8b80f278c + - 0a5c785ac6db - a68aa6c1204a - - 589e7e57fd6d + - b28e0cfa7ba1 + - dde39ba9c031 + - a1a923cd89e8 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/blast.yml b/staging.gvl.org.au/blast.yml index f286fb37e..a5228d252 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -8,10 +8,10 @@ tools: - name: diamond owner: bgruening revisions: - - f921014aba5a + - 62c9df8382c2 - e8ac2b53f262 - 54f751e413f4 - - 62c9df8382c2 + - f921014aba5a tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,15 +23,15 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - 6f386c5dc4fb - - 2889433c7ae1 - - e25d3acf6e68 - - acf4e47b734c + - cbf3f518b668 - 0e3cf9594bb7 - 5edc472ec434 - - d999e774072a - - cbf3f518b668 + - 6f386c5dc4fb - a52d2d93e595 + - acf4e47b734c + - d999e774072a + - 2889433c7ae1 + - e25d3acf6e68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus @@ -43,8 +43,8 @@ tools: - name: taxonomy_krona_chart owner: crs4 revisions: - - 1334cb4c6b68 - e9005d1f3cfd + - 1334cb4c6b68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index 9f4f16b2d..dc5ff122f 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 6ca543ec1bf8 - - da6bd1975a71 - - f4230f116196 - - 095ad4d096d1 - 710301bc46fa + - 6ca543ec1bf8 - c8cdde00b105 - 27ee142314a9 + - f4230f116196 + - da6bd1975a71 + - 095ad4d096d1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -130,50 +130,50 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 0fac8e2afc13 - - 3b8a9d5ced85 - - 79cfd9ead848 - bfb65cb551d8 - 88076940fa94 + - 3b8a9d5ced85 + - 0fac8e2afc13 + - 79cfd9ead848 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - d532b7e5f64b - - eb6564a60136 - - b46d4b4d995c + - 55918daa5651 - f5d979cb4b54 + - eb6564a60136 + - d532b7e5f64b - 715cd0e87781 - - 55918daa5651 + - b46d4b4d995c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - fdf2cc80adb5 - - 5579659312e6 - - f26afd1b7104 - - 97872d87ba80 - d2f955aea23a + - 97872d87ba80 + - f26afd1b7104 + - 5579659312e6 + - fdf2cc80adb5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - bc31d02be922 - - 319a28774da9 - d1d0efda35c0 + - 319a28774da9 + - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 4da9ee404eab - cac1886249a2 + - 4da9ee404eab + - 2c349b027a01 - 070e3ecc3fda - ed736e6eee39 - - 2c349b027a01 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim @@ -181,23 +181,23 @@ tools: revisions: - f197e34c33a9 - 525ca7c8065f + - d1f803b5943c + - da8753545526 - 2e219a2d9327 - - 73008ef1f487 - 807aa4c9293d - - da8753545526 - - d1f803b5943c - c0c9a5024177 + - 73008ef1f487 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 2c8ed1b52bf7 - - 27ea4e1a3f95 - - 1809414a9454 - - c4fbab8e03c5 - 7568ae18908a + - c4fbab8e03c5 + - 27ea4e1a3f95 - 61094e01eff9 + - 2c8ed1b52bf7 + - 1809414a9454 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -210,17 +210,17 @@ tools: owner: chemteam revisions: - 730ef07b90ae - - ba83f0923369 - - ccfbd956a2d3 - d7ec25187599 - 79e8ab8f1e81 + - ba83f0923369 + - ccfbd956a2d3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 48d6a6eb438b - 9a3a1f698fc6 + - 48d6a6eb438b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_dihedral @@ -269,9 +269,9 @@ tools: owner: bgruening revisions: - b59c91adeac1 + - 1400d1977e7b - e6011617c748 - 4242b4d68e9c - - 1400d1977e7b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -297,15 +297,15 @@ tools: - name: qcxms_neutral_run owner: recetox revisions: - - 33b7a99b6de3 - 8f465c0c3b6c + - 33b7a99b6de3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_production_run owner: recetox revisions: - - 356f7916ac07 - e97bfe7ac906 + - 356f7916ac07 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: rem_complex @@ -341,9 +341,9 @@ tools: - name: sucos_max_score owner: bgruening revisions: + - d4c67ced6abc - 9b48456a96fe - 85fad59f8168 - - d4c67ced6abc - bf99565cec1f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index fa6862719..882bd8d6c 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -2,10 +2,10 @@ tools: - name: diffbind owner: bgruening revisions: - - fa56d93f7980 - c97a786e8fb5 - - f907216064f6 + - fa56d93f7980 - 163688bb8f73 + - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -23,18 +23,18 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 4124781932db - 11cf21ee4242 + - 4124781932db tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - - 86e2413cf3f8 - 424aefbd7777 - - f5d67c722d67 - - 495a4173006f - 640d3af5d833 + - 86e2413cf3f8 + - 495a4173006f + - f5d67c722d67 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -53,9 +53,9 @@ tools: - name: sicer owner: devteam revisions: - - 4a14714649b4 - - 74c9214cc8e6 - 5c2cc3b58c7d + - 74c9214cc8e6 + - 4a14714649b4 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/staging.gvl.org.au/collection_operations.yml b/staging.gvl.org.au/collection_operations.yml index 7005d4b3b..9629aad6c 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -2,24 +2,24 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: + - 33151a38533a - 25136a2b0cfe - - 830961c48e42 - 90981f86000f - - 33151a38533a + - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - baabc30154cd + - 6cbe2f30c2d7 - 0046692724f9 + - baabc30154cd - 2dae863c8f42 - - 6cbe2f30c2d7 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 57f0914ddb7b - 38eec75fbe9b + - 57f0914ddb7b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index 7848dac50..9339d0bfa 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -2,8 +2,8 @@ tools: - name: agat owner: bgruening revisions: - - abba05ead5d7 - e7449b2c14bf + - abba05ead5d7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -15,39 +15,39 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 5e1240a87bcb - - 6ef0b5664c69 - 367b1ed91207 - - e3cbd2287f63 - - a3b86937ead6 + - 0b3c3ad92827 + - 5e1240a87bcb - ab9350a8ab4d - 3b6f97e7094c - 4a6ee918c13a + - a3b86937ead6 - f3a19509108a - - 0b3c3ad92827 + - e3cbd2287f63 + - 6ef0b5664c69 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 091bb5922a82 - - 501c21cce614 + - 72ed72122deb + - e525f9ffb9ac + - bd46669113b9 - 584008e574b2 - - 33c99804a32f - d4d4e9febf5c - - e177a8ea0bf1 - - 1b5fc03380d4 - - 72ed72122deb + - 501c21cce614 - 54ccb7e1f49a - - bd46669113b9 - - e525f9ffb9ac + - 091bb5922a82 + - 1b5fc03380d4 + - 33c99804a32f + - e177a8ea0bf1 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 owner: iuc revisions: - - a0d092f27fdf - 11c3eb512633 + - a0d092f27fdf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: compress_file @@ -59,8 +59,8 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - e7ed3c310b74 - 7e801ab2b70e + - e7ed3c310b74 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta @@ -74,8 +74,8 @@ tools: - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - 4b347702c4aa + - 614a63f14adf - 43807a65369f tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -88,8 +88,8 @@ tools: - name: gfa_to_fa owner: iuc revisions: - - 8e9d604e92f4 - e33c82b63727 + - 8e9d604e92f4 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -101,9 +101,9 @@ tools: - name: gffread owner: devteam revisions: - - 154d00cbbf2d - - 3e436657dcd0 - 4dea02886337 + - 3e436657dcd0 + - 154d00cbbf2d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -115,8 +115,8 @@ tools: - name: intermine_galaxy_exchange owner: iuc revisions: - - c24014d80001 - faef2b1622a3 + - c24014d80001 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: mz_to_sqlite @@ -143,19 +143,19 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 68f57cc8fad0 - - 2dcfbbf9071a - 78fb18899c99 + - 2dcfbbf9071a + - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: + - b9b385097f13 + - 92ac8e086317 + - 26c6706bfb07 - 63769c4217a7 - 19e45916daf9 - - 26c6706bfb07 - - 92ac8e086317 - - b9b385097f13 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index 71d165679..a71e9f386 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,71 +2,71 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - a1ca9bccc7f2 - - de72ba3ed6f2 - 268e91e540ee + - 29451af70c52 + - a1ca9bccc7f2 - c929a006727f + - de72ba3ed6f2 - e821645ef8fc - 5f6d123679f4 - - 29451af70c52 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 7a7fd0f5f15d - - 2d2cf5c1ea8a + - 0e143b4c3987 - bb1e4f63e0e6 + - 7a7fd0f5f15d - 12af64f93288 + - 2d2cf5c1ea8a - 5d11599b8a7d - 0e49b109abc2 - - 0e143b4c3987 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: + - 195e98217334 - dc059492a995 - - 7c1beb6d6eca + - 1d848bc4585f - c06951d10364 - - 195e98217334 + - 7c1beb6d6eca - 81b1e3e1fc6c - - 1d848bc4585f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: + - a67ac707496a + - 93eb012d9eed + - 07418a30ed01 - 3d211717a775 - - bfff7454b59a - 71aa86af6762 - - 07418a30ed01 - 26e7304d6737 - - a67ac707496a - - 93eb012d9eed + - bfff7454b59a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 29fcfd36e90a + - 5be24eba848d - b8858746dc1f - - 26983857c91a - 56d5b797ce84 - - 5be24eba848d - - 2bc10a9ca58b - dd0b7398bb96 + - 29fcfd36e90a + - 2bc10a9ca58b + - 26983857c91a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - e6d0bff01239 - ee3a1b0f45f1 + - e6d0bff01239 - 7e6bcd2e5128 - 9384cd033f30 - - 72bfafe3330b - c3e012dfe21f + - 72bfafe3330b - 7ef978dc1b8a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -74,133 +74,133 @@ tools: owner: bgruening revisions: - a60c359ec43c - - 514fa53b5efb - - d9a637e83828 - 167788df3b46 - 9470f29702f8 - - fb9cf9c97ec4 - fd1275e01605 - b73e213add0c + - 514fa53b5efb + - d9a637e83828 + - fb9cf9c97ec4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - e479c7ca5570 + - c34d11ea4ba6 - 86febdcc4283 - ca0616bb2cdf + - a02cfa31e9cb - 5bffaa8354a1 - 2c37ce318bc3 - - c34d11ea4ba6 - - a02cfa31e9cb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - 192ef85c0b0b - - 2d466b530754 - - 01fb6a7654e6 - 1fcb7adc39b8 - - 69a8621ca2f0 - - 004aea905d4d - 78f405266706 + - 004aea905d4d + - 01fb6a7654e6 + - 2d466b530754 + - 69a8621ca2f0 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - d9ce4897dbb2 - - 3c9f0c486cca - d580d6acd1df - 459cfa861f0b - - db940c262830 - 137c4beed34b + - 3c9f0c486cca - 2f9e4843f480 + - db940c262830 + - d9ce4897dbb2 - 9ecba5e225a6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - 32e451def88c - - 2c66e43f1c86 - bad3ca889618 - - f264afa9fa6f - - bd7db9e2f2cb - fd408d755394 - fbe773640707 + - 2c66e43f1c86 + - f264afa9fa6f + - 32e451def88c + - bd7db9e2f2cb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - 4e12ea27f788 - - 7fda5607e777 - 7e361d147872 + - 231994413f89 + - 3b9d990a0a0e - 56bce3c82278 + - 7fda5607e777 - 9368fbc49c8b - - 3b9d990a0a0e - - 231994413f89 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - e65d16fb2724 - - b1779366c8e9 - - 94ca68515826 - - d9114ef1c8a5 - ce4ce3316f74 + - d9114ef1c8a5 + - e65d16fb2724 - 4431f39ede55 + - b1779366c8e9 - c03c3384cd81 + - 94ca68515826 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - d57251071381 + - 2da482e408b8 - b88ebb3672a1 - - 793665fff0f8 - 4ed32329e0ed - - d57251071381 - f8fc4e5aff9d - - 2da482e408b8 + - 793665fff0f8 - 23f7c5f1fdaf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - c60570fa602f - - a7849312d328 - - e4c7985d4585 + - 010e58e9d822 - a4dfb122e52b + - ba6efa77fb79 - 512155688d98 + - e4c7985d4585 + - c60570fa602f - 25d830337d31 - - 010e58e9d822 - - ba6efa77fb79 + - a7849312d328 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 69264da0ce77 - c899e0ccff8c - 00d869ea03a1 + - 38e3f226248b - 443d9a9d6d11 - aa200e4f3939 - 4d678170d29b - - 38e3f226248b + - 69264da0ce77 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - c361b12d207a - - 6662b1a8d326 - - a2d70c4fd406 - - aac8444d6681 - 10301d137111 + - aac8444d6681 + - 6662b1a8d326 - d806504e96d9 + - a2d70c4fd406 + - c361b12d207a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/dna_metabarcoding.yml b/staging.gvl.org.au/dna_metabarcoding.yml index dfa46c5bd..a4d828dfc 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -9,8 +9,8 @@ tools: - name: obi_clean owner: iuc revisions: - - 7d16de45c021 - 08d873cdd5f6 + - 7d16de45c021 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -23,8 +23,8 @@ tools: - name: obi_grep owner: iuc revisions: - - e9e49cf06b42 - 02bab5ff7c37 + - e9e49cf06b42 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend @@ -44,8 +44,8 @@ tools: - name: obi_sort owner: iuc revisions: - - 12b9e285ca1c - b6d9ea2fb41b + - 12b9e285ca1c tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_stat @@ -65,7 +65,7 @@ tools: - name: obi_uniq owner: iuc revisions: - - d4bea99366f9 - c0f7b58b4ce4 + - d4bea99366f9 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index caecd371d..df5ff4121 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - dba489bfcd62 - - ce385837c160 - - 832c20329690 - 63dd26468588 + - 832c20329690 + - ce385837c160 + - dba489bfcd62 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index 557952f6c..cf8b05588 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -8,10 +8,10 @@ tools: - name: bwameth owner: iuc revisions: - - d82648ad25a3 - - 6da3972210ee - 62f5fab76dfb - cf1322aeb137 + - d82648ad25a3 + - 6da3972210ee - 29bdbc353f20 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -24,7 +24,7 @@ tools: - name: pileometh owner: bgruening revisions: - - 183cb55b1729 - d6787bab7b11 + - 183cb55b1729 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 91c610c91..13c15528c 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: - - 8665bcc8b847 + - c053d4cad713 + - e4691e1589d3 + - 44e2cc14f75b + - 093678460093 - 135b80fb1ac2 - - 64172f1c1202 - - de6cebe3c043 - fe74900d6dc7 - b1c926deaa2d - - c5e2e5902201 - - c053d4cad713 - - 44e2cc14f75b + - de6cebe3c043 + - 48f587c13075 + - 49370cb85f0f + - 64172f1c1202 + - 8c0175e03cee - 4e5056fefd88 - - 5eb7e84243f2 - - c4b82dce8335 - - 660cffd8d92a + - c5e2e5902201 + - 8665bcc8b847 - 5915ea1ec9b1 - - e4691e1589d3 - - 8c0175e03cee - - 093678460093 + - 660cffd8d92a + - c4b82dce8335 - 288f97432497 - - 49370cb85f0f - - 48f587c13075 + - 5eb7e84243f2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -39,9 +39,9 @@ tools: - name: fasta_clipping_histogram owner: devteam revisions: - - 9db07fd39f85 - - 8889eb864cef - f666895cbebd + - 8889eb864cef + - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -53,8 +53,8 @@ tools: - name: fasta_compute_length owner: devteam revisions: - - 5cbde03c1103 - 7d37cfda8e00 + - 5cbde03c1103 - de2db1bdfbf8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -87,8 +87,8 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 516b97a23d7e - 859422bcb689 + - 516b97a23d7e - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -109,8 +109,8 @@ tools: owner: devteam revisions: - ec0b5076173a - - f81d4362b6c1 - f773e98b26cf + - f81d4362b6c1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -122,10 +122,10 @@ tools: - name: fasta_stats owner: iuc revisions: - - 0dbb995c7d35 + - cd0874854f51 - 9c620a950d3a + - 0dbb995c7d35 - 56022eb50bbd - - cd0874854f51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -138,11 +138,11 @@ tools: owner: iuc revisions: - d60c3f704da0 - - c59d48774d03 + - dbf9c561ef29 - dbfc505896e9 + - c59d48774d03 - 1d8fe9bc4cb0 - 65b93b623c77 - - dbf9c561ef29 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -154,9 +154,9 @@ tools: - name: fastq_combiner owner: devteam revisions: + - 9115b978ce10 - b05e39b9c170 - f1dc2a761c30 - - 9115b978ce10 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -168,9 +168,9 @@ tools: - name: fastq_filter owner: devteam revisions: - - '144275714590' - 81a9090d6df3 - 10b75444feae + - '144275714590' tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -183,8 +183,8 @@ tools: owner: devteam revisions: - 47e5dbc3e790 - - e9f8633db0a2 - 8611b80a14d6 + - e9f8633db0a2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -196,9 +196,9 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 7861f3b10c68 - - e30352e889fe - 5b87038565bb + - e30352e889fe + - 7861f3b10c68 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation @@ -211,8 +211,8 @@ tools: owner: devteam revisions: - 4e1d64e6385f - - 9dfda4e310ed - 9282652e7234 + - 9dfda4e310ed tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality @@ -238,8 +238,8 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - 3e396e702cea - 2ccb8dcabddc + - 3e396e702cea - b41c2c1bcfbf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -266,8 +266,8 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - 397dc333436b - 35e38452bb3f + - 397dc333436b - e39cc71d3ed6 - 249c8393f2d4 tool_panel_section_label: FASTA/FASTQ @@ -281,9 +281,9 @@ tools: - name: fastq_quality_converter owner: devteam revisions: - - 54053ea6c77e - - 74db4cffab1f - 045f0e1043f7 + - 74db4cffab1f + - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -295,9 +295,9 @@ tools: - name: fastq_stats owner: devteam revisions: - - f0e7deab6518 - b1cea1b2fcd0 - f86c27295151 + - f0e7deab6518 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats @@ -323,17 +323,17 @@ tools: - name: fastqtofasta owner: devteam revisions: - - ac3fed111eb6 - 297962e79f39 + - ac3fed111eb6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter owner: devteam revisions: - - 529bccd5e4a1 - 567d5b3c52b1 - 09070cacefd8 - d5e9e83cd3d8 + - 529bccd5e4a1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter @@ -359,10 +359,10 @@ tools: - name: fastx_clipper owner: devteam revisions: - - cb1e251cac37 - - 736b8f6ee456 - 90858c306551 + - cb1e251cac37 - bdf1ce174e39 + - 736b8f6ee456 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -375,8 +375,8 @@ tools: owner: devteam revisions: - 421f0af4ee95 - - 7ce1891db6f5 - 07497255281e + - 7ce1891db6f5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -388,10 +388,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - 3599f5451ee2 + - 02f8a17a4ebd - f984bb114520 - b29d37ca9e41 - - 02f8a17a4ebd + - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -404,9 +404,9 @@ tools: owner: devteam revisions: - 0c2907307ba4 - - e246088b6e34 - 177f0621c266 - 6027ef51ef91 + - e246088b6e34 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -418,9 +418,9 @@ tools: - name: fastx_trimmer owner: devteam revisions: + - 61b4cedc8934 - 73194cdd4f57 - 377ac2829eac - - 61b4cedc8934 - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -445,10 +445,10 @@ tools: - name: pear owner: iuc revisions: + - 2f804526f5fd + - b4c6f054210a - f69501361cec - 037f0acc7830 - - b4c6f054210a - - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -460,8 +460,8 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 3b0a14722175 - 8e1a90917fa7 + - 3b0a14722175 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort @@ -474,23 +474,23 @@ tools: - name: seqkit_stats owner: iuc revisions: - - 812705bcf39c - fe1ae2ebf63d + - 812705bcf39c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - a019807f4e67 - - 4b494533146a - 3da72230c066 + - 4b494533146a + - a019807f4e67 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - a019807f4e67 - 4b494533146a + - a019807f4e67 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: split_paired_reads @@ -502,16 +502,16 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - dfa082f84068 - 51b771646466 + - dfa082f84068 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - - d3f58a0dc09d - - bf04bd405d5b - 71f649c23021 + - bf04bd405d5b + - d3f58a0dc09d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -523,11 +523,11 @@ tools: - name: umi_tools_count owner: iuc revisions: - - a535cf1e5da4 - 8250ea3a1501 - b557acca0b56 - e654095ab143 - 71ad4a56c40c + - a535cf1e5da4 - 24013bf85a6f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -547,14 +547,14 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 9fa7803d1c51 - - 7accf7407811 - - f3759eec3018 - 015cf18f4a15 + - 7accf7407811 - 27ac32a22ad2 - - 6a675c3aa610 - - 828dba98cdb4 - 7a7e33d28f62 + - f3759eec3018 + - 828dba98cdb4 + - 6a675c3aa610 + - 9fa7803d1c51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract @@ -566,15 +566,15 @@ tools: - name: umi_tools_group owner: iuc revisions: - - 428735be9764 - d6255614afd7 + - 428735be9764 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_whitelist owner: iuc revisions: - 4c8a1c7d3608 - - 953b4821b183 - e4e12f0b3af1 + - 953b4821b183 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index bfae47da4..1df66655d 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,10 +2,10 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - e41385662e5e - - ce9cd02d5b88 - 64e9a6afdd0c - 7b4468117008 + - e41385662e5e + - ce9cd02d5b88 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -19,35 +19,35 @@ tools: owner: devteam revisions: - 5ec9f6bceaee - - 9da02be9c6cc - - 3d0c7bdf12f5 - - 2c64fded1286 - f2e8552cf1d0 - 2b0c9d9fc6ca - - ff9530579d1f - e7b2202befea + - 2c64fded1286 + - 9da02be9c6cc + - ff9530579d1f + - 3d0c7bdf12f5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - a252d8415583 - 89d299153577 + - a252d8415583 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - b6b54ba71bd8 - - ad116ae3f4d9 - 18a51655db17 + - ad116ae3f4d9 + - b6b54ba71bd8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - cc0fd298cc17 - 7306ec78632a + - cc0fd298cc17 - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu @@ -55,30 +55,30 @@ tools: owner: iuc revisions: - a72af9de6bf5 - - 8880fb74ef56 - 1f296803dfa3 + - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 9a913cdee30e - - b2f1f75d49c4 + - bf675f34b056 + - 3d93dd18d9f8 - f7e2f1eb3a16 - f7985e0479b9 - - 5e33b465d8d5 - - 3d93dd18d9f8 + - 1c2db0054039 + - 9a913cdee30e + - b2f1f75d49c4 - 75c93c70d094 - abfd8a6544d7 - - 1c2db0054039 - - bf675f34b056 + - 5e33b465d8d5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 084bbd8ba7b8 - - cd7e644cae1d - 949f01671246 + - cd7e644cae1d + - 084bbd8ba7b8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index e6d5e9548..54bbfa7ed 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -15,8 +15,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: - - 141612f8c3e3 - 83a19df00eab + - 141612f8c3e3 - 85ef5f5a0562 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index ae5360954..70d2f265f 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -2,30 +2,30 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 3630a6e624d4 - 142d95ab942e + - 3630a6e624d4 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend owner: iuc revisions: - - be828b79bd4d - 4bd4870ecd33 + - be828b79bd4d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - - f2f3bc622a16 - - 8f53b238a360 - 0c8f7322f8fc + - 8f53b238a360 + - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden owner: iuc revisions: - - 1a4c5adcd587 - df57188562f0 + - 1a4c5adcd587 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets @@ -38,8 +38,8 @@ tools: - name: gemini_db_info owner: iuc revisions: - - 7d75673f4d6f - 4c5f4e9b1931 + - 7d75673f4d6f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo @@ -59,15 +59,15 @@ tools: - name: gemini_fusions owner: iuc revisions: - - 8151a5a0e4f6 - 91d53f89ca54 + - 8151a5a0e4f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -79,16 +79,16 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 184aa4e686e2 - 2550239feed5 + - 184aa4e686e2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load owner: iuc revisions: - - cf61daf064fe - - b2c25142267e - 45296e47d565 + - b2c25142267e + - cf61daf064fe tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -101,8 +101,8 @@ tools: - name: gemini_mendel_errors owner: iuc revisions: - - 61343646155c - 00c2734b3bea + - 61343646155c tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways @@ -115,23 +115,23 @@ tools: - name: gemini_qc owner: iuc revisions: - - 86e46972e183 - 9e83673fa6d2 + - 86e46972e183 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query owner: iuc revisions: - - 666f60a9331a - - da74170c55c7 - 840fb4850be3 + - da74170c55c7 + - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant owner: iuc revisions: - - 86f3aac4418d - 05124dc72dba + - 86f3aac4418d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region @@ -151,15 +151,15 @@ tools: - name: gemini_set_somatic owner: iuc revisions: - - e4e2128460e3 - ef9991a4a9a7 + - e4e2128460e3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats owner: iuc revisions: - - 5c9efee9cb1e - ee894347fcd6 + - 5c9efee9cb1e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 9844ff03b..451dd80c8 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -9,28 +9,28 @@ tools: - name: mageck_gsea owner: iuc revisions: - - b946929d31c4 - d46e36492bff + - b946929d31c4 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle owner: iuc revisions: - - 26126538a86f - b36c85e37a48 + - 26126538a86f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway owner: iuc revisions: - - 39a996d44e16 - 9744e1124d0f + - 39a996d44e16 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test owner: iuc revisions: - - 688a8eccea71 - 9b4f4533c9ee + - 688a8eccea71 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index fb7ae550e..0dbe70133 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - 983bf725dfc2 + - e9df53a75f3c - b39347891609 + - 983bf725dfc2 - c1b437242fee - - e9df53a75f3c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,53 +17,53 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - 1c58de56d587 - e063168e0a81 + - 1c58de56d587 - 28587613264f tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 69ebb7f46e45 - - 516a54ddf218 - - 5e6237d58b0c - - 9a776b080193 - - e407b9da183a - - 653e89d73fc4 - - 1ec814014652 - - 4df8de2d0e48 - - f8054ea1c365 - - aad3885b3216 + - 83c7d564b128 - 4317d3cb6cba - - f5ea3ce9b9b0 - - 8848455c0270 - - 1790dcf3c32d - - e08a7ad4378b + - 734abc7ac21d - ba931a59dd59 + - e407b9da183a + - 1790dcf3c32d + - f5ea3ce9b9b0 - 7068f48d0ef9 + - e08a7ad4378b + - 69ebb7f46e45 - 6ea73833cf67 - - c441583adae5 - - 734abc7ac21d + - 1ec814014652 + - f8054ea1c365 + - 8848455c0270 + - 5e6237d58b0c + - 516a54ddf218 - 6591f049cf7e - - 83c7d564b128 + - 653e89d73fc4 + - aad3885b3216 + - 9a776b080193 + - 4df8de2d0e48 + - c441583adae5 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 75b3b3d0adbf - - 21a560af5913 - 34758ab8aaa4 - 9aaa46d45472 + - 75b3b3d0adbf + - 21a560af5913 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - bfdc6a7ffd3a + - 468c71dac78a - 054483e27a35 + - bfdc6a7ffd3a - af5eccf83605 - - 468c71dac78a tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index 37de18cf4..0935cf247 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - 7f13dc906cb9 - - 4b519282a05b - - 740057a5126d + - 290a11559985 - fd59d783248a + - 4b519282a05b - ae9994cf526f + - 7f13dc906cb9 + - c4bde687c846 - df7356989ac1 - a64dc31ab7f2 - - c4bde687c846 - - 290a11559985 + - 740057a5126d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -34,9 +34,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 7cf5b1d072b5 - - f95284aa2946 - 867ab348287d + - f95284aa2946 + - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -48,30 +48,30 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: + - 53460afd5115 + - 3b37b1b1c3a7 + - 51c6ccaace7e - ca7cb0eaad62 - 374e9062d874 - - 3b37b1b1c3a7 - '566197475670' - - 53460afd5115 - - 51c6ccaace7e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - da4c086cff5b - - 1a72f938213e - - 391a4cc45fea - - 3d059e9c2fba - d3a9e32672ec - 10515715c940 + - 3d059e9c2fba + - 1a72f938213e + - da4c086cff5b + - 391a4cc45fea tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram owner: iuc revisions: - - b0d96516e6a5 - 6fc8bab811da + - b0d96516e6a5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_pca @@ -84,19 +84,19 @@ tools: - name: ggplot2_point owner: iuc revisions: - - 299307abd804 - - e3a675da7fd0 - - 5298e06f14f9 - 1acf88921176 + - 299307abd804 - 5fe1dc76176e + - 5298e06f14f9 + - e3a675da7fd0 - d0fc8b746d57 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - - 0e7290688b50 - 17b666467c32 + - 0e7290688b50 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -108,8 +108,8 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - 97e3b735ed22 + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan @@ -135,17 +135,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 1cfc579079a6 - - 112eb40ba6cf - - ca2def38369c - fd5dbf0f732e - - 6cd09d7b5f37 + - 836d1aa3e89a - 2bb2e07a7a21 - - 667e17248bfe - - a6e57ff585c0 - 17359b808b01 + - a6e57ff585c0 + - ca2def38369c + - 6cd09d7b5f37 + - 667e17248bfe + - 1cfc579079a6 - 4542035c1075 - - 836d1aa3e89a + - 112eb40ba6cf tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -178,18 +178,18 @@ tools: - name: plot_ragtag_paf owner: galaxy-australia revisions: + - c1bed78b9ed5 - 94e0834ae4ed - 501dcf66c0ce - - c1bed78b9ed5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: - - 85da91bbdbfb - - f234e2e59d76 - 1c5dcef5ce0f + - f234e2e59d76 - 62e3a4e8c54c + - 85da91bbdbfb tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -208,9 +208,9 @@ tools: - name: pretext_snapshot owner: iuc revisions: + - 7c9417381ad5 - 44c66e8d21e6 - 6c571966cfb9 - - 7c9417381ad5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -222,23 +222,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 4ac4e7083b7e - - 326a3db8d9d1 - - 7dd841a32245 - 36b848d5f3ec - - a1abfa420d9d - 360df4999907 - - 2824d77cd8f8 - 14e7c35f3d00 + - 4ac4e7083b7e + - 7dd841a32245 + - 326a3db8d9d1 + - 2824d77cd8f8 + - a1abfa420d9d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - 44608d0193ed - - 73b8cb5bddcd - 83c573f2e73c - 2f557f6abbfb + - 73b8cb5bddcd tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index 78d9d25f5..95e7e0623 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph @@ -35,15 +35,15 @@ tools: - name: scanpy_filter_cells owner: ebi-gxa revisions: - - 361608369dda - bf1e0bdec1db + - 361608369dda tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes owner: ebi-gxa revisions: - - 23d838d1569d - cc64914b0cf4 + - 23d838d1569d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster @@ -63,8 +63,8 @@ tools: - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 79da59a0b180 - 64dd8bb151e1 + - 79da59a0b180 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn @@ -84,16 +84,16 @@ tools: - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - 6903bc865d63 - c354af93f567 + - 6903bc865d63 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - ff6decc0f432 - - 94697510d55f - 9a2f72d7dbd2 + - 94697510d55f + - ff6decc0f432 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -106,15 +106,15 @@ tools: - name: scanpy_normalise_data owner: ebi-gxa revisions: - - 3027cb62adbd - 28b1546857b0 + - 3027cb62adbd tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - 73d43034c860 - d4c9061c8fef + - 73d43034c860 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed @@ -127,15 +127,15 @@ tools: - name: scanpy_plot_scrublet owner: ebi-gxa revisions: - - 6f5509cf3176 - 4a74b45c1ce4 + - 6f5509cf3176 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory owner: ebi-gxa revisions: - - d3df472a21dc - cb1992d1804b + - d3df472a21dc tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x @@ -155,8 +155,8 @@ tools: - name: scanpy_run_diffmap owner: ebi-gxa revisions: - - 6a6364b488db - 79cc06a557b0 + - 6a6364b488db tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt @@ -176,15 +176,15 @@ tools: - name: scanpy_run_paga owner: ebi-gxa revisions: - - 6d4f88995e40 - b2768cae00a1 + - 6d4f88995e40 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_pca owner: ebi-gxa revisions: - - 4428dba93375 - 0cf90e01d9f8 + - 4428dba93375 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne @@ -197,15 +197,15 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: + - ea91cfd0444e - 0f98603d0116 - 767a675b5254 - - ea91cfd0444e tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - e2d0dc8a50ca - 4cc9362782b4 + - e2d0dc8a50ca tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 410763e5b..ed6b65bc5 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,41 +2,41 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - ed2cca6b5de4 + - a4c13ddcc8ee - 29f66c353bcb - - 921a2da49a0c - 9edf8894a22d - - a4c13ddcc8ee + - ed2cca6b5de4 + - 921a2da49a0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - 755df866ad0c - - d404277cc87a - ec4b948dc6f0 - - 5746d61f0a91 - 78fb5e286609 + - 5746d61f0a91 + - d404277cc87a tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 977dc15add20 + - 03dd3c16ae4e - 11fa44ee0603 - - 4d511437b1e5 - 9e357a8b2ec3 - - 03dd3c16ae4e + - 4d511437b1e5 + - 977dc15add20 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: + - 77919cc3618e + - c3e5e2cf12b7 - 3b5b54ed6392 - 0ba4f56a3613 - 41dbf4d162a2 - - 77919cc3618e - - c3e5e2cf12b7 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix @@ -45,8 +45,8 @@ tools: - 9939786dd9c9 - b63363075c2e - 5308ca68ef3d - - 7babd8a46fe0 - 12d51d7be66f + - 7babd8a46fe0 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index ba3afba8f..f07ab9c85 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,29 +2,29 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 3df9f0a4bf34 - - 8bccb36e055a - - 7db4fc31dbee + - 699a5e9146b3 - 81f0cbca04a7 - 0c777d708acc - - 699a5e9146b3 + - 7db4fc31dbee + - 3df9f0a4bf34 + - 8bccb36e055a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 0a53256b48c6 - - 5bc8cdc17fd0 - 2436a8807ad1 + - 5bc8cdc17fd0 + - 0a53256b48c6 - 5791a7f65275 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - 9d47aabda459 - e576b73a2e2f - 6ad1d3cfdea1 + - 9d47aabda459 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization @@ -38,18 +38,18 @@ tools: - name: 2d_simple_filter owner: imgteam revisions: + - d51310ab328a - f70b215d155c - dba87c4b32d3 - - d51310ab328a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - - fcadded98e61 - 10eed33aa9b2 - - b07f4839ca77 - 85edbb7a436b + - b07f4839ca77 + - fcadded98e61 - f3360fbeda64 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -63,9 +63,9 @@ tools: - name: count_objects owner: imgteam revisions: + - b58447a2eed2 - 5bf8eb50b280 - 664232d2a3f7 - - b58447a2eed2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler @@ -79,72 +79,72 @@ tools: - name: cp_color_to_gray owner: bgruening revisions: - - e8f822eeb9fd - bad171ed1e96 + - e8f822eeb9fd tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - - e7273daa5ae2 - 670975e92458 - 6070780813d9 + - e7273daa5ae2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - cdf8e3c57dae - ef4aed1d34c4 + - cdf8e3c57dae - df3ad3ba5c6f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 6a7da2e5f696 - - 2484086dee41 - 5d28ac336861 + - 2484086dee41 + - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - bace5a93a97c - - f2ed92b011a9 - 11f177b1a59e + - f2ed92b011a9 + - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: + - d0178bdcd00e - f24c370e5ea4 - f8fa0f6718a3 - - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: + - 31d195bedf6d - ad271f78a87a - 3245681b2f6d - - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - 993faa34333b - - 87d4d92d7487 - b6eec6087271 + - 87d4d92d7487 + - 993faa34333b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: + - ff1a86a87364 - c09dcda1143f - 6100a22bf4f2 - - ff1a86a87364 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image @@ -159,47 +159,47 @@ tools: owner: bgruening revisions: - a1a961c46d4b - - 2564f461de62 - ac5bea85a391 + - 2564f461de62 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - 91e03287f285 - - a32c3f810ade - 20dbb1f7ec7b + - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - 8536b1ae0254 - - b64af54c5c09 - 5499dc6f8ac1 + - b64af54c5c09 + - 8536b1ae0254 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - 6f4715b8540a - d3890df07463 - e972e07c7845 + - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - 980aed9e8fd5 - - 407925835dd9 - e52c75a28c4b + - 407925835dd9 + - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - d85f11570109 - acf3aa487283 + - d85f11570109 - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -228,9 +228,9 @@ tools: - name: cp_save_images owner: bgruening revisions: - - 33f4fa1413fb - - 4ecf93628f97 - 27edbb90ab2b + - 4ecf93628f97 + - 33f4fa1413fb tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -242,23 +242,23 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 972d2c365739 - 1fd453cd757b + - 972d2c365739 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: idr_download_by_ids owner: iuc revisions: - - f92941d1a85e - 4b794652dcdc + - f92941d1a85e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info owner: imgteam revisions: - 236ec78b2e53 - - f8b4eada923c - 7b6d9412c7f8 + - f8b4eada923c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images @@ -270,7 +270,7 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 22e573b7dcb1 - 8ad39f493587 + - 22e573b7dcb1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index f7b65f7d5..89fb826a7 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - a38934e303b9 - - 3a72fede57ce - - 78bbd17d0703 - 1069f6db0a0e - - d6e72da3ec35 - - 40737febe339 + - 3e4f434a69c6 - e319b5b65879 - e4ee04da1c19 + - 40737febe339 + - 3a72fede57ce + - 78bbd17d0703 - f362150bef41 - - 3e4f434a69c6 + - a38934e303b9 + - d6e72da3ec35 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 8f8df367470d - - f91cfb73d369 + - 72ddd32392cd - c88553ec696e - - 618297d23022 - 0135f1d487a0 + - 7fe36019c073 + - f91cfb73d369 - 2b95d5c04908 - - 9537184d421f + - 618297d23022 - fcbeda41d0ac - - 72ddd32392cd - - 7fe36019c073 + - 8f8df367470d + - 9537184d421f tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - d7e79eb3bcb3 - - 2cf4a1cafc16 - - ad0dc9f4c9e2 - fafb3d685fa9 + - ad0dc9f4c9e2 + - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 8c05afb547fa + - 5dc33613c288 - ee29337f905c - - a1c2aecd7a0d - - 9eaadf03e0df + - 8c05afb547fa - ee2beb764a7b - - 5dc33613c288 + - 7f1cfa4c0e32 + - 28a6f1908fcc - 3d18f8c3c0f6 + - a1c2aecd7a0d - 8d36959b000d + - 6a1515bb0687 - 94df24c6bc00 - - 7f1cfa4c0e32 - bd2a7d1316b9 - - 28a6f1908fcc - - 6a1515bb0687 + - 9eaadf03e0df - 43aac8d29685 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: + - 5d6ed46cc101 - cb903c9dc33d - - 5671e1d3d5ee - - a250929be21b - - 364f4ffec275 - 8858fa037a15 + - 9f978da6528a + - 5671e1d3d5ee - d37ede8589b2 - bcaa0d571ce2 - - c092052ed673 - - 86a20ae274fc + - 364f4ffec275 + - a250929be21b - db536ad45f28 - - 5d6ed46cc101 + - 86a20ae274fc - e3bb03cf207a - - 9f978da6528a + - c092052ed673 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 49236b03e4fd - abbc8041e8ec - - 38b91a3190cd - - f95f403841ad - - e1a015876aa9 - - c5c9f02b6167 - - 584beffa972b - - 194e3ceee923 - - 3b6a16d82c1b - 12d66d0d05ac - - 230b05597996 + - 584beffa972b - ed28dd32141c + - 230b05597996 + - c5c9f02b6167 + - 3b6a16d82c1b + - 194e3ceee923 + - 38b91a3190cd + - e1a015876aa9 + - f95f403841ad + - 49236b03e4fd tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/join_subtract_and_group.yml b/staging.gvl.org.au/join_subtract_and_group.yml index 3afdd087c..27c33e99e 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: - - 0f1724dd59d2 - b8a457820315 - f198773344e4 - 17e3b698dd52 + - 0f1724dd59d2 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: + - ac092723240d - ba0c40780ecf - - 374cb875d38a - a513e3fbb4c5 + - 374cb875d38a - 22c2a1ac7ae3 - - ac092723240d tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/machine_learning.yml b/staging.gvl.org.au/machine_learning.yml index 5e8999787..a50bce582 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,47 +2,47 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 522137aaa9c4 - - 66d7efc06000 - 772e0e89fc68 + - 66d7efc06000 + - 522137aaa9c4 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - 4d81e3e2fb63 - - f22a9297440f - 8a794e6d3388 + - f22a9297440f + - 4d81e3e2fb63 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - f1b9a42d6809 - - 2af1346e68c9 - e1317b5502fa - b6ef6d0cb6b7 + - 2af1346e68c9 - 818f9b69d8a0 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 947c2eacccb8 - 1588f9076e32 - 8334dc98c48e - - 05143043ca13 - c80db5d6fd8c + - 05143043ca13 + - 947c2eacccb8 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - 25b46af53232 - - 83228baae3c5 + - 9991c4ddde14 - 1552b8cb4a94 + - 83228baae3c5 - 29e4122c90de - - 9991c4ddde14 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble @@ -50,8 +50,8 @@ tools: revisions: - 53616c8b0865 - 1a53edc4b438 - - f3dfa4bdf87e - a07ab242b0b5 + - f3dfa4bdf87e - 060ca94ac049 - 841a6cc5fc58 tool_panel_section_label: Machine Learning @@ -59,42 +59,42 @@ tools: - name: sklearn_generalized_linear owner: bgruening revisions: - - 91c4e3331208 - d4808d5b83da - - 2fc89dcd41c8 - 40f4447733b2 - - 927586a18553 - dc4b5fd604a6 + - 91c4e3331208 + - 2fc89dcd41c8 + - 927586a18553 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - 7626ea9c2e1b - - 25ab6b4e376e - - 301e07345c93 - - 36e8d6d5d01b - e5a5ad882f1f - c6ae57f774c6 + - 36e8d6d5d01b + - 301e07345c93 + - 25ab6b4e376e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - b7c3e9a3b954 - - 02d2be90dedb - f9639b488779 + - 02d2be90dedb - 80852884053f - - 4ed102b922cb - 0630258dcf35 + - b7c3e9a3b954 + - 4ed102b922cb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: + - ec69cbe34b73 - caeb57858702 - 14180f9c831e - 61634a87efc7 - - ec69cbe34b73 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index 997f83c3b..a50b68f1d 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - a6d65b0c67af - - d5ceb9f3c25b - cd659e8cc5fa - - 749c918495f7 - - f6877ad76b00 - - 17062a0decb7 - - 017aba02828d + - 03e9b2fbc005 + - 3ba8d4563129 - 937aa69e715f + - 749c918495f7 - 0d4acadabb04 - - 3ba8d4563129 - - 03e9b2fbc005 + - 017aba02828d + - d5ceb9f3c25b + - a6d65b0c67af + - 17062a0decb7 + - f6877ad76b00 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -24,19 +24,19 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - b4a22d90cce9 - bfaa0d22c2e4 + - b4a22d90cce9 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - - 2477830927ec - - 64f11cf59c6e + - 3fe632431b68 - 53646aaaafef + - 2477830927ec - dfd8b7f78c37 + - 64f11cf59c6e - e188dc7a68e6 - - 3fe632431b68 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: - - 37b497aa133f - 3e1ea2facca6 - - 60afcc2c1d05 - 2ff111fac1d7 - e7f19d6a9af8 + - 37b497aa133f + - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: + - 11a0d50a54e6 + - 8c6cd2650d1f + - 77b2770508f6 + - 6b1e195506a3 - be1d967337e4 - 09b53c1d4ab1 - - 77b2770508f6 + - 5cc34c3f440d - b3eab4b67562 - - 6b1e195506a3 - - 11a0d50a54e6 - - 037c6e54df11 - 53c0b7a1a0c3 - c0c2d0941de8 - - f54f5baedfdd - - 5cc34c3f440d + - 037c6e54df11 - 3f4d6399997b - - 8c6cd2650d1f + - f54f5baedfdd tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 1cd2511a396e - - 13022c3d3076 - - 5ef7ec16b04f - - 178bdbdb6d24 - - 79b885ce78d7 - - b8f5f6e87f5c - - ec9cbd6b9a49 + - 45795f582ae9 - 00fbfac99d39 + - e403d27e8f24 + - ec9cbd6b9a49 - 42ce70172b72 + - 178bdbdb6d24 + - 5ef7ec16b04f - 9ee34ba73ebf - - e403d27e8f24 - - 45795f582ae9 + - 79b885ce78d7 + - b8f5f6e87f5c + - 1cd2511a396e + - 13022c3d3076 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/staging.gvl.org.au/metabolomics.yml b/staging.gvl.org.au/metabolomics.yml index 5ed2438e3..afa5641b6 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -14,8 +14,8 @@ tools: - name: biotransformer owner: recetox revisions: - - 90dc951da294 - 6cd2a9e6ac49 + - 90dc951da294 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_annotate @@ -93,15 +93,15 @@ tools: - name: matchms_convert owner: recetox revisions: - - b9cc12600553 - c990df6afc24 + - b9cc12600553 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering owner: recetox revisions: - - 00e66c401366 - a177ac3c752c + - 00e66c401366 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity @@ -114,15 +114,15 @@ tools: - name: matchms_formatter owner: recetox revisions: - - 1b09315a3f87 - 9e3c83d2afc3 + - 1b09315a3f87 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export owner: recetox revisions: - - f04610d25411 - b576ed720711 + - f04610d25411 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match @@ -192,8 +192,8 @@ tools: - name: msmetaenhancer owner: recetox revisions: - - b5467dead5b1 - 90745ecc5e9f + - b5467dead5b1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msnbase_readmsdata @@ -255,8 +255,8 @@ tools: - name: recetox_aplcms_align_features owner: recetox revisions: - - 7b42ee54d757 - 79ad928a0dae + - 7b42ee54d757 - c53a97599181 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -264,8 +264,8 @@ tools: owner: recetox revisions: - 149b9cc7499b - - 18ec7635bac6 - f3a18e020cdd + - 18ec7635bac6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template @@ -279,26 +279,26 @@ tools: - name: recetox_aplcms_correct_time owner: recetox revisions: - - 02c772a49998 - - 51332c2520c7 - 9064aecc78a7 + - 51332c2520c7 + - 02c772a49998 - 501a232f3cd5 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - b3413f335327 - - b341cfd4baf8 - e7305ba0dd38 + - b341cfd4baf8 + - b3413f335327 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: + - dd7bbc2b99d1 - 17a48d0a80f4 - cf061712a184 - - dd7bbc2b99d1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals @@ -312,9 +312,9 @@ tools: - name: recetox_aplcms_remove_noise owner: recetox revisions: + - ffbabefbd2e2 - ea0758b41473 - d90187b0f247 - - ffbabefbd2e2 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -326,8 +326,8 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 6b5dec818827 - 2c6fa447f6a0 + - 6b5dec818827 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature @@ -345,8 +345,8 @@ tools: - name: rmassbank owner: recetox revisions: - - 0b28816c1c2c - 5a6bb93ec656 + - 0b28816c1c2c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: spec2vec_similarity @@ -376,8 +376,8 @@ tools: - name: use_theoretical_mz_annotations owner: recetox revisions: - - b3d41b1fcb18 - e0cac9994a72 + - b3d41b1fcb18 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: w4mclassfilter diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index 2bd622bca..1d382c72c 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -8,8 +8,8 @@ tools: - name: cat_bins owner: iuc revisions: - - 0e63d03c8790 - 18676df0cb3a + - 0e63d03c8790 - 0094893f5001 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -22,8 +22,8 @@ tools: - name: cat_summarise owner: iuc revisions: - - a8216def322b - 7f1aaa1932d8 + - a8216def322b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -96,29 +96,29 @@ tools: owner: iuc revisions: - 7c2100246a2f - - 65db807336bc - - 5b5a7af9fbb4 - 76d3d2b10738 - 63f86089423e + - 65db807336bc + - 5b5a7af9fbb4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 84fd33a60b35 - 18a502a9d287 - - 96336c6a2bb7 - - 1c35dadbe76f - 00f5005840fa + - 1c35dadbe76f + - 96336c6a2bb7 + - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: + - 34e55239e68b + - f732237754fc - e8fba04706d3 - a9f4a217dcd6 - - f732237754fc - - 34e55239e68b - addaf9d22850 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -126,18 +126,18 @@ tools: owner: iuc revisions: - 0776d824d896 - - 04c15826a0b8 - 75403243703a - - 5fe3edf19b9c - 8c202e741d68 + - 04c15826a0b8 + - 5fe3edf19b9c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 43c99742158b - - 1c9b3bcd4261 - e96bbb9e24ea + - 1c9b3bcd4261 + - 43c99742158b - 8470de786d47 - 75c8945b0da2 tool_panel_section_label: Metagenomic Analysis @@ -145,19 +145,19 @@ tools: - name: dada2_mergepairs owner: iuc revisions: + - 84743da21318 - 5c865a382933 - 35176674168c - - 306a40d4bb8f - 1d75bd0595e2 - - 84743da21318 + - 306a40d4bb8f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 8daf4564ccda - 78faebd0879c - 32c9ea835770 + - 8daf4564ccda - ac72310b038a - 555ccac8a4c5 tool_panel_section_label: Metagenomic Analysis @@ -165,31 +165,31 @@ tools: - name: dada2_plotqualityprofile owner: iuc revisions: + - 7b8cb2b02978 - cae017b76acb - - f947b4bb5107 - a58e4a43f49c + - f947b4bb5107 - d60df8727f59 - - 7b8cb2b02978 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: + - 073608a50ac3 - 04144473e59e - 1bc3657cd694 - - 7136e9ab70db - - 073608a50ac3 - 7f3b59dee073 + - 7136e9ab70db tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - a7817705348e - - 0a1224c4b781 - - d943081510da - 9058d8943303 + - d943081510da - 19299bb1c6af + - 0a1224c4b781 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -202,29 +202,29 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - a68b985913ab - - b907a3c0434f - - f8f56dd6449f - - 65d52c693b8e - 4d9445dff47b - - dbf1798c0dcc + - 65d52c693b8e - c4db8c4de66f - 5c7ba3d85a01 + - a68b985913ab + - f8f56dd6449f + - dbf1798c0dcc + - b907a3c0434f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 15dbb444df71 - 213df31ba341 + - 15dbb444df71 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: + - 6d364c65c946 - 6c84982ee6f7 - 654548ae1357 - - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -244,17 +244,17 @@ tools: - name: humann2_renorm_table owner: iuc revisions: - - c6676a890f50 - b084117133af - d77397f09da1 + - c6676a890f50 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - cad93abecac9 - 7f208f1eb64f - 9704f1a3b32d + - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -293,33 +293,33 @@ tools: - name: humann_regroup_table owner: iuc revisions: + - e88b731dad59 - 31c6d107e7a5 + - 79706f10d680 - c409a495841f - 8237a0f225db - - e88b731dad59 - - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - 714d5a28cc5c + - aabf8cfb8fef - d24841f5c3d2 - - 094ad9c068af - 172920f67a84 - - aabf8cfb8fef - 71ea608ddfa3 + - 094ad9c068af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - d7e9a3c41657 - 4137b492233e - a4d7148ccee4 - a293a742194f - 12fb63b5f63f - 2bdd84912a2b + - d7e9a3c41657 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -331,20 +331,20 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - 75bedfb2078b - - 6fcb8ac37a3e - cf87759761eb - a92c06a3afa7 - - e2c71b852aba + - 6fcb8ac37a3e - 97f7bb0851e7 - 64bc7acc22a9 + - 75bedfb2078b + - e2c71b852aba tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - 81c5dd1c777f - e9d12c223a80 + - 81c5dd1c777f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler @@ -356,21 +356,21 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: + - 4033827c76b8 - c82508e76ad1 - 5e5a999ffaa9 - - 4033827c76b8 + - 2d35528d2141 - 4e5e73d03f0d - 080ea153677c - - 2d35528d2141 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - fc6c328c292f + - 95bf7479d53c - 6b7622dda516 + - fc6c328c292f - c2803012bbb3 - - 95bf7479d53c - 2cd76b089570 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -390,22 +390,22 @@ tools: - name: khmer_abundance_distribution_single owner: iuc revisions: - - 385a965c6f87 - 65b382bf9b7c + - 385a965c6f87 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution owner: iuc revisions: - - e699e2747356 - 7624945cacd3 + - e699e2747356 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_count_median owner: iuc revisions: - - 570505540a7b - b3d513c7093e + - 570505540a7b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_extract_partitions @@ -418,22 +418,22 @@ tools: - name: khmer_filter_abundance owner: iuc revisions: - - 29a4d6e2ae9c - b86562b4f3fd + - 29a4d6e2ae9c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_below_abundance_cutoff owner: iuc revisions: - - 00f7064c564b - 19607c740d19 + - 00f7064c564b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_normalize_by_median owner: iuc revisions: - - 4d23ab83ea29 - b1fe2ef3d244 + - 4d23ab83ea29 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition @@ -452,17 +452,17 @@ tools: - name: kraken2 owner: iuc revisions: - - cdee7158adf3 - - 328c607150ff - 20e2f64aa1fe + - 328c607150ff + - cdee7158adf3 - 4a9da2b6c2e3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax owner: devteam revisions: - - f03c7ba8d8bc - 50bd98b3ae5a + - f03c7ba8d8bc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -474,8 +474,8 @@ tools: - name: kraken_filter owner: devteam revisions: - - 5bee9adae474 - 67236d921e83 + - 5bee9adae474 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report @@ -501,8 +501,8 @@ tools: - name: kraken owner: devteam revisions: - - 8ba2174315aa - 766d5f63b0f4 + - 8ba2174315aa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_alpha_diversity @@ -570,22 +570,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 2cff76cf35c6 + - 0270541aaf46 - 3cc4a60615c0 - - 327d9f4cc95f - 7f5d7b0e9884 - - e073891b2afc - - 27250f92a01a - - 0270541aaf46 + - 2cff76cf35c6 - 4fd3b5d8706b + - 27250f92a01a + - 327d9f4cc95f + - e073891b2afc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 76bc4efa1aeb - - 708abf08a626 - eb50e7eca3dc + - 708abf08a626 + - 76bc4efa1aeb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -651,33 +651,33 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - ebb74774457e - fdbd63e92b01 + - ebb74774457e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - 2131d7dca455 - - 740fd2d16a28 - - a16313517e55 + - 6dee4abadccb + - 1a6cdf55390f - ff8f55893e7d + - b89b0765695d - fd69c607b43f - - 1a037928504c - - ef65b083bd0c - - ec368db926f4 - - 6dee4abadccb + - a16313517e55 - a92a632c4d9b - 289b3807e80c - - b89b0765695d - - 1a6cdf55390f + - 2131d7dca455 + - ef65b083bd0c + - ec368db926f4 + - 1a037928504c + - 740fd2d16a28 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning owner: galaxy-australia revisions: - - 2a8bc1d26d06 - e3a64a1d2a6e + - 2a8bc1d26d06 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -702,22 +702,22 @@ tools: - name: picrust2_hsp owner: iuc revisions: - - 6eafc1e01a8c - 3b133b8d578a + - 6eafc1e01a8c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 415cb5d91168 - 709adbfcf308 + - 415cb5d91168 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline owner: iuc revisions: - - 6077821e8ae7 - f53beb324696 + - 6077821e8ae7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline @@ -730,8 +730,8 @@ tools: - name: picrust2_place_seqs owner: iuc revisions: - - 73b56418e7f4 - 680fb3eb574c + - 73b56418e7f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions @@ -769,8 +769,8 @@ tools: - name: picrust_normalize_by_copy_number owner: iuc revisions: - - 65e5f9caefcc - 2e62e32d4f33 + - 65e5f9caefcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_predict_metagenomes @@ -813,13 +813,13 @@ tools: - name: staramr owner: nml revisions: - - 3b22de20bd4b - - aeaa20b96ef2 - - 4d83eccf5f81 - 2fd4d4c9c5c2 - 4b9a8031ab74 - - be818ae858e4 + - 3b22de20bd4b + - 4d83eccf5f81 - 141afacabcfa + - be818ae858e4 + - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -849,8 +849,8 @@ tools: - name: vsearch owner: iuc revisions: + - 576963db5f1b - 9495df9dd6ef - b3c7199d8786 - - 576963db5f1b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index c8656b62d..fe21f7ff7 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - 67cb43432196 - e866e31f6da3 + - 67cb43432196 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index 5df9e22e3..3f42408bd 100644 --- a/staging.gvl.org.au/multiple_alignments.yml +++ b/staging.gvl.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 80f03df2e2ce - bdfbaf0c10aa - - 48c13389050d - - 8b67dd48fec1 - 6ae5a7b5a0a2 - - 098506c54016 - - 9baa871cb1d1 - - cd07731e4434 - - a74dbfee5a86 - 2263989660f5 + - 48c13389050d + - a74dbfee5a86 + - 9eeb13a92d79 + - 8b67dd48fec1 - 94b8c6013083 + - 9baa871cb1d1 - 9422c5a87ee2 - - 9eeb13a92d79 + - cd07731e4434 + - 098506c54016 + - 80f03df2e2ce tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - c44f824c051a + - 3ff17bad4006 - f0af8936ed41 - 5abf2c2249aa + - bc3831dd65c1 - 2e093badc689 - - aaa0d6a8b808 + - c18157c68134 + - be78f13134e2 + - d7ce0ec78e51 + - c44f824c051a + - f14193ec1f50 + - '764845535798' - 4a60927aaca5 - d390fe1567dc - - '764845535798' + - aaa0d6a8b808 - fc2e49f91e52 - - c18157c68134 - - f14193ec1f50 - - d7ce0ec78e51 - - 3ff17bad4006 - - bc3831dd65c1 - - be78f13134e2 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,75 +46,75 @@ tools: - name: chromeister owner: iuc revisions: - - e483be1014b6 - b768cc4cca40 + - e483be1014b6 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw owner: devteam revisions: - - d6694932c5e0 - 5b097fde95dd + - d6694932c5e0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko owner: iuc revisions: - - 5efbd15675ca - 1de657a3198d + - 5efbd15675ca tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mafft owner: rnateam revisions: - - 15974dd17515 - bf28a8cff401 - - f1a5908ea2cb - - c5908940967d - f0d493f8f84f + - 8e649f27aa0d + - c5908940967d - a65296ffb4a0 + - 15974dd17515 - 6f28e90db932 - - 8e649f27aa0d + - f1a5908ea2cb tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - b3acbb3a6af0 - e8fdceffea4c + - b3acbb3a6af0 - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 5561a1193611 - - 60698466facd - c9685bc0407c + - 60698466facd + - 5561a1193611 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - 57f042937ba7 - 48823c9635a4 + - 57f042937ba7 - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: + - 4fc0cb2ac8ae - fb43e8887350 - ebe3b0f84de9 - - 4fc0cb2ac8ae tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - 636b049e6141 - 7cd7a55a678d - e18267f90096 + - 636b049e6141 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords diff --git a/staging.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index d63178fa0..05b697da3 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,17 +8,17 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 28928576e1ea - 1145758d2f0b - 7c47b3c9e493 + - 28928576e1ea - 18a8d140ec6f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado owner: galaxy-australia revisions: - - 63d8ecfcfab1 - fc5b6491cf78 + - 63d8ecfcfab1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: guppy_basecaller @@ -30,21 +30,21 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: + - a7228a7ea146 - 79e9a869f40e - 72b5e9dda577 + - cb34f00cc10f - 0e9e7fcdd543 - fc8804320156 - - a7228a7ea146 - - cb34f00cc10f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - 18505fe2bdb1 - - db25ec99c3ea - d6cddc06aeae - fa11aa8103b2 + - db25ec99c3ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -56,15 +56,15 @@ tools: - name: medaka_variant owner: iuc revisions: + - cc36773a3681 - ec699520444c - - 222669c4afb6 + - edf6d4003fad - 2bf63b38ee9b - - 19f3b583a9b3 - - cc36773a3681 - eb746fa6f514 - 43815fa60f3a - 0f5f4a208660 - - edf6d4003fad + - 222669c4afb6 + - 19f3b583a9b3 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -83,36 +83,36 @@ tools: - name: nanoplot owner: iuc revisions: - - a38bdcec9e4c - 7b379e98b9a9 - - 0f1c34698076 + - a38bdcec9e4c - a3c4fe6f49ab + - 0f1c34698076 + - 645159bcee2d - a02b8b3f5a0c - edbb6c5028f5 - - 645159bcee2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 85a394edc247 - 3b6f94fc7e1d - d219b6d8158a + - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: + - be95355fef8d - a8d4be409446 - 90a922f32523 - - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 449e9aeded2d - 4857d5bcce52 + - 449e9aeded2d - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -120,23 +120,23 @@ tools: owner: bgruening revisions: - bec636361cfd - - a3afc5f0a96c - de5b3d8f5b90 + - a3afc5f0a96c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 543cbeef3949 - 93d623d9979c - 5f76b20953e5 + - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - daf8518d243a - 1d835c691480 + - daf8518d243a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -149,30 +149,30 @@ tools: - name: poretools_hist owner: iuc revisions: - - 47936349f3e9 - d1805f9c4c82 + - 47936349f3e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist owner: iuc revisions: - - a57b6350fd5d - 5c4fa65f5733 + - a57b6350fd5d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_occupancy owner: iuc revisions: + - 336791b5665f - 338d15b8d6fb - 0433aad600e9 - - 336791b5665f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist owner: iuc revisions: - - ae9060e764b5 - 72dfdbfab3cc + - ae9060e764b5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualpos @@ -185,9 +185,9 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - ce8af9373061 - - 34553d0caa5e - 26e6c9362b7b + - 34553d0caa5e + - ce8af9373061 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -199,8 +199,8 @@ tools: - name: poretools_tabular owner: iuc revisions: - - 2cb2feb94f0e - 5f5f1da94d7f + - 2cb2feb94f0e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_times @@ -219,8 +219,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - 64a83664b814 - c5c5a3e84989 + - 64a83664b814 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index d254f3b43..a313061fc 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -21,8 +21,8 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: - - 71186bb66ca2 - 4e85a3a5dbd1 + - 71186bb66ca2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_frameshifts @@ -59,11 +59,11 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - 3e73c97f025d - - 97b1b5ad1cda + - baceff842902 - d74850cf4e42 + - 3e73c97f025d - adfd6bf710bd - - baceff842902 + - 97b1b5ad1cda tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder @@ -83,18 +83,18 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 1e34d2e3d285 - - 2f27f3b86827 - - e4b4837f06f5 - ed1518ce2237 + - 1e34d2e3d285 - edacc4bcd3cb + - e4b4837f06f5 + - 2f27f3b86827 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -106,23 +106,23 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 472dabcb03bf - 74af283d8ebd + - 472dabcb03bf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_dada2 owner: iuc revisions: + - 38ccd4589990 - 5711fc06a63e - 48a42ca61006 - - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 5a0d0bee4f8d - 4a08b7b76b78 + - 5a0d0bee4f8d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -155,17 +155,17 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 6287d0ee459e - 9a40272f56d0 + - 6287d0ee459e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: + - 27a6a256cd23 - 172815da3d41 - b4b2b284230a - 5bcf0e24f42c - - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -192,8 +192,8 @@ tools: owner: iuc revisions: - 19bbd19b74b3 - - 87febc68b45b - fea85c467896 + - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -206,8 +206,8 @@ tools: - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 15c2fc266540 - 4c7ebbad42cf + - 15c2fc266540 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -225,11 +225,11 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 2c61c30a57e7 - 9c43baa60906 - - d8dc037e3c13 - - 0cb27ea69dc1 - 5fe20c915fa6 + - 0cb27ea69dc1 + - 2c61c30a57e7 + - d8dc037e3c13 - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -243,18 +243,18 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - aec831b54a5b - 9d09724f2bf1 + - aec831b54a5b - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - df30a2f1db55 - - 6e24e79d3d69 - ed7a967cb11b - 29c738066906 + - df30a2f1db55 + - 6e24e79d3d69 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -280,8 +280,8 @@ tools: - name: data_manager_snpeff owner: iuc revisions: - - def511e8e005 - d107d20dc6bd + - def511e8e005 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -294,16 +294,16 @@ tools: owner: iuc revisions: - 64deddb6a8ec - - d63c1442407f - c520a52b5174 + - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 9946bc39c834 - - 94a50db37d1a - 625fd9476402 + - 94a50db37d1a + - 9946bc39c834 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1060,8 +1060,8 @@ tools: - name: rdock_rbcavity owner: bgruening revisions: - - 7e5c2e4bc227 - 744a777e9f90 + - 7e5c2e4bc227 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rdock_rbdock @@ -1081,11 +1081,11 @@ tools: - name: salsa owner: iuc revisions: - - ab5b7f6b7198 - 9a22227bb6d0 - - ba7b0f11e470 - - 58a870ef434c - f77f7a7f3b83 + - ab5b7f6b7198 + - 58a870ef434c + - ba7b0f11e470 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_merge diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index c9c04ad88..a597da6f2 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -26,8 +26,8 @@ tools: - name: gubbins owner: iuc revisions: - - 96e6283e4745 - 637ec5d5368c + - 96e6283e4745 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -39,66 +39,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: + - f04a1264e2a2 - d7c7ef3353fe - - 8834daeb9892 - - b89cac5156ec - - 6a457678efcb - - c78f3d7dd1db - - 26de3a7b1cb9 - - a6619171428e - - 107d3ba7024a - cce7b18495e4 - - f73435dc282b - d033ffc1c161 - - f04a1264e2a2 + - f73435dc282b + - 3f59ebfbfe3d - '841557158611' - 81e66674859e - - 3f59ebfbfe3d + - 26de3a7b1cb9 + - 8834daeb9892 + - 107d3ba7024a + - a6619171428e + - 6a457678efcb + - c78f3d7dd1db - 3b8b5bde0bd9 - 5a7c56a5cc08 + - b89cac5156ec tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - b0af57c1a968 - - 7a2092844346 - - 5b777002c2de - - e75442c7f4da - - 659517798cc4 - - 3b96e92e8ec3 - - 5fcd1ece3a6e - 6223845127ea - - 02b8758214b0 - - 6a726db04d4b - - df47d4845b62 - 4755f52427c4 - a185b079b095 - - aa8cc71438cf - - 88c4aa435ded + - 02b8758214b0 + - e75442c7f4da - 6283babe736e + - 5fcd1ece3a6e + - 6a726db04d4b + - 88c4aa435ded + - aa8cc71438cf + - b0af57c1a968 + - 5b777002c2de + - df47d4845b62 + - 3b96e92e8ec3 + - 7a2092844346 + - 659517798cc4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: + - d1c340a5664b - b8476e82ac20 + - 111bd54f6bc4 + - 24d024316465 - f87ac61981f0 - - d1c340a5664b + - 70acec670c30 + - 0878b7fd5260 - 524d31add34a - - 24d024316465 - - 111bd54f6bc4 - f97743d52b87 - - 0878b7fd5260 - - 70acec670c30 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - daddf188c13f - 9e10ba792be2 - feb40665d7cd + - daddf188c13f - 4f6349228462 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -111,26 +111,26 @@ tools: - name: pangolin owner: iuc revisions: - - ca337cce3888 - - b6abccb1f25b - - 36912871ccdc - - 9d61d3fa046c - - 42a174224817 - 2fa9d4f1b48f + - 8ad84c5753ea - 3a43c3982401 - - 2f1019071464 - - 5f8727ff21e7 - - 03ed9524dcd1 - b7e297c2ede6 - - 83a69484cb87 - - 437e28791761 + - 42a174224817 + - 36912871ccdc + - b6abccb1f25b - a2099fb98cdb - - 7bb8726be37c + - 03ed9524dcd1 + - 437e28791761 + - 9d61d3fa046c + - 5f8727ff21e7 + - 81804a978fc0 + - 83a69484cb87 - abf6dbe8c9d7 - 14ae456b8cc5 - - 81804a978fc0 - - 8ad84c5753ea - ca0d8cf80567 + - 7bb8726be37c + - ca337cce3888 + - 2f1019071464 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -149,23 +149,23 @@ tools: - name: raxml owner: iuc revisions: + - 73a469f7dc96 - ea30d3089354 - ba29b5e2a4be - - a4b71be30c3c - - 73a469f7dc96 - - 29ff6a849eac - b1e68bbe4cef + - 29ff6a849eac + - a4b71be30c3c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - 15ac71df11a0 - - e88a7de55d6e - - f1ccc8a6eb05 - 809e42326fc2 + - f1ccc8a6eb05 - 9b2b122d0415 - dbe2b2204555 - 91887494eb97 + - e88a7de55d6e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/picard.yml b/staging.gvl.org.au/picard.yml index 3281fb54a..14a194b51 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -3,13 +3,13 @@ tools: owner: devteam revisions: - f9242e01365a - - b502c227b5e6 - - fc288950c3b7 + - 1aac2a13842a - f6ced08779c4 - a1f0b3f4b781 + - b502c227b5e6 + - fc288950c3b7 + - 3f254c5ced1d - 881d7645d1bf - 7d34178f2812 - - 1aac2a13842a - - 3f254c5ced1d tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomic_ai.yml b/staging.gvl.org.au/proteomic_ai.yml index d165e3f8a..4f49da93e 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -2,17 +2,17 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - c0e71cb2bd1b + - ca90d17ff51b - e7f1b552a695 - - 6ab1a261520a + - c0e71cb2bd1b + - a58f7eb0df2c + - 3bd420ec162d - e4a053d67e24 - - 5b85006245f3 - - 7fbec959cf2b - - d00e15139065 - - ca90d17ff51b - eb085b3dbaf8 - - a58f7eb0df2c - 2f7702fd0a4c - - 3bd420ec162d + - 7fbec959cf2b + - 5b85006245f3 + - 6ab1a261520a + - d00e15139065 tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomics.yml b/staging.gvl.org.au/proteomics.yml index d7d827005..fe0e5e2b7 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,94 +2,94 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - 4c177985028a - - 277dc652246e - - ece627528a78 - b18329a8ac14 + - 277dc652246e + - 4c177985028a - b574b84afc4d - - 0a18ac48ac53 - f28ad96b76dc + - 0a18ac48ac53 + - ece627528a78 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - e988563cc6e5 - - bf06d196e23d + - e215f71d7983 + - b41107d8fe89 - 525f201b86c1 + - bf06d196e23d - a9a28e46d54a - - b41107d8fe89 - - e215f71d7983 + - e988563cc6e5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - bb6397b94018 + - 56da27be956a - 4fbffddde8cd + - bb6397b94018 - 8da3511c9467 - - 56da27be956a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - 528fb09022be - - a8157342d9a3 + - b8c79e70516d - f23d67e28cc8 - 890845926d4b - - b8c79e70516d + - 528fb09022be + - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 59e85306eae5 + - a95a82eb4d50 + - a69865da6f80 - 80600735685d - ae304a72db7b - 25b83cbd596a - - a69865da6f80 - - a95a82eb4d50 + - 59e85306eae5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - f1897eb07081 - - 83aac7741200 + - 798da6bdff3d - e0669b1854b1 - ed9ed1e6cca2 - - 798da6bdff3d - 611d80c0e29d + - f1897eb07081 + - 83aac7741200 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - a7fb9b395ddf - - 5a35e3a8d013 - d426a9107a6c + - a7fb9b395ddf - 74b61bf5bc4b + - 5a35e3a8d013 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - df2187f9013b - - 91f0f5922011 - - cc430977c8ff - 82f6c2f4332d + - cc430977c8ff + - 91f0f5922011 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 1693b2126f30 - - 043f9c91f686 - c5aa9fca18c6 - - ba92b59cd529 + - 043f9c91f686 - d2483487e077 - 10566783d718 + - ba92b59cd529 + - 1693b2126f30 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -129,16 +129,16 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 4081e4faa4ab - - 0fa397f4f40b - 1c5cbf8f79ce + - 0fa397f4f40b + - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib owner: galaxyp revisions: - - 36880dfd9fa7 - fb192dd6658a + - 36880dfd9fa7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut @@ -158,9 +158,9 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - 160538a890a6 - - d286ff4600dd - e66f552a3c47 + - d286ff4600dd + - 160538a890a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing @@ -173,23 +173,23 @@ tools: - name: maxquant_mqpar owner: galaxyp revisions: - - 3fc2116ac6d9 - 9cb7dcc07dae + - 3fc2116ac6d9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - f522c08e900c - - 97a7f34fcb6a + - 2133b0be850a - 837224ad1694 + - 97a7f34fcb6a + - 1f39c833f65f + - e42225f8a659 + - 37d669de2828 - 7f432d87c82c - 9c52362ae7bb - - e42225f8a659 - 4d17fcdeb8ff - - 2133b0be850a - - 37d669de2828 - - 1f39c833f65f + - f522c08e900c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -201,45 +201,45 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - a72ac2c7cc5b - 0ed07016d668 - - e63db1aa82ee + - a72ac2c7cc5b - 85b8866f06d7 + - e63db1aa82ee tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: + - 352b37c66d97 - 767c1d761aaf - 1974224d63c2 - - 352b37c66d97 - 990b4560ead7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 35cc7ca0bdc7 - - deaf035bbe9f - - 99450519d727 - 4f359549383c + - 99450519d727 + - deaf035bbe9f + - 35cc7ca0bdc7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: + - c1343e3389ca - e79958768a2c - 06f6826d380c - c7745841de24 - - c1343e3389ca tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - d46d64e7964d - - da986f83631b - d2eac53666f0 + - da986f83631b - b9d453dca8d3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -248,15 +248,15 @@ tools: revisions: - 1199751329b0 - 944b43462104 - - 8bd7734309f6 - 9bf325045235 + - 8bd7734309f6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus owner: galaxyp revisions: - - 8295d959ca28 - e0104a9f20f0 + - 8295d959ca28 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert @@ -269,10 +269,10 @@ tools: - name: msstats owner: galaxyp revisions: - - 28434abe6c5c - 8212e342e482 - - de7593c29499 - 593839e1f2c3 + - 28434abe6c5c + - de7593c29499 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -285,10 +285,10 @@ tools: - name: openms_consensusid owner: galaxyp revisions: - - 4e77b8f12cd3 - - 8960fb791701 - f4be248c3d47 - 01dbaf6a57e0 + - 4e77b8f12cd3 + - 8960fb791701 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -302,137 +302,137 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 9cdf15d3cfc8 - - 518b1730cf2a - c9eff69a7c62 - - f7fef900f5b2 + - 9cdf15d3cfc8 - 6ccbf9a2072c + - f7fef900f5b2 + - 518b1730cf2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: + - dff6c756eee5 - 9876bda3ec53 - - ca88bd28f116 - 5e948629bc73 - - dff6c756eee5 + - ca88bd28f116 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 1595601708ec - - 41859bbdc16e - 890025d6e426 + - 41859bbdc16e + - 1595601708ec - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 6634cad7d797 - 9b7977080f6d - - 2a93a25f0599 - 5ad0b5bf1deb + - 2a93a25f0599 + - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - 05d5e1ddc985 - - d6878d27f051 - fe4e4587d265 - 0bb5056cb775 + - 05d5e1ddc985 + - d6878d27f051 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 4af67edd5aef - 52ba9695e752 - 5ad830edc021 - febd569ad26f + - 4af67edd5aef tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - 39e8fde08881 - - 27cba4c5fc42 - 92352a475eed + - 27cba4c5fc42 - b2fc8da99bcc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - d3546bb9fd8e - - 0efbc235f314 - d413dc49d650 + - 0efbc235f314 + - d3546bb9fd8e - 9e26f5c770f8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - c28f13cab67a - - 3720e349ba2a - 8a04ed1c1d1b + - 3720e349ba2a + - c28f13cab67a - ca1740533b59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: + - c427a8628cbe - 382cde407f81 - a5d785af0ad8 - c55dddc5844a - ca799a7246e7 - - c427a8628cbe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - adca857b4884 - - 8ddb7bab1138 - b5d0905419da + - adca857b4884 - 39caaa778d2e + - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - 1c5f31b8d632 - - f817513840a9 - 34e7afee141d - - 18f93351f8b6 - 8d4db262964c + - f817513840a9 + - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 5d9f175dff81 - 986e03d3201e - - 111c3a00136d + - 5d9f175dff81 - c69f69d7867a + - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 476b5e296979 - - be74a8cd7d66 - 4204882495f2 + - be74a8cd7d66 - 0e52c85f3b15 + - 476b5e296979 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter owner: galaxyp revisions: - - 9866e1170611 - e133b5c8878f + - 9866e1170611 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter @@ -447,50 +447,50 @@ tools: - name: openms_multiplexresolver owner: galaxyp revisions: - - d0304fb829c0 - 021fdb80f204 + - d0304fb829c0 - 4e66c4e73909 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: + - ee860980edc6 + - 2735db4dd8d9 - 8098330f6d91 - bf32e0bcf554 - - 2735db4dd8d9 - - ee860980edc6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: + - 0ced5bc9f4dd - a2a6e9551046 - 08488066d588 - - 0ced5bc9f4dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - - 8c01da82292c - de7a553552a6 + - 8c01da82292c - 2a9ff56cb279 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - e8f64a7dc470 - - 1bf940c18d93 - c1809c05ae8c + - 1bf940c18d93 + - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 9f505cd4428f - 496cf619e311 - f861ec9fbe59 + - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring @@ -512,92 +512,92 @@ tools: - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - 05ec9fb05ed1 - f9ed7e074900 - f82b320ceb90 + - 05ec9fb05ed1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: + - 18826fb8e5db - d31426ef20f6 - 6e8cc5ed2a9b - - 18826fb8e5db tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - - 4a7b96835140 - bc63b4d12779 - 2aebe58de46e + - 4a7b96835140 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - decc397c3b7e - 6b01678ec2fc - - 3d8d4ada5405 + - decc397c3b7e - 5ae104d0da6e + - 3d8d4ada5405 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - e039cc5c7aed - - 539a3a4dcc9e + - d6aca689dd48 - dd173849c3d8 + - 539a3a4dcc9e - 5182338d5e7c - - d6aca689dd48 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - d426affe977c - - 16026cdb1330 - 8a45fd5a608a + - 16026cdb1330 + - d426affe977c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - dd71e020e2aa - 43b9ed22e8ce - 9c70a651a53e + - dd71e020e2aa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: + - d063e2fe4ba4 - 9020199dba0a - 1b03536aa3c9 - - d063e2fe4ba4 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - 78c080d36945 - - f036e8cf1a55 - ad2ba3a95a02 + - f036e8cf1a55 + - 78c080d36945 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - 7f6a1f27553e - - c8b225c69a7f - fb52e95a370c - 5c2a97a234d6 + - 7f6a1f27553e + - c8b225c69a7f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - 073a2965e3b2 - a6282baa8c6f + - 073a2965e3b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pepquery2 @@ -617,13 +617,13 @@ tools: owner: galaxyp revisions: - 1beff3ddce58 - - da885ca16cb2 - - 7fdd9119cc4f - 3ec27b4cee7c - a72c48001f7c - - 07ff622ec007 - - 943a34df6047 - 3634c90301af + - 7fdd9119cc4f + - da885ca16cb2 + - 943a34df6047 + - 07ff622ec007 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -683,10 +683,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 265c35540faa - 1a5690a5eedc - - a371252a2cf6 + - 265c35540faa - 12692567c7f9 + - a371252a2cf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index d7c374a9a..9a90ee393 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,11 +2,11 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 42201b90e3f4 + - e345aadf914f - 289b7d6b69a4 - - 110a346daf36 + - 42201b90e3f4 - cd5f98911089 - - e345aadf914f + - 110a346daf36 - 2f1d464ebfd2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -19,12 +19,12 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - 0345dbaaa79b - 42d9087b4789 - - 0cd2df8af811 - - fcce77c09289 - c207119ba5f6 + - 0cd2df8af811 + - 0345dbaaa79b - 8501601a118d + - fcce77c09289 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: - - 421c33b8bf17 - - 33486216eec0 - 89eb29319bf4 + - 405a212b32ab + - 33486216eec0 + - 421c33b8bf17 - 04db7fd6b238 - ad5ab22ffe24 - - 405a212b32ab tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -53,12 +53,12 @@ tools: - name: stacks2_gstacks owner: iuc revisions: - - 1d839ead7ad3 - - 7b72fde3d27e - - fa51dc5e8386 - - eb784fa07f80 - f6e91108b7b1 + - eb784fa07f80 + - fa51dc5e8386 - 7370bb65bad4 + - 7b72fde3d27e + - 1d839ead7ad3 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -70,12 +70,12 @@ tools: - name: stacks2_kmerfilter owner: iuc revisions: - - d30e36c48c93 - - 1544278c272e - - c9b77ced9a78 + - 8a55d29c8fcf - 3d70c2996730 + - 1544278c272e - a3e86cd9cac7 - - 8a55d29c8fcf + - c9b77ced9a78 + - d30e36c48c93 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -87,12 +87,12 @@ tools: - name: stacks2_populations owner: iuc revisions: - - b242deb58952 - - 564c33e5c3e3 - - e2db212d64ad - 7b881f5f5ad5 - - a5969aa9347e + - e2db212d64ad + - 564c33e5c3e3 + - b242deb58952 - 887cf585cafc + - a5969aa9347e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,11 +104,11 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - bd5ff77e2036 - e897c74a48bb - - 8cff84759bf6 - 9a171f9a450b - b4bab607eb05 + - 8cff84759bf6 + - bd5ff77e2036 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 6dafad990086 - 33f0793edf93 - - adc7a7610d4f - 5e10f396979e - - 4f65e343ecdf + - 6dafad990086 + - adc7a7610d4f - 887e0991eb24 + - 4f65e343ecdf tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -137,12 +137,12 @@ tools: - name: stacks2_shortreads owner: iuc revisions: - - c287418eb288 - - c5d7050e4ad7 - 4e280b27a831 + - c287418eb288 - 43e3eeb2e0ec - - 97575d01f06b + - c5d7050e4ad7 - 17d39bf0a63a + - 97575d01f06b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,12 +154,12 @@ tools: - name: stacks2_sstacks owner: iuc revisions: - - a819ec3b362d - 0b8c84a7fdb5 - - 09b8edb56d80 - - 9586f08634c0 + - a819ec3b362d - d9bf483266a1 + - 9586f08634c0 - cd034465d4a4 + - 09b8edb56d80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -171,12 +171,12 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: - - bf0e43ab0416 - 69842dd5aa48 + - a4b4bd84f69e + - bf0e43ab0416 + - 95351dd0fd3f - 2645575d1bf2 - a9c34a289493 - - 95351dd0fd3f - - a4b4bd84f69e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,11 +188,11 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - 912f904a6e1e - bb0475c884ff - cfb504394ae1 - 8a35a3bc6752 - d1fda11e602f + - 912f904a6e1e - d033e1ccb386 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -235,9 +235,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - d504d945a655 - d1fad35bdb4a - 95286af4139b + - d504d945a655 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 649942d45..0c19fb928 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,18 +2,18 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: + - 31f8063eedea - cf01dd6c6b1f - - 2d4e3aff9dc7 - 7acb00fc980a - - 31f8063eedea + - 2d4e3aff9dc7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - 703a2cb3fb38 - - 125d20cb23d7 - 32e542c2a773 + - 125d20cb23d7 - 7a5a2d28c539 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -21,8 +21,8 @@ tools: owner: iuc revisions: - 3d61a698e5e1 - - 01ccd366690d - 45c2ec061cf9 + - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -34,8 +34,8 @@ tools: - name: blockclust owner: rnateam revisions: - - aab6cf87b40a - dbb6ee3179bc + - aab6cf87b40a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockclust @@ -77,9 +77,9 @@ tools: - name: cuffcompare owner: devteam revisions: + - ad5d061fbdf2 - f648e5180e40 - e66b9b5b8580 - - ad5d061fbdf2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffcompare @@ -105,10 +105,10 @@ tools: - name: cuffmerge owner: devteam revisions: - - cf747d1bd79a - - 22cf48ad7b16 - - 6a6717a5f421 - 86285ddd4512 + - 6a6717a5f421 + - 22cf48ad7b16 + - cf747d1bd79a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -120,9 +120,9 @@ tools: - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - - 9a854107dbb2 - 28b94cfbfdb9 + - 9a854107dbb2 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -134,8 +134,8 @@ tools: - name: cuffquant owner: devteam revisions: - - 679d93c99757 - 93148c05136f + - 679d93c99757 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -159,10 +159,10 @@ tools: - name: describe_samples owner: iuc revisions: - - e3b16fd7dd08 - 8f0181aacb7a - 3b36efd62b3e - 0693ccd171c4 + - e3b16fd7dd08 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -174,13 +174,13 @@ tools: - name: deseq2 owner: iuc revisions: - - 6a3a025714d3 - - 9a882d108833 - - 24a09ca67621 - - cd9874cb9019 + - 8fe98f7094de - 0696db066a5b + - cd9874cb9019 + - 9a882d108833 + - 6a3a025714d3 - d027d1f4984e - - 8fe98f7094de + - 24a09ca67621 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -192,11 +192,11 @@ tools: - name: dexseq owner: iuc revisions: + - df929f257179 + - 62adf13b86ea - 2872c633f07e - b47c006d90c5 - - df929f257179 - 9a7c5b6d8f1e - - 62adf13b86ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -208,18 +208,18 @@ tools: - name: edger owner: iuc revisions: - - 334ce9b1bac5 - df0c8d0a5992 + - 3d89af8a44f0 - 070900306913 - - 555659de7321 - 9bdff28ae1b1 - - 0cb907a2a810 + - 6e53e565fc6a - f2843df56434 - 5bf899c13979 + - 555659de7321 - ae2aad0a6d50 - - 6e53e565fc6a - a8305cf0c951 - - 3d89af8a44f0 + - 334ce9b1bac5 + - 0cb907a2a810 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -231,8 +231,8 @@ tools: - name: egsea owner: iuc revisions: - - 31ea4992b948 - fba1660fb717 + - 31ea4992b948 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -250,16 +250,16 @@ tools: - name: featurecounts owner: iuc revisions: + - af814359d244 + - 38b6d12edc68 + - ea04b737afa0 + - 7db9d3ea71c9 + - e6a2a912677a - a56fbe2d6ba7 - - f3a5f075498f - 90d16db017d7 - - e6a2a912677a - - 38b6d12edc68 - - af814359d244 - a37612abf7f9 - f9d49f5cb597 - - 7db9d3ea71c9 - - ea04b737afa0 + - f3a5f075498f - 6f66ae7c5f7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -291,8 +291,8 @@ tools: owner: iuc revisions: - 3c97c841a443 - - 0f710191a66d - 3c5e024a18cf + - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -310,13 +310,13 @@ tools: - name: hisat2 owner: iuc revisions: - - 6c19daec423d - - 3fb01a8c902d - - d4b55e2beb12 - 6ab42baa56e9 - - 26371a1df031 - - f4af63aaf57a + - d4b55e2beb12 - a86e80d3c09c + - f4af63aaf57a + - 26371a1df031 + - 6c19daec423d + - 3fb01a8c902d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -334,9 +334,9 @@ tools: - name: htseq_count owner: lparsons revisions: + - 4418229c501e - 67b0b160903a - 916cb26bd9d3 - - 4418229c501e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -355,10 +355,10 @@ tools: owner: iuc revisions: - 1c75aa5de15e - - ce5d418183c5 - 87c11c05d238 - - 01247aaf0a10 - 5ae5c312d718 + - 01247aaf0a10 + - ce5d418183c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -370,10 +370,10 @@ tools: - name: kallisto_quant owner: iuc revisions: - - 40985510cd98 - - 10c98fab6c5a - c971db6f0fe5 - 4f9c4e6566e5 + - 40985510cd98 + - 10c98fab6c5a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -385,14 +385,14 @@ tools: - name: limma_voom owner: iuc revisions: - - e827f9aae031 + - 708348a17fa1 - 32511f586472 + - 58c35179ebf0 - 0921444c832d - - 97e06a4c7c75 - 119b069fc845 + - e827f9aae031 + - 97e06a4c7c75 - d6f5fa4ee473 - - 58c35179ebf0 - - 708348a17fa1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -410,8 +410,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_mapper @@ -441,8 +441,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - 72927fc9e9ed - d696cf0a9622 + - 72927fc9e9ed tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -460,21 +460,21 @@ tools: - name: rgrnastar owner: iuc revisions: + - c7c55b694974 + - 980d2a2e1180 + - c772497b2c32 + - 5ec75f5dae3c + - e132e7d02a3e + - 4074fc1940e2 + - b0f2be869d6d - 79de45b5069b - 4df95e2d7f61 - - c772497b2c32 + - 0a563fd2f22e + - 3ea5a2a63fa2 - 4014de1b6daf - - 4074fc1940e2 - - e132e7d02a3e + - 99b17b74a8cd - 7ed2edc1337f - - c7c55b694974 - - 3ea5a2a63fa2 - - 0a563fd2f22e - b9e04854e2bb - - 980d2a2e1180 - - b0f2be869d6d - - 5ec75f5dae3c - - 99b17b74a8cd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -498,14 +498,14 @@ tools: - name: salmon owner: bgruening revisions: + - 2c0ca397d302 + - 49121db48873 - 53e9709776a0 + - 15cd64d7c58b + - cc05793bb896 - ebab418107f5 - f4d5237a84f6 - - cc05793bb896 - - 15cd64d7c58b - e3d32471da11 - - 49121db48873 - - 2c0ca397d302 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -517,23 +517,23 @@ tools: - name: seurat owner: iuc revisions: - - c0fd285eb553 - - 8c28affc7c48 - 56242ff81c84 - fab6ff46e019 + - c0fd285eb553 + - 8c28affc7c48 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 258d696dbd7e + - 914cfcba0ec8 - 1ebd14235b92 - cef79931dda5 + - ae618321f34a + - cbf488da3b2c - 76d290331481 + - 258d696dbd7e - dd4df992d93d - - cbf488da3b2c - - ae618321f34a - - 914cfcba0ec8 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -569,10 +569,10 @@ tools: - name: transdecoder owner: iuc revisions: - - 0db979fead3a - - c6334cb383ff - - d0d4cef4f967 - ffd1300599a1 + - d0d4cef4f967 + - c6334cb383ff + - 0db979fead3a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -584,10 +584,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: + - 74217fbfba4d - bcc5f03f1900 - - ba3720d7e68b - d6a479fd4281 - - 74217fbfba4d + - ba3720d7e68b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -599,10 +599,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 56162e446004 - - 2fb4ee002432 - c2b82a94493e + - 2fb4ee002432 - 478f36effca1 + - 56162e446004 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -615,8 +615,8 @@ tools: owner: iuc revisions: - 9ff3765e7172 - - 3f4094b6a565 - fab23c3b5258 + - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -628,10 +628,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 4687ecf0eb2d - be3f26533209 - - 34a018cbee9c - 870ac06dff8e + - 4687ecf0eb2d + - 34a018cbee9c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -643,10 +643,10 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: + - 65e7dea767ea - 5192f657f305 - 05ab8d5e04a2 - c5fbddcac63a - - 65e7dea767ea - 33406f5a445c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -660,9 +660,9 @@ tools: owner: iuc revisions: - 1fdb25a8384d - - 6f0fb35b799c - - e406ac71165d - a35cba31d904 + - e406ac71165d + - 6f0fb35b799c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -674,10 +674,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - 37a1129c89d2 - 7c7fbf13aadd - - 964b7efe2639 - c2c039e421af + - 964b7efe2639 + - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -689,10 +689,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 24e94d84adc9 - - eafea3083352 - 047c22569787 + - 24e94d84adc9 - 1d689e4e1caf + - eafea3083352 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -704,9 +704,9 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 1812dbc5bb7b - - 3a4ac03d1266 - 9871104ea630 + - 3a4ac03d1266 + - 1812dbc5bb7b - 04bb8bb7c198 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -732,13 +732,13 @@ tools: owner: iuc revisions: - cee61b3fcf78 - - 9fa24d5aac68 - - 32b86cd8eb50 - c9cfec002f71 - 8f1c3df4dd49 - - d2bc35f3d1c5 - - 48636f857c4b + - 9fa24d5aac68 - db1f362cca3e + - 32b86cd8eb50 + - 48636f857c4b + - d2bc35f3d1c5 - d84caa5a98ad tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -751,10 +751,10 @@ tools: - name: trinotate owner: iuc revisions: - - 6fd16fad465d - - 2b093007fab9 - - 4383070d29ed - 9e61bc67866f + - 4383070d29ed + - 2b093007fab9 + - 6fd16fad465d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index 97ef01662..9eed3b471 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: - - 473382134e56 - 1a052c827e88 - - 27e16a30667a - 080fd5739bb4 + - 27e16a30667a + - 473382134e56 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/sambam.yml b/staging.gvl.org.au/sambam.yml index 99fe5b051..2e612b425 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -2,9 +2,9 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 3c661e57a88f - 88eedb4abea0 - 10184eaa85fc + - 3c661e57a88f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -16,8 +16,8 @@ tools: - name: bamtools_filter owner: devteam revisions: - - 108db6635177 - cb20f99fd45b + - 108db6635177 - 1dfd95ee241e - 993b19f20c76 tool_panel_section_label: SAM/BAM @@ -44,8 +44,8 @@ tools: - name: bamtools_split_tag owner: iuc revisions: - - e9b9c489aacc - e30af4e78cd3 + - e9b9c489aacc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamutil_diff @@ -83,9 +83,9 @@ tools: owner: iuc revisions: - e7fd6754d093 - - 19ece8afbaab - 5f8e69cc4c6e - 30a201c9c310 + - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_bamqc @@ -110,8 +110,8 @@ tools: - name: sam2interval owner: devteam revisions: - - 75557c0908a9 - 8c737b8ddc45 + - 75557c0908a9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_bitwise_flag_filter @@ -150,8 +150,8 @@ tools: owner: devteam revisions: - 56c31114ad4a - - dc6ff68ea5e8 - 649a225999a5 + - dc6ff68ea5e8 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip @@ -163,10 +163,10 @@ tools: - name: samtools_bedcov owner: devteam revisions: + - 9149ad20699a - 6856f8a01905 - 12749212f61b - 46c6639921f1 - - 9149ad20699a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -179,9 +179,9 @@ tools: owner: devteam revisions: - 06dc50b7b711 - - 92ec40abcdcf - 33208952b99d - 26b4f9f98aca + - 92ec40abcdcf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -206,9 +206,9 @@ tools: owner: iuc revisions: - b3d99709fe1a - - a8d69aee190e - b906586a6596 - 720217c23995 + - a8d69aee190e - 66e23b11feae tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -221,8 +221,8 @@ tools: - name: samtools_fixmate owner: iuc revisions: - - d2df79922531 - e5ece8fa99de + - d2df79922531 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -230,9 +230,9 @@ tools: revisions: - 22970df7a40e - cc61ade70eb8 + - fefd89ab563c - fe34990e5ce7 - db17d5321bad - - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -244,11 +244,11 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - fa5d3e61e429 - - 7def34e6cf4d - - 88b8c2916784 - - 7a6034296ae9 - 811fc2d75ad4 + - 7a6034296ae9 + - 88b8c2916784 + - 7def34e6cf4d + - fa5d3e61e429 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -260,28 +260,28 @@ tools: - name: samtools_markdup owner: iuc revisions: - - 40fa6c240105 - a389f74c3630 + - 40fa6c240105 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - 740ce0a18f0d - - 65a38e8c8e2a - b40e2d865d52 + - 740ce0a18f0d - 36677f429310 + - 65a38e8c8e2a - cae2794d2deb tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 329deb17a9f7 - 583abf29fc8e - - fa7ad9b89f4a - - b61f5d6a7f25 + - 329deb17a9f7 - 9da0311ab1dd + - b61f5d6a7f25 + - fa7ad9b89f4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -306,10 +306,10 @@ tools: - name: samtools_reheader owner: devteam revisions: + - db000c6007a0 - 30388d878f81 - 85e38b31e8b3 - bb8cfc6f6e0c - - db000c6007a0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -327,9 +327,9 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - 344fc91e1bfd - b8beef827165 - a4a10c7924d1 + - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -341,10 +341,10 @@ tools: - name: samtools_sort owner: devteam revisions: - - 6c2c1836728b - e613c1ad4c4c - - d54a4df48867 - cab3f8d35989 + - 6c2c1836728b + - d54a4df48867 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -356,11 +356,11 @@ tools: - name: samtools_split owner: devteam revisions: + - 5d9ae78f34d3 - 135c85f4cfaf - - bd850490c7f1 - b7f7826ef1cd - bcedabb53ddf - - 5d9ae78f34d3 + - bd850490c7f1 - 818030fa6bbf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -374,11 +374,11 @@ tools: owner: devteam revisions: - 541082d03bef - - 145f6d74ff5e - - 1cc79f49b8d5 - - 3a0efe14891f - 5a08c09b9311 + - 1cc79f49b8d5 - 24c5d43cb545 + - 3a0efe14891f + - 145f6d74ff5e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats @@ -390,16 +390,16 @@ tools: - name: samtools_view owner: iuc revisions: - - b72793637686 - - 5826298f6a73 - - 32dc5f781059 + - 2dce91e11ca7 + - 350bbc5c2ffd + - c370440f901e - 0dbf49c414ae + - b72793637686 - bf328cec6a42 - - b01db2684fa5 - - c370440f901e - 6be888be75f9 - - 350bbc5c2ffd - - 2dce91e11ca7 + - 32dc5f781059 + - b01db2684fa5 + - 5826298f6a73 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view diff --git a/staging.gvl.org.au/send_data.yml b/staging.gvl.org.au/send_data.yml index 8554b8578..d587efb9f 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -9,12 +9,12 @@ tools: owner: iuc revisions: - 6f6537780379 - - 5cb6146337d8 + - ea5e944f447d + - d147d6455873 + - 4aab5ae907b6 - a62c4a11a67d - 59bb6d34fca6 + - 5cb6146337d8 - 480d9e9d156b - - 4aab5ae907b6 - - d147d6455873 - - ea5e944f447d tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/single_cell.yml b/staging.gvl.org.au/single_cell.yml index 3637e0467..034e9d426 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -8,32 +8,33 @@ tools: - name: alevin owner: bgruening revisions: - - e4c01dcece8b - - f2000bc73102 + - e32b215b7c04 - c9944a2600f1 - ecb9ea6269ee - - e32b215b7c04 + - e4c01dcece8b + - f2000bc73102 + - b0fe3e482cb7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - cfaf5a405371 - - e1c3c2f2a834 - c0b037b12765 + - cfaf5a405371 - 707023fa62fe + - e1c3c2f2a834 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: + - 32e547223c9e - d330b3082107 + - 00712416fdaa + - 55e35e9203cf + - 93dd15e13e6a - cfc3f5a57dc6 - fb9e030ffae4 - - 93dd15e13e6a - - 32e547223c9e - - 55e35e9203cf - - 00712416fdaa tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -45,13 +46,13 @@ tools: - name: anndata_inspect owner: iuc revisions: - - 688357ad5e61 + - ee98d611afc6 + - b9fac48532eb - 6f0d0c784f09 - 038e32885fec - - 39e945f0b2c1 - 0bf7fddf90c7 - - b9fac48532eb - - ee98d611afc6 + - 39e945f0b2c1 + - 688357ad5e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -63,13 +64,13 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - ed4996a16f7f - - 43cb7b5a6fe7 + - 7e8c677a7b71 + - 9bd945a03d7b - 3d748954434b - d4af736e7b83 - b85871dd69f9 - - 9bd945a03d7b - - 7e8c677a7b71 + - 43cb7b5a6fe7 + - ed4996a16f7f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -98,27 +99,27 @@ tools: - name: baredsc_2d owner: iuc revisions: - - 344c2af50552 - - c29e7bb492bf - a90f8efe08b4 - aa4a6f0916b4 + - 344c2af50552 + - c29e7bb492bf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - b13d3e4c48e1 - 5b7c81b35b89 - - 050cf43887d3 - c32347702e12 + - 050cf43887d3 + - b13d3e4c48e1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - ae969fdb8442 - - 02fc39c8610d - 1d77986f9ddc + - 02fc39c8610d + - ae969fdb8442 - 239193b96d72 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -155,11 +156,11 @@ tools: - name: dropletutils owner: iuc revisions: + - cdf4443d5625 - cfe1e6c28d95 - - a9caad671439 - 8855361fcfc5 - - cdf4443d5625 - 2c1200fba922 + - a9caad671439 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -195,8 +196,8 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 01c37e54e86e - fb7068d30ec9 + - 01c37e54e86e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest @@ -209,8 +210,8 @@ tools: - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 23b8d6b8960c - 163fd744e235 + - 23b8d6b8960c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint @@ -223,15 +224,15 @@ tools: - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - - a63e9713c39d - b892fa1fcaec + - a63e9713c39d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - 640e0e45518a - 45a386d18509 + - 640e0e45518a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel @@ -244,15 +245,15 @@ tools: - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - 40fee49bc6c3 - f881c94fb3b3 + - 40fee49bc6c3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - - e06265d204f6 - 2dccb6bb0add + - e06265d204f6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts @@ -286,22 +287,22 @@ tools: - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - 2ba6cee8e4db - c0737631eea1 + - 2ba6cee8e4db tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - 62b720dceb56 - ea19190ce5e0 + - 62b720dceb56 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - 2b4d6a8dab36 - 2786a931cad2 + - 2b4d6a8dab36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops @@ -328,8 +329,8 @@ tools: - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 409396ea5cf0 - 7f7c6ead2d0d + - 409396ea5cf0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo @@ -363,15 +364,15 @@ tools: - name: hicexplorer_hicnormalize owner: bgruening revisions: - - 6d042c96aceb - f34ab9882252 + - 6d042c96aceb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: - - ea5d67ec94ab - dd9988943f53 + - ea5d67ec94ab tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts @@ -384,8 +385,8 @@ tools: - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - b4e780e93c91 - 337705015ee8 + - b4e780e93c91 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint @@ -398,15 +399,15 @@ tools: - name: hicexplorer_hicquickqc owner: bgruening revisions: - - ea8fb5e899e8 - 21d859ad4502 + - ea8fb5e899e8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - 36dfa2825a59 - 1d6af10874d5 + - 36dfa2825a59 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -424,15 +425,15 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - 27fe5cd1729c - f36828ebdc54 + - 27fe5cd1729c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 1d201e8378b3 - 11a3385e03b5 + - 1d201e8378b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom @@ -440,10 +441,10 @@ tools: revisions: - 0f1aaff9b22d - 4b0adaa31c95 + - e98619de2776 - 7784821452ac - 59be31ac9dc3 - eeab712b0b99 - - e98619de2776 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -455,9 +456,9 @@ tools: - name: music_construct_eset owner: bgruening revisions: + - 282819d09a4f - 2cfd0db49bbc - 7ffaa0968da3 - - 282819d09a4f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution @@ -470,8 +471,8 @@ tools: - name: music_inspect_eset owner: bgruening revisions: - - 7705cc75ac18 - 8c64a2da3869 + - 7705cc75ac18 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -489,10 +490,10 @@ tools: - name: raceid_clustering owner: iuc revisions: - - 0bff0ee0683a - a4b734cd253b - - 7e014059a88d + - 0bff0ee0683a - f911a64454fb + - 7e014059a88d - c4f39bf4a068 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -506,9 +507,9 @@ tools: owner: iuc revisions: - b83fbc90161e - - 43c146e25a43 - - d45f092caf24 - 7608d5faee41 + - d45f092caf24 + - 43c146e25a43 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf @@ -520,9 +521,9 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: + - f3eb2291da05 - 2b0d3e2f402a - 37a47c4fd84d - - f3eb2291da05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -534,9 +535,9 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - a6821f856a1e - 69018f285aa3 - df8e4e54d367 + - a6821f856a1e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -549,10 +550,10 @@ tools: owner: iuc revisions: - 2af7c5086a96 - - 72979cac22b2 + - c92d0f9338c5 - e93b008c637a - 44b935f2271b - - c92d0f9338c5 + - 72979cac22b2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -576,17 +577,17 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: + - 4d8f983cd751 + - 77b91b9bdf52 + - 6acb08931836 - 38db3fef7aad - 6f83f8fd381f - aaa5da8e73a9 - - 4d8f983cd751 - - 8983e7a04ba7 - - 77b91b9bdf52 - cb43c5d3acd3 + - b2df381a6004 + - 8983e7a04ba7 - edec35114f72 - f9353ee6a0d4 - - 6acb08931836 - - b2df381a6004 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -598,16 +599,16 @@ tools: - name: scanpy_filter owner: iuc revisions: - - 8cb783c81905 + - 3c86f71498bc + - a97abb8cd15b - fc0321c000a3 - - 277313130da5 - - 64388be6d510 - - 72a6bebab2a5 - - d636ce5cde16 - b409c2486353 + - 72a6bebab2a5 + - 8cb783c81905 - a03ff8633507 - - 3c86f71498bc - - a97abb8cd15b + - 64388be6d510 + - 277313130da5 + - d636ce5cde16 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -619,17 +620,17 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - f54f0f0598ad + - 6c145a6868cc - c5d3684f7c4c - cc0deb593fc8 - - 5c3ebe2adc77 + - 5e9171dc8244 + - d86cb2ce311b - 3081ff5c84a3 + - 5c3ebe2adc77 + - f54f0f0598ad + - 18262103fa61 - c0a80a16560f - - 6c145a6868cc - 6bd82ed14acd - - d86cb2ce311b - - 5e9171dc8244 - - 18262103fa61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -642,16 +643,16 @@ tools: owner: iuc revisions: - 146ae5d70b47 - - d844935c906c - - 94c19fb1281c - - 9f354c7c8c92 - - c9cb76cf8d6c - - 3bcd5445cd7a + - a407e7f8bdc1 - 7b9fafe32c86 - - ab55fe8030b6 + - 94c19fb1281c - 56c0d4acef02 + - d844935c906c + - 3bcd5445cd7a + - c9cb76cf8d6c + - 9f354c7c8c92 - 4bda4412b8c2 - - a407e7f8bdc1 + - ab55fe8030b6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -663,18 +664,18 @@ tools: - name: scanpy_plot owner: iuc revisions: - - 7647e5cd1b8b - - 6adf98e782f3 - - f7446fd8d5e7 - - dbbe1ea8ecb1 - - 6f5349dd5c49 - - aa0c474463c2 + - 9b0cdb8cf6be - 0185bd174ea0 - - 95777145cb92 + - aa0c474463c2 - 40812a65a78b - - 9b0cdb8cf6be - 1072ce66b426 + - 7647e5cd1b8b + - 95777145cb92 + - 6f5349dd5c49 + - f7446fd8d5e7 + - dbbe1ea8ecb1 - 62acdd96d4a0 + - 6adf98e782f3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -686,17 +687,17 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - 73ab2ac53d06 - - a39040ae0a38 - - f2f6c703da06 - bf2017df9837 - - 974bb00b2f43 - fe8f16c594ec - - d18e7a6e5cd4 - - c65fce500915 - 9fb627495ec2 - - 458e8f43a775 + - 73ab2ac53d06 + - c65fce500915 - 215733a383f2 + - f2f6c703da06 + - 974bb00b2f43 + - 458e8f43a775 + - a39040ae0a38 + - d18e7a6e5cd4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -709,8 +710,8 @@ tools: owner: iuc revisions: - b834074a9aff - - 8f333f90d8d6 - fd808de478b1 + - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -722,9 +723,9 @@ tools: - name: scater_filter owner: iuc revisions: - - b7ea9f09c02f - 652923ce664f - 7a365ec81b52 + - b7ea9f09c02f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -742,8 +743,8 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 2e41b35b5bdd - 81e5bdff4853 + - 2e41b35b5bdd - ef4c80837bc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -1013,8 +1014,8 @@ tools: - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 88192fe25375 - 588c811fdd48 + - 88192fe25375 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting @@ -1027,8 +1028,8 @@ tools: - name: snapatac2_preprocessing owner: iuc revisions: - - cec3e76eaf05 - fef8f61cb34c + - cec3e76eaf05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: squidpy diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index 508fd0435..ff2764f9f 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: + - 4c07ddedc198 - 746e8e4bf929 + - 562f3c677828 - 419027d822d6 - 2f3c6f2dcf39 - - 562f3c677828 - - 4c07ddedc198 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all @@ -56,8 +56,8 @@ tools: - name: dwt_ivc_all owner: devteam revisions: - - 506ae7b0d85d - 0b89b03ad760 + - 506ae7b0d85d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass @@ -71,8 +71,8 @@ tools: owner: devteam revisions: - 7a15159140d1 - - 6c29c7e347e8 - cb1c59d69557 + - 6c29c7e347e8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,21 +120,21 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 9c3e1d3235c8 + - aef56d0e7a61 - 4c4ec859c31a + - 9c3e1d3235c8 - 840f29aad145 - b1eda492f063 - - aef56d0e7a61 - 7442b94d6a1e tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 30d21a6041f6 - - 07843f917990 - d0352e8b4c10 - 9fda0b82f419 + - 30d21a6041f6 + - 07843f917990 - 375bbd555f4a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -143,20 +143,20 @@ tools: revisions: - 7ae443e6217d - 4cc980df6265 - - 8b1b2b91f8d0 - cd02bf168d23 + - 8b1b2b91f8d0 - 2c58b83c9bad tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - 7dd3fb35904f - - 4bbaf77573ef - e10e776f2109 - - ad7e0b4291ee + - 4bbaf77573ef - 1dd433d2c92c - bb9fc9d46ea4 + - 7dd3fb35904f + - ad7e0b4291ee tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/staging.gvl.org.au/text_manipulation.yml b/staging.gvl.org.au/text_manipulation.yml index 5de6eb1eb..0db524bc1 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -14,8 +14,8 @@ tools: - name: add_value owner: devteam revisions: - - 023f0a3760b3 - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -34,15 +34,15 @@ tools: - name: column_maker owner: devteam revisions: + - 6e8d94597139 + - be25c075ed54 + - 464b9305180e - aff5135563c6 + - 6595517c2dd8 - 9cd341095afd - - 626658afe4cb - - 464b9305180e - 02026300aa45 - - 6e8d94597139 - - be25c075ed54 + - 626658afe4cb - 13b6f0007d9e - - 6595517c2dd8 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -54,8 +54,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 3a4694d4354f - 6f54dc6b37da + - 3a4694d4354f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -79,11 +79,11 @@ tools: - name: filter_tabular owner: iuc revisions: + - 34d29339abab + - 557ec8d7087d - 90f657745fea - 9cc411a62277 - - 557ec8d7087d - 37cde8134c6a - - 34d29339abab tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -107,30 +107,30 @@ tools: - name: merge_cols owner: devteam revisions: - - dd40b1e9eebe - f2aac0c5c60d + - dd40b1e9eebe - ae7843d06f8f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - cf4397560712 - - 3a6b78c39dca - - 83069b38aa85 + - cf34c344508d - 623f3eb7aa48 - - 33d61c89fb8d - - 2e8f945f7285 - 1ea4e668bf73 - - cf34c344508d + - 83069b38aa85 + - 2e8f945f7285 + - 33d61c89fb8d + - cf4397560712 + - 3a6b78c39dca tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: + - 503bcd6ebe4b - ae8c4b2488e7 - 399da6b5ec21 - - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -142,10 +142,10 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - f768f6183386 - b722161a845a - - c4d18aa4ec4a - bce29ec10b78 + - f768f6183386 + - c4d18aa4ec4a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -158,15 +158,15 @@ tools: - name: text_processing owner: bgruening revisions: - - 86755160afbf + - d698c222f354 - 9ff72e942410 - - ddf54b12c295 - - a6f147a050a2 - f46f0e4f75c4 + - 86755160afbf - 12615d397df7 - - 0a8c6b61f0f4 - - 74a8bef53a00 + - ddf54b12c295 - fbf99087e067 - - d698c222f354 + - 74a8bef53a00 + - 0a8c6b61f0f4 + - a6f147a050a2 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/variant_calling.yml b/staging.gvl.org.au/variant_calling.yml index 7dd02bca8..5519d7480 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -14,9 +14,9 @@ tools: - name: breseq owner: iuc revisions: - - 82fb5e3bb93e - - 85c57cc9b558 - 0d18a3ba2d1c + - 85c57cc9b558 + - 82fb5e3bb93e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -28,65 +28,65 @@ tools: - name: cutesv owner: iuc revisions: - - c0f8fe52948e - 23d7e75d850e + - c0f8fe52948e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: freebayes owner: devteam revisions: - - 57def2d7c093 - - 156b60c1530f - ef2c525bd8cd - - 04fa42777df9 - a5937157062f + - 04fa42777df9 + - 156b60c1530f + - 57def2d7c093 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - e61c9ac190ad + - 791f73caa0c8 - 09d6e4693887 + - e61c9ac190ad - 435b157bed6d - - 791f73caa0c8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - e1461b5c52a0 - - 4805fe3d8fda - - 3b4b2121842f - - dfadc322b065 - - b11e8e9c23bf - 03627f24605f + - 3b4b2121842f - 65432c3abf6c + - 4805fe3d8fda + - b11e8e9c23bf + - e1461b5c52a0 - 074d44697036 + - dfadc322b065 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 701d134358ad - 9cb929f21cfa + - 701d134358ad - 7dfca164d2e3 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - 426d707dfc47 + - f4473557ffc7 - 971e07ca4456 + - 426d707dfc47 - c27549b9aa1f - - f4473557ffc7 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: + - aa35ee7f3ab2 - cdaab621d454 - dbd9f2db9ed8 - - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -98,18 +98,18 @@ tools: - name: sniffles owner: iuc revisions: - - 43fffeed243f - 93c4b04a0769 + - 43fffeed243f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: - - 5bbf9eada9c2 - - d220115f882b - 9bccc8404a3c - fa016f1eea1a + - d220115f882b - c9a8ef2aa380 + - 5bbf9eada9c2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -151,21 +151,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - 32f14a2723ec - - e7aff4a85df5 - - ee4a90760848 - 3b1e7c170b10 + - ee4a90760848 - 40f0591deda0 + - 32f14a2723ec + - e7aff4a85df5 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: + - 9793bc5d741b + - 02d81b994ef5 - 4934c0ac6197 - adc0645b945c - - 02d81b994ef5 - 42818629ec4c - - 9793bc5d741b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_copynumber diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index e86fbf621..a52dd33eb 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -2,13 +2,13 @@ tools: - name: bcftools_annotate owner: iuc revisions: + - e075b1be5abb + - 95815a0bb307 + - 265fe0f9ea64 - b7ea370b8f5d + - 2c372041ed8c - 6a88248893c4 - - 265fe0f9ea64 - ebe5fc018e72 - - 95815a0bb307 - - e075b1be5abb - - 2c372041ed8c - 8a2e296c07ef tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -21,13 +21,13 @@ tools: - name: bcftools_call owner: iuc revisions: - - 1001172b5089 - - 22637b1a55bf + - b03984136ce4 - 0fba2c15b40d + - 1001172b5089 + - 544cb432072b - c37b684e7f4e - 21687e35f066 - - b03984136ce4 - - 544cb432072b + - 22637b1a55bf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -39,15 +39,15 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - ccb83bf54de0 + - 3a7084316a6e - bf1f4994f104 - 8ca3647c90fd - - 0238f68ad641 - - 3a7084316a6e - 01d6b7d6365e - - 8408bffd5616 - - 143796b504eb + - ccb83bf54de0 - 8627b2b383b4 + - 143796b504eb + - 0238f68ad641 + - 8408bffd5616 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -59,14 +59,14 @@ tools: - name: bcftools_concat owner: iuc revisions: - - 81426b3cf18b - - 03e0645395d2 - - 6b6c992d3a14 - f430a1ec7ee4 + - d144af39073a + - 81426b3cf18b - 9b5abbf50d23 - 62ca6da715bf - abd489215f73 - - d144af39073a + - 6b6c992d3a14 + - 03e0645395d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -79,13 +79,13 @@ tools: owner: iuc revisions: - 8aa352093d73 - - d3081540d175 - - 95c6f3f4c77f - 1171446da5db - - d37e313a41be - 2363ef414c9b - - e522022137f6 + - 95c6f3f4c77f + - d3081540d175 - 1829900b5dcd + - d37e313a41be + - e522022137f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -97,14 +97,14 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - 92c0aff8b53e - - 09f37afb3621 + - 1137ce8efc1e - 9b29129fb491 + - 348cd212dbad + - 09f37afb3621 + - 012656fd329f - b14ff40958cb + - 92c0aff8b53e - d58d2e8c7a57 - - 012656fd329f - - 348cd212dbad - - 1137ce8efc1e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -116,13 +116,13 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - cfd81f17580b - - de68c11034f6 - 367ba501b6eb + - de68c11034f6 - ecc9192912b8 + - 1f2183a23823 - 55c0e906c14c - 7291189e98b4 - - 1f2183a23823 + - cfd81f17580b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -134,13 +134,13 @@ tools: - name: bcftools_csq owner: iuc revisions: - - d237eaef451f - - 6c790a091c7c - - 039ea3f1dea9 - e6f4badbe6f3 + - 6c790a091c7c + - ae68ceb4cca3 - 64a8f7dae3ad + - 039ea3f1dea9 + - d237eaef451f - 7cbf3c66d4ad - - ae68ceb4cca3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -152,14 +152,14 @@ tools: - name: bcftools_filter owner: iuc revisions: - - 6ea7170a016d - - e7452697afd9 - - 5d6653c989cb - - 33bd9301568c - 963a3635b2e1 - 277719af4dd7 - 46fcafba49ec + - 33bd9301568c + - 6ea7170a016d - cdb7b4927742 + - e7452697afd9 + - 5d6653c989cb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -171,14 +171,14 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - 91c1e57d5c7f - - 26d97cdd5410 - - 501bfb078342 + - a1213a0b7b66 - 5a321fab1fe4 + - 26d97cdd5410 + - b7f0f59baa7e - a29a2f40b665 - - a1213a0b7b66 - 7b4454382d39 - - b7f0f59baa7e + - 501bfb078342 + - 91c1e57d5c7f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -190,15 +190,15 @@ tools: - name: bcftools_isec owner: iuc revisions: - - 709dd8291b83 - - 15da1ddcfeff - - 5f27e814a119 - - 39bca000353d - 97d19c008d15 - - d7d1663559e9 - - 768d04526638 - 81e4014fa809 + - 5f27e814a119 + - d7d1663559e9 + - 709dd8291b83 - c803c34361e0 + - 15da1ddcfeff + - 768d04526638 + - 39bca000353d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -210,14 +210,14 @@ tools: - name: bcftools_merge owner: iuc revisions: - - b931e65638b8 - b1eba148b35b - - 2215287d5cc9 - - 86296490704e - - 85ee7e6c4204 - 7ba36babba2d - - b84fda8ebef0 - 5b006286a458 + - b931e65638b8 + - 2215287d5cc9 + - b84fda8ebef0 + - 85ee7e6c4204 + - 86296490704e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -229,16 +229,16 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - 37757ffb4c5f - - 5660b21a0dbd + - 4e1d23e5c691 - 0a5dcc9a8ec2 + - 5660b21a0dbd - f506df85c652 - - 9c711df3258d + - ce9396ddcb2b - 56556e1267de - - 4e1d23e5c691 + - 9c711df3258d - cf06b44624c7 - 31ea13dfe5e6 - - ce9396ddcb2b + - 37757ffb4c5f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -250,13 +250,13 @@ tools: - name: bcftools_norm owner: iuc revisions: - - 48291658fdf6 - - 19905c025d2a - - 271965b55437 - - 021693fdadaa - - 1ca7418e46ee - a404f786a94c + - 021693fdadaa - 6deb4d549bc9 + - 1ca7418e46ee + - 19905c025d2a + - 271965b55437 + - 48291658fdf6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -268,14 +268,14 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: + - 3f6fadf8b8ff - 97e8145d7e30 - - 69d8b7567281 - 5ad5d4243987 - - f7879f1e77f9 - dadbd61dc4cf - - 3f6fadf8b8ff - - c450406f722b - 71c78e0eea52 + - f7879f1e77f9 + - c450406f722b + - 69d8b7567281 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -287,13 +287,13 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: - - 52f9e4a660e3 - 0fe007201caf - - 2514e684f8a3 - - 79f7a1acc2cd + - 283911fe7e1a - d31a2e310a52 - cc7f9a4e186b - - 283911fe7e1a + - 2514e684f8a3 + - 79f7a1acc2cd + - 52f9e4a660e3 - 6cf13a657cf6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -306,14 +306,14 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - a12844ca467a - - 230e424bde67 - - 0a62420cb9cd - - 026a989b7cee + - 6963a6841d22 - 1411bef27a75 + - 026a989b7cee + - a12844ca467a - 80e6e399ccd0 - - 6963a6841d22 - 75ddd081f608 + - 230e424bde67 + - 0a62420cb9cd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -326,13 +326,13 @@ tools: owner: iuc revisions: - 444e6a756c35 - - 5808f77b2bb6 - - e493702b19eb - - 5acfca5a76af - - b10d1510fa84 - - ba20340426fe - bca7ce81688f - 450a265f92e8 + - 5acfca5a76af + - e493702b19eb + - ba20340426fe + - b10d1510fa84 + - 5808f77b2bb6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -344,13 +344,13 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - d52b8947b269 - - 12152af85697 - - 4d236c696844 - 68fec03a63b7 - - 157ffcdd3fa7 - f2482aa4862e + - d52b8947b269 + - 157ffcdd3fa7 + - 12152af85697 - dd72ff87cfd0 + - 4d236c696844 - c43399f161f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -363,13 +363,13 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: - - 29ba253e2e05 - - 75becf493cd3 - - 0e5d11004815 - - 8dbce095986c - 8f2fc0ab30fb - - 6f8e223f78f3 + - 0e5d11004815 - cbe39e530cbf + - 29ba253e2e05 + - 6f8e223f78f3 + - 8dbce095986c + - 75becf493cd3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -381,13 +381,13 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - a367a15c6de5 - - a8630d4fbaf8 + - e0a856def0b0 - 88bb477f45f7 - - 9708e3086f32 - 8f5962c43868 + - 9708e3086f32 + - a8630d4fbaf8 + - a367a15c6de5 - 3ff5654b4e7d - - e0a856def0b0 - f544f71adb73 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -401,13 +401,13 @@ tools: owner: iuc revisions: - 8b260d252ff4 - - 5c9729d54721 - 31c096c6b156 - - 34dc0bbc7e93 - 6ce175385dd9 + - 5c9729d54721 + - 34dc0bbc7e93 - 4ed46189d6c6 - - 03e30f06f15f - 96d0145c041a + - 03e30f06f15f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -419,14 +419,14 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: - - 46eb13bc2c73 - - 2c4941386820 - - a730269af659 - - a1aad8b559c6 - - 40daf124be88 - - 11af7fce71cf - 681bdf1e22ff - 09f5e45a8212 + - 11af7fce71cf + - 40daf124be88 + - 2c4941386820 + - 46eb13bc2c73 + - a1aad8b559c6 + - a730269af659 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -438,15 +438,15 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - 8cb121b6a1d2 - - 882b2e649602 - - f272b8ba0983 - - 6cbb9c47795c - 3897eaadfbff - 743cd1472aeb - - 12038f59c0f4 + - 6cbb9c47795c - 0594ea1417c8 + - 12038f59c0f4 + - f272b8ba0983 + - 882b2e649602 - b74b8cbfc1f1 + - 8cb121b6a1d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -458,13 +458,13 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: - - 238f78e38a8b - - eccb508bb678 - 18cf9de1cf73 - adee7e8b746f + - 238f78e38a8b - dba06328556a - - cced6715f926 - a9826db86d9a + - cced6715f926 + - eccb508bb678 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples @@ -476,14 +476,14 @@ tools: - name: bcftools_query owner: iuc revisions: - - f64e7ca2efd2 - - e53501abf992 - fdec14f69010 + - 31a1b89eab9b + - 9f36041495a3 - e0ad88dec40d - - c9935c9e8a24 - 3ce32adc55b2 - - 9f36041495a3 - - 31a1b89eab9b + - e53501abf992 + - c9935c9e8a24 + - f64e7ca2efd2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -495,14 +495,14 @@ tools: - name: bcftools_reheader owner: iuc revisions: + - 3b7b1fe7b937 + - 2331ddcbd5aa - b7be725976b6 + - d68c43202172 - 4db0695a6fc7 - - 2331ddcbd5aa - d43eb39b989e - - 79489d5685dd - - d68c43202172 - fd3539749127 - - 3b7b1fe7b937 + - 79489d5685dd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -514,13 +514,13 @@ tools: - name: bcftools_roh owner: iuc revisions: - - 58091e1be01b - 6a636d58dfc2 - 1a989b4110da - 5296d26b0373 - b0d39ef600a7 - 1ccf0e7fb4f6 - 78cd8b69da4c + - 58091e1be01b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -532,14 +532,14 @@ tools: - name: bcftools_stats owner: iuc revisions: + - bf8325a07ce7 + - b17394940c7a + - 4d3ce9dc1525 - e8af591435d1 - - 591cc8518033 - b641062a2587 - - 4d3ce9dc1525 - '388983871932' - - b17394940c7a - baa8823f8073 - - bf8325a07ce7 + - 591cc8518033 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -551,14 +551,14 @@ tools: - name: bcftools_view owner: iuc revisions: - - 3a233c8eb814 + - e6b5cbbf449b - d1f8f55f564d - - 59fa8742285e - - c2ab91a0d506 + - 3a233c8eb814 + - 1a2ef636f48e - 3ca3de4e5291 - 38d75661c235 - - e6b5cbbf449b - - 1a2ef636f48e + - c2ab91a0d506 + - 59fa8742285e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -577,22 +577,22 @@ tools: - name: vcfaddinfo owner: devteam revisions: - - 6ea73d6151ec - afc0ba768690 + - 6ea73d6151ec tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives owner: devteam revisions: - - a8a4f94aa321 - 57a16b310fe8 + - a8a4f94aa321 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate owner: devteam revisions: - - 6faa2c4c71d2 - 01e0321aca98 + - 6faa2c4c71d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes @@ -612,15 +612,15 @@ tools: - name: vcfbreakcreatemulti owner: devteam revisions: - - 690b1d846263 - 9fd5d91eb91b + - 690b1d846263 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcheck owner: devteam revisions: - - 5e850c85ba32 - aa8e8c96ca06 + - 5e850c85ba32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -648,9 +648,9 @@ tools: owner: devteam revisions: - 6b935ab36d7b - - eae7c08ebb6f - fa24bf0598f4 - 4bdc111b2470 + - eae7c08ebb6f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup @@ -670,43 +670,43 @@ tools: - name: vcfgeno2haplo owner: devteam revisions: - - b890055e07bd - a3dea556218d + - b890055e07bd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes owner: devteam revisions: - - f5653ed90dfd - a60ae8af21a1 + - f5653ed90dfd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom owner: devteam revisions: - - 8254e0fe7358 - b07ef36cf7e6 + - 8254e0fe7358 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfleftalign owner: devteam revisions: - - d2406f98a782 - 29f9b782727e + - d2406f98a782 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfprimers owner: devteam revisions: - - 17096387c0e6 - d226a7327946 + - 17096387c0e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample owner: devteam revisions: - - 6257ee3b50d3 - 12b570dd0bc5 + - 6257ee3b50d3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfselectsamples @@ -719,9 +719,9 @@ tools: - name: vcfsort owner: devteam revisions: + - f0580efedada - 5b7120c66efc - ee60203e68d9 - - f0580efedada tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate @@ -751,7 +751,7 @@ tools: - name: vcfvcfintersect owner: devteam revisions: - - 6f6bf10618d7 - 166c4f50525f + - 6f6bf10618d7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/viral_tools.yml b/staging.gvl.org.au/viral_tools.yml index 06370d956..15250eab7 100644 --- a/staging.gvl.org.au/viral_tools.yml +++ b/staging.gvl.org.au/viral_tools.yml @@ -2,7 +2,7 @@ tools: - name: quasitools owner: nml revisions: - - 18aad692772a - 9def47f3c1e4 + - 18aad692772a tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 168eaa6d8..0260e5a07 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 6e9aea89e388 - - 3f3e247c053d - 78c75f134c16 - - 4efdca267d51 - c2ef298da409 + - 4efdca267d51 + - 6e9aea89e388 + - 3f3e247c053d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -26,37 +26,37 @@ tools: - name: aegean_locuspocus owner: iuc revisions: - - c4ac24510b55 - 1fdc517743e6 + - c4ac24510b55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_parseval owner: iuc revisions: - - 1b52f0c8ad7f - d6c074a93c51 + - 1b52f0c8ad7f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - 4f2967b27e67 - - fe3ca740a485 - - 133f36c29579 - f29602ae449e - - cd2480f35935 - - 3e1f6f6d557e + - 1aae04680c4b - 44018dd6b447 - - b5d8e5475247 + - cd2480f35935 + - 133f36c29579 - a79ee60b6926 - - 1aae04680c4b + - b5d8e5475247 + - 3e1f6f6d557e + - 4f2967b27e67 + - fe3ca740a485 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - bc88856eddab - e78e25d3b4bd + - bc88856eddab tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training @@ -64,34 +64,34 @@ tools: revisions: - 7be22100e5e1 - f1e653756174 - - 6519ebe25019 - dc027fa56d55 + - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - ca6d970d931c - bd0e53f3a891 - 28433faa6e42 + - ca6d970d931c - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - d77802fe76f7 - 728dacaf08a9 - - 92eee5f31117 - da5f1924bb2e + - 92eee5f31117 + - d77802fe76f7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - - 7355bbf5e05f - fe48aa4ccd5e - 8fd427007e93 + - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -103,8 +103,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 8bd92f2404dd - 1b9a9409831d + - 8bd92f2404dd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -116,17 +116,17 @@ tools: - name: cpat owner: bgruening revisions: - - 8e9e228c54c4 - 7ccc6234b54e - 1ac12c0cc7a0 + - 8e9e228c54c4 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - 9d1fbff733cf - - 63662ae295d6 - d9c3016f7283 + - 63662ae295d6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -150,61 +150,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - b6b5cd37f2a2 - - 9c15ca7e764e - - 14f588312c56 + - 582fd74dc2a1 - 756376aeb1ae - 3bbe70fef6df + - 14f588312c56 + - 9c15ca7e764e - 9f2455341fac - - 582fd74dc2a1 + - b6b5cd37f2a2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - 0ffe5be70caf + - 1691af4a0d17 - 73428a792541 - a230ea445788 + - 30fb23d4c31c - 989f7c061f35 - - 1691af4a0d17 - 8e1ace8f77c6 - - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - 494f0bb4a993 - - 563a19373357 - - 57c6718cbfcc - e94187d661df - - 30f08d74024f - - 5a5ae61da69c - 0418d28136de + - 57c6718cbfcc + - 5a5ae61da69c + - 563a19373357 + - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - d6c7106b7b2e + - 4b96ced19f75 - f77d7b685bb3 - - 7abc5f6dd595 - 1bc5a03faf2e - - 4b96ced19f75 - - 2bba2ff070d9 - f31125bb85ea + - d6c7106b7b2e + - 2bba2ff070d9 + - 7abc5f6dd595 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - b3cf4684e9c7 - d77fdcca400e - 54961e026fe4 - - d3af38b9c7e1 - - 520e30695ec3 - fed64e676186 - 52af33194019 + - 520e30695ec3 + - d3af38b9c7e1 + - b3cf4684e9c7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -216,9 +216,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 79261884facd - - 07d7991bf205 - 2aea122fbd25 + - 07d7991bf205 + - 79261884facd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -231,8 +231,8 @@ tools: owner: iuc revisions: - ef2ad746b589 - - 602de62d995b - 43798b4caee0 + - 602de62d995b - 8b3e3657034e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -264,8 +264,8 @@ tools: - name: interproscan owner: bgruening revisions: - - 74810db257cc - 98cafcbd2578 + - 74810db257cc - c55643c3d813 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -284,26 +284,26 @@ tools: - name: maker_map_ids owner: iuc revisions: - - e906fa778440 - 326f9c294b09 + - e906fa778440 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: - - 3c1a01127868 - - 370c210d9541 - d46d803ca6cc + - 370c210d9541 + - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 624606f7c996 - - b815ec682418 - e95d52d295d7 + - 624606f7c996 - 033755194fe9 - c8ac28e8ac44 + - b815ec682418 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -351,10 +351,10 @@ tools: - name: prokka owner: crs4 revisions: + - 8a22554cdde2 - a17498c603ec - - bf68eb663bc3 - d643e3b03500 - - 8a22554cdde2 + - bf68eb663bc3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -373,8 +373,8 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 41bfbaf3c959 - 8661b2607b7e + - 41bfbaf3c959 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -398,23 +398,23 @@ tools: - name: snpeff owner: iuc revisions: - - 68693743661e - - 5c7b70713fb5 - - 5b80f544c67f - cfcf33df7fc0 - 6322be79bd8e + - 5c7b70713fb5 + - 8f92c2b26e6d - ca2b512e8d7c - - 268d162b9c49 - 5a29ab10dba6 - - 8f92c2b26e6d + - 268d162b9c49 + - 68693743661e + - 5b80f544c67f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 5fab4f81391d - 09d6806c609e - 2b3e65a4252f + - 5fab4f81391d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna @@ -433,24 +433,24 @@ tools: - name: tbprofiler owner: iuc revisions: - - 809dfc93d593 - - 200c378d85f3 - - ba6f87115e13 - - 37213cf56392 - 037a11682176 - - 51dd22484644 - - e1a9d6fd258d - - 45083d070fb8 - d03af1c7002c - - ac8250086ac3 - 4839e590cb26 + - 37213cf56392 + - e1a9d6fd258d + - ac8250086ac3 + - 51dd22484644 + - 809dfc93d593 + - 200c378d85f3 + - 45083d070fb8 + - ba6f87115e13 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - f50807720df1 - 8fc50fe60127 + - f50807720df1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_hmm diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 4ca811fa7..2777c066a 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,27 +2,27 @@ tools: - name: abyss owner: iuc revisions: - - 0e93176640ac - - 841084c5fc46 - - a929ce596a34 + - d6d5ccc2c581 - 890b794c997d - 7547fcab5d19 - - d6d5ccc2c581 - - fa5259cc561b + - a929ce596a34 + - 0e93176640ac - 553bfe8bd0b5 - - 0124fce4654a + - fa5259cc561b - 8f1b150a2487 + - 0124fce4654a + - 841084c5fc46 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - b9e31c5c01c7 - - 94fe43e75ddc - - 21e491ad532a - b2860df42e16 - - ddddce450736 + - 21e491ad532a + - b9e31c5c01c7 - 067592b6b312 + - ddddce450736 + - 94fe43e75ddc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -35,46 +35,46 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - faee8629b460 - 22286dab5aa1 - - 5258e18bbe23 + - faee8629b460 - a7f16f24e9a1 - 3371c5bdc17a + - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - 8c2167481e72 - 53dd00a4ab68 + - 8c2167481e72 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - 94170eee0ad8 - 41030a6c03b7 - e4bd1e99bacf - - 0d243f458b53 + - 602fb8e63aa7 + - ea8146ee148f + - e824f5d958d0 + - 2babe6d5c561 + - 94170eee0ad8 + - cf13a1e03e5b + - 2dd755c1c6ff - 46ae58b1d792 - 1e62c28ba91d - - e824f5d958d0 - 1440ae06552f - - 2babe6d5c561 - bb935709506a - - 2dd755c1c6ff - 4048d82f0c88 - - 602fb8e63aa7 - - ea8146ee148f + - 0d243f458b53 - 5ecdeca79a0d - - cf13a1e03e5b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 86f150c8019d - c5b7390290b1 + - 86f150c8019d - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -87,23 +87,23 @@ tools: - name: flye owner: bgruening revisions: - - 3e4f8642c77e - 8d4f03b5fe9d - 1f0769f0b56b + - 1ce9b1d72ec3 - 3ee0ef312022 - - cb8dfd28c16f - - 276f5d8712d5 - 291923e6f276 + - 3e4f8642c77e - e27815e82dd4 - - 1ce9b1d72ec3 + - 276f5d8712d5 + - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - 460fad600dce - - 01210c4e9144 - 3169a38c2656 + - 01210c4e9144 - b2f674562a18 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -111,8 +111,8 @@ tools: owner: iuc revisions: - 7348b69e5109 - - ba88bc5a6446 - 06bcf65179fb + - ba88bc5a6446 - 8b330a577046 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -120,10 +120,10 @@ tools: owner: bgruening revisions: - 5127a713de83 - - 690c2caa367e - 6ec1b853c8fd - - 3ef480892a9f - 3fba9c77550a + - 3ef480892a9f + - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -135,23 +135,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - df25d4fb79b7 - - ec9e21e9c71b - - 41cea2aa2dce - - da9d8bf98802 - - 60024a528cbd - 2061fb3b81b4 + - 60024a528cbd + - f3c89da3af16 - 5f625c63b8bc - - 045c7c3d8e59 - 284a1cb82b61 + - 9ef6920c3089 - 5bec28269d95 - - 71740308d412 + - 366a11d316a7 + - ec9e21e9c71b - 0ee0c3089254 + - 045c7c3d8e59 - 3f7be05a1597 - - 9ef6920c3089 - - f3c89da3af16 + - da9d8bf98802 - 6505bd37670d - - 366a11d316a7 + - 41cea2aa2dce + - df25d4fb79b7 + - 71740308d412 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -175,43 +175,43 @@ tools: - name: megahit owner: iuc revisions: + - de387b2b2803 - a96f3ad4e0d8 - 14ddfc8ffb93 - 7518ee87b53d - - de387b2b2803 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 9d79beb19ac3 - - f8113c25bc6b - - 09c589057ee8 - eb7b00ec347d + - 09c589057ee8 - d7edbc9c3a07 - 39edec572bae + - 9d79beb19ac3 + - f8113c25bc6b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - eadfd71dde37 - - 29dabd8db6f2 - 51c2360aa807 + - 29dabd8db6f2 + - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: + - f369ef5f210b - 606b09cc9860 - - f338e9942b27 - - fd128c111ab0 - e731ea24e48d + - fd128c111ab0 + - 99ecfdafc64f + - eb7a370f6588 - 2ecf5a570907 - - f369ef5f210b - 3ca2d2a9068c - - eb7a370f6588 - - 99ecfdafc64f + - f338e9942b27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -223,10 +223,10 @@ tools: - name: miniasm owner: iuc revisions: - - 8dee0218ac7d + - 8b6d0d85252b - b799a615995d + - 8dee0218ac7d - a7b889b90140 - - 8b6d0d85252b - 73a3846701e1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -259,44 +259,44 @@ tools: - name: pretext_map owner: iuc revisions: - - 2b16ba799da9 - - 02831bf9e95f - - 8fef980d48b5 + - 79b48f02db49 - bbe19ef04a74 + - 8fef980d48b5 - dfb8a4497339 - - 79b48f02db49 + - 02831bf9e95f + - 2b16ba799da9 - d256a51a656b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - 76d4cbefff85 - e9bd16ba5ebd + - 76d4cbefff85 - a315c25dc813 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: + - 6fcbee531de6 + - 875d0f36d66f + - 7594365c546b + - 3061c8b029e5 - 59db8ea8c845 + - 342a1d1fed7b - 72472698a2df - - 875d0f36d66f - ebb0dcdb621a - - 342a1d1fed7b - - 7594365c546b - 675488238c96 - - 6fcbee531de6 - - 3061c8b029e5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - a199cd7ac344 + - aa39b19ca11e - d865b62f501c - cd06929b224b - - aa39b19ca11e + - a199cd7ac344 - 39bed8de8017 - 78c533842eeb tool_panel_section_label: Assembly @@ -310,12 +310,12 @@ tools: - name: raven owner: iuc revisions: - - 33b7d8481a76 - 3edba9afc9bc - - f8564b2d7f63 - - f11b994b7eb2 - 2b2a352488fa + - f11b994b7eb2 + - 33b7d8481a76 - 5c55448d0f33 + - f8564b2d7f63 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast @@ -328,13 +328,13 @@ tools: - name: rnaspades owner: iuc revisions: - - ef69617ecb42 - - 378e55aeeb25 + - 1d06c8b38e77 - 28189050e437 - 5fc94b3a4704 - - 1d06c8b38e77 - e122f9101584 + - ef69617ecb42 - 53c2bc8c2ae3 + - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -346,189 +346,189 @@ tools: - name: shovill owner: iuc revisions: - - ad80238462c1 - - 83ead2be47b2 + - ee17a294d3a3 - 865119fcb694 + - 83ead2be47b2 + - d9f6a00b6db7 - f698c7604b3b - 196a599ec43d - - ee17a294d3a3 - - d9f6a00b6db7 + - ad80238462c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 5e0825476fb7 - 015283de3004 + - 5e0825476fb7 - 24e471d13fe9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 904bf932cf78 - - 1fc82fe7ebef - - 604782a8a53a - 7490b213baa9 - c33a476f4001 - - 1bb12736175c - 051fd2db8a27 + - 904bf932cf78 + - 1bb12736175c + - 1fc82fe7ebef + - 604782a8a53a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - 655fa188c3cc + - 9678993ca5bd + - 34305b013402 - fee85957cebe - 808b3a0a6716 - d6e617c4e338 - - 34305b013402 - ad8b536d1caa - - 9678993ca5bd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: + - b8002c3f7141 + - 7e27faaad80e + - e5a3b75a271f + - 037f9927c4ff - 6b5a5842531e - 8d4b90bf9caf - 21da31ed41a1 - - e5a3b75a271f - - 037f9927c4ff - - b8002c3f7141 - - 7e27faaad80e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 86f66ab58e14 - f1532cb33c75 - - 5b26685e5d3b + - 86f66ab58e14 - 2a10645aeadd - 7922870efcca - - 9de69775f512 - 328aa71f0f3c + - 5b26685e5d3b + - 9de69775f512 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 6aad515a5270 - - e41dcb0e913b - - 85fb02c43042 - 340bc17f49cf + - 6aad515a5270 - 8cc856b935ee - 1708851f8804 + - e41dcb0e913b + - 85fb02c43042 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - b3490b036c5a - - 6357b127161e - - d5fb354f745d + - b65a43f70b99 - d159735a6a9f - - 249f6a28c751 - de1260f8a300 - - b65a43f70b99 + - d5fb354f745d + - 249f6a28c751 + - b3490b036c5a + - 6357b127161e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: + - 9006e5836729 + - 7897763d14ec - 33368fec3b70 + - b7829778729f + - d5887ace0dd4 - dd7ad84f3943 - a90db5dbaaf3 - - 7897763d14ec - - 9006e5836729 - d2d1df21dfb9 - - d5887ace0dd4 - - b7829778729f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 505a9833ab5d + - ced385aa976d - ed2425b9fd27 - 8f631679571f - - 189e837009c9 - - ced385aa976d - 6f4c8ad6ea01 + - 189e837009c9 + - 505a9833ab5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 19bdfd1e6fe3 + - d40ed4eb0c0e - 9ded6109434a - f31d376ce725 - 356afed970b4 + - 19bdfd1e6fe3 - e59bee4565b3 - - d40ed4eb0c0e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 6dd935e4984b - 80a17897564d - - 4688ae3b49b5 + - af40e971a8cc - ebd801e712bc + - 4688ae3b49b5 + - 6dd935e4984b - b23249f81bc4 - - af40e971a8cc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - cb1e3db43020 - - 59bd28f6265d - - bb11fefb23a3 - b5e35a2ca4f3 - - 937ea677d437 + - bb11fefb23a3 + - 59bd28f6265d - b64696992ee9 + - 937ea677d437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - cb4768eeca3b - - 6015aa0303f2 - - 2628f6790eda - 05bd7504fdb2 - - 6bfab4a4a988 + - 2628f6790eda + - 6015aa0303f2 + - cb4768eeca3b - 383bb5ad32e2 + - 6bfab4a4a988 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - e92675014ac9 + - 6e26c9afd301 - 0a3a602cd1e3 + - 8f9f06995f98 - 3e44ef016b45 - 9e3e80cc4ad4 - - 8f9f06995f98 + - e92675014ac9 - e022dff952df - - 6e26c9afd301 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: + - 5da9a0e2fb2d - 8d09f8be269e - - 08256557922f - 920677cd220f - - 5da9a0e2fb2d + - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - 37d88f41c810 - - 4a53b89fa703 - 82398ba86ba7 + - 4a53b89fa703 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko @@ -540,8 +540,8 @@ tools: - name: yahs owner: iuc revisions: - - 425e63adcc5d - 39495e107274 - ff4031bfaa22 + - 425e63adcc5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index e4ca414e6..48bc15b66 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,19 +2,19 @@ tools: - name: integron_finder owner: iuc revisions: - - bfd290fe1588 - - 392f100eebcd - 4768f7f8e93f + - 392f100eebcd - 1ae00120dd24 + - bfd290fe1588 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - 31812e7a1315 - - 1f5641a52664 - ded48b36f3b7 + - 1f5641a52664 - 8e8dc9a1e3e5 + - 31812e7a1315 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index 0cb973fd0..6f3627c26 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,12 +2,12 @@ tools: - name: bbtools_bbduk owner: iuc revisions: + - 1c427e24fb79 + - d1f62024a08b - 159b04e36791 - - a9c9d768b751 - 7beb76ffbc0f - - 1c427e24fb79 - 0840ba83860c - - d1f62024a08b + - a9c9d768b751 - 204a131e47db tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index d42c64f3b..f7e31f101 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: + - 0a5c785ac6db + - e19bebe96cd2 + - a1a923cd89e8 - a68aa6c1204a - - dde39ba9c031 - 87ee588b3d45 + - b28e0cfa7ba1 + - dde39ba9c031 + - ce3c7f062223 + - a8eabd2838f6 - 589e7e57fd6d - 64e2edfe7a2c - - a8eabd2838f6 - - e19bebe96cd2 - - 0a5c785ac6db - 07e8b80f278c - - ce3c7f062223 - - b28e0cfa7ba1 - - a1a923cd89e8 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/blast.yml b/usegalaxy.org.au/blast.yml index 422078388..cffc8cd7d 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,24 +8,24 @@ tools: - name: diamond owner: bgruening revisions: - - e8ac2b53f262 - - f921014aba5a - 54f751e413f4 + - f921014aba5a + - e8ac2b53f262 - 62c9df8382c2 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - a52d2d93e595 - - d999e774072a - - 5edc472ec434 - e25d3acf6e68 - - 6f386c5dc4fb - - 0e3cf9594bb7 + - 5edc472ec434 - acf4e47b734c - cbf3f518b668 + - a52d2d93e595 + - d999e774072a - 2889433c7ae1 + - 6f386c5dc4fb + - 0e3cf9594bb7 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 860ba4b32..78e4e5852 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -9,12 +9,12 @@ tools: owner: chemteam revisions: - 095ad4d096d1 - - 710301bc46fa + - c8cdde00b105 - 27ee142314a9 - - f4230f116196 + - 710301bc46fa - da6bd1975a71 - - c8cdde00b105 - 6ca543ec1bf8 + - f4230f116196 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -92,8 +92,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 8e214e52e461 - 7255688c77f3 + - 8e214e52e461 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_conformers @@ -130,31 +130,31 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 3b8a9d5ced85 - 0fac8e2afc13 - - bfb65cb551d8 - 88076940fa94 - 79cfd9ead848 + - 3b8a9d5ced85 + - bfb65cb551d8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - b46d4b4d995c - 715cd0e87781 - - d532b7e5f64b - - 55918daa5651 - eb6564a60136 + - b46d4b4d995c + - d532b7e5f64b - f5d979cb4b54 + - 55918daa5651 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: + - d2f955aea23a - f26afd1b7104 - 5579659312e6 - fdf2cc80adb5 - - d2f955aea23a - dae135dfd519 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -162,17 +162,17 @@ tools: owner: chemteam revisions: - 319a28774da9 - - d1d0efda35c0 - bc31d02be922 + - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - 4da9ee404eab - - 2c349b027a01 - 070e3ecc3fda - cac1886249a2 + - 2c349b027a01 - ed736e6eee39 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -180,23 +180,23 @@ tools: owner: chemteam revisions: - da8753545526 + - d1f803b5943c + - 525ca7c8065f + - 73008ef1f487 - c0c9a5024177 - f197e34c33a9 - - 525ca7c8065f - 2e219a2d9327 - - d1f803b5943c - 807aa4c9293d - - 73008ef1f487 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 7568ae18908a - - c4fbab8e03c5 - - 61094e01eff9 - 2c8ed1b52bf7 + - 61094e01eff9 + - c4fbab8e03c5 - 1809414a9454 + - 7568ae18908a - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -209,11 +209,11 @@ tools: - name: md_converter owner: chemteam revisions: - - d7ec25187599 + - 79e8ab8f1e81 - 730ef07b90ae - ccfbd956a2d3 - - 79e8ab8f1e81 - ba83f0923369 + - d7ec25187599 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -268,10 +268,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - e2c36f62e22f + - b59c91adeac1 - 4242b4d68e9c + - e2c36f62e22f - e6011617c748 - - b59c91adeac1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -296,8 +296,8 @@ tools: - name: qcxms_neutral_run owner: recetox revisions: - - 33b7a99b6de3 - 8f465c0c3b6c + - 33b7a99b6de3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_production_run @@ -351,9 +351,9 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 85fad59f8168 - - bf99565cec1f - 9b48456a96fe + - bf99565cec1f + - 85fad59f8168 - d4c67ced6abc tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 445e40947..c60a701a7 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,11 +2,11 @@ tools: - name: diffbind owner: bgruening revisions: + - f907216064f6 + - c97a786e8fb5 - fa56d93f7980 - 2605cbdaa7d8 - - c97a786e8fb5 - 163688bb8f73 - - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -18,8 +18,8 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 11cf21ee4242 - 4124781932db + - 11cf21ee4242 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -27,16 +27,16 @@ tools: revisions: - 495a4173006f - 640d3af5d833 - - 86e2413cf3f8 - f5d67c722d67 - 424aefbd7777 + - 86e2413cf3f8 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator owner: pjbriggs revisions: - - 087d9872fb0d - b695071de766 + - 087d9872fb0d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index de16e7aa4..4e8ef6863 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -9,10 +9,10 @@ tools: - name: collapse_collections owner: nml revisions: - - 33151a38533a - 830961c48e42 - - 90981f86000f - 25136a2b0cfe + - 33151a38533a + - 90981f86000f tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - baabc30154cd + - 0046692724f9 - 2dae863c8f42 - 6cbe2f30c2d7 - - 0046692724f9 + - baabc30154cd tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 57f0914ddb7b - 38eec75fbe9b + - 57f0914ddb7b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index d55379548..005c10975 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -2,8 +2,8 @@ tools: - name: agat owner: bgruening revisions: - - abba05ead5d7 - e7449b2c14bf + - abba05ead5d7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -15,32 +15,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 0b3c3ad92827 - - 3b6f97e7094c - e3cbd2287f63 - ab9350a8ab4d + - 0b3c3ad92827 + - 3b6f97e7094c + - 6ef0b5664c69 - 5e1240a87bcb - f3a19509108a - - 6ef0b5664c69 - - 367b1ed91207 - - a3b86937ead6 - 4a6ee918c13a + - a3b86937ead6 + - 367b1ed91207 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 1b5fc03380d4 - - bd46669113b9 - - 33c99804a32f - - 091bb5922a82 - - 501c21cce614 - 584008e574b2 - - e177a8ea0bf1 - - 72ed72122deb - e525f9ffb9ac - - 54ccb7e1f49a + - 72ed72122deb + - e177a8ea0bf1 - d4d4e9febf5c + - 091bb5922a82 + - 501c21cce614 + - bd46669113b9 + - 54ccb7e1f49a + - 33c99804a32f + - 1b5fc03380d4 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -58,31 +58,31 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - 7e801ab2b70e - e7ed3c310b74 + - 7e801ab2b70e tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: - - 77b41c89d856 - - 8979c288aefb - 186b8d913e6c + - 8979c288aefb + - 77b41c89d856 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: + - 4b347702c4aa - 43807a65369f - 614a63f14adf - - 4b347702c4aa tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa owner: iuc revisions: - - e33c82b63727 - 8e9d604e92f4 + - e33c82b63727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -94,8 +94,8 @@ tools: - name: gffread owner: devteam revisions: - - 4dea02886337 - 154d00cbbf2d + - 4dea02886337 - 3e436657dcd0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -121,8 +121,8 @@ tools: - name: samtools_bam_to_cram owner: iuc revisions: - - b9ea85dfaf45 - 18dbde5680c0 + - b9ea85dfaf45 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta @@ -135,18 +135,18 @@ tools: owner: devteam revisions: - 2dcfbbf9071a - - 68f57cc8fad0 - 78fb18899c99 + - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - - 92ac8e086317 - 63769c4217a7 - - 26c6706bfb07 - - b9b385097f13 - 19e45916daf9 + - b9b385097f13 + - 26c6706bfb07 + - 92ac8e086317 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf @@ -158,15 +158,15 @@ tools: - name: ucsc_twobittofa owner: iuc revisions: - - 8067dfa00ed2 - 3c6f9e8a4c17 + - 8067dfa00ed2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig owner: iuc revisions: - - 98704d357ede - a2f83a375bf2 + - 98704d357ede tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index fbf3c4290..f8ffc4b40 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,120 +2,120 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 5f6d123679f4 - 29451af70c52 - - a1ca9bccc7f2 - - c929a006727f - - e821645ef8fc - - de72ba3ed6f2 - 268e91e540ee + - 5f6d123679f4 + - de72ba3ed6f2 + - e821645ef8fc + - c929a006727f + - a1ca9bccc7f2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 0e143b4c3987 - - 5d11599b8a7d - 2d2cf5c1ea8a + - bb1e4f63e0e6 + - 0e143b4c3987 - 0e49b109abc2 - 12af64f93288 + - 5d11599b8a7d - 7a7fd0f5f15d - - bb1e4f63e0e6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - c06951d10364 - - 195e98217334 - - dc059492a995 - - 7c1beb6d6eca - 81b1e3e1fc6c + - dc059492a995 + - 195e98217334 - 1d848bc4585f + - c06951d10364 + - 7c1beb6d6eca tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - a67ac707496a + - 07418a30ed01 + - 26e7304d6737 - 3d211717a775 - 93eb012d9eed - - bfff7454b59a - - 26e7304d6737 - 71aa86af6762 - - 07418a30ed01 + - bfff7454b59a + - a67ac707496a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 5be24eba848d - - 2bc10a9ca58b - - 26983857c91a - 56d5b797ce84 - b8858746dc1f - - 29fcfd36e90a + - 26983857c91a + - 2bc10a9ca58b + - 5be24eba848d - dd0b7398bb96 + - 29fcfd36e90a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: + - 9384cd033f30 - c3e012dfe21f + - ee3a1b0f45f1 - e6d0bff01239 - 7e6bcd2e5128 - - 9384cd033f30 - - 7ef978dc1b8a - - ee3a1b0f45f1 - 72bfafe3330b + - 7ef978dc1b8a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - 167788df3b46 + - 9470f29702f8 - fb9cf9c97ec4 - - 514fa53b5efb - - a60c359ec43c - b73e213add0c - - fd1275e01605 + - 167788df3b46 - d9a637e83828 - - 9470f29702f8 + - 514fa53b5efb + - fd1275e01605 + - a60c359ec43c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - 5bffaa8354a1 - - c34d11ea4ba6 - ca0616bb2cdf - a02cfa31e9cb + - c34d11ea4ba6 + - 86febdcc4283 - e479c7ca5570 - 2c37ce318bc3 - - 86febdcc4283 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: + - 2d466b530754 - 004aea905d4d - - 69a8621ca2f0 - - 192ef85c0b0b - 78f405266706 - - 2d466b530754 - - 1fcb7adc39b8 - 01fb6a7654e6 + - 69a8621ca2f0 + - 1fcb7adc39b8 + - 192ef85c0b0b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - d9ce4897dbb2 - - 3c9f0c486cca - - 137c4beed34b - - d580d6acd1df - 2f9e4843f480 - 9ecba5e225a6 + - 137c4beed34b + - 3c9f0c486cca + - d9ce4897dbb2 + - d580d6acd1df - db940c262830 - 459cfa861f0b tool_panel_section_label: DeepTools @@ -123,84 +123,84 @@ tools: - name: deeptools_plot_correlation owner: bgruening revisions: - - bd7db9e2f2cb - - 2c66e43f1c86 - - f264afa9fa6f - - fbe773640707 - - fd408d755394 - 32e451def88c + - f264afa9fa6f + - 2c66e43f1c86 - bad3ca889618 + - fd408d755394 + - fbe773640707 + - bd7db9e2f2cb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 231994413f89 - - 7fda5607e777 - 56bce3c82278 - - 4e12ea27f788 - 9368fbc49c8b + - 4e12ea27f788 + - 7fda5607e777 - 7e361d147872 - 3b9d990a0a0e + - 231994413f89 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - 94ca68515826 - ce4ce3316f74 - - d9114ef1c8a5 - - 4431f39ede55 - b1779366c8e9 - c03c3384cd81 + - d9114ef1c8a5 + - 94ca68515826 + - 4431f39ede55 - e65d16fb2724 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - 2da482e408b8 - 793665fff0f8 + - b88ebb3672a1 - d57251071381 - f8fc4e5aff9d - - 2da482e408b8 - - b88ebb3672a1 - - 4ed32329e0ed - 23f7c5f1fdaf + - 4ed32329e0ed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - a7849312d328 - - ba6efa77fb79 - - 512155688d98 - - c60570fa602f + - a4dfb122e52b - 010e58e9d822 - e4c7985d4585 - - a4dfb122e52b + - c60570fa602f + - ba6efa77fb79 - 25d830337d31 + - a7849312d328 + - 512155688d98 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 69264da0ce77 - - c899e0ccff8c - - aa200e4f3939 + - 443d9a9d6d11 - 00d869ea03a1 - 4d678170d29b - - 443d9a9d6d11 + - aa200e4f3939 + - 69264da0ce77 - 38e3f226248b + - c899e0ccff8c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: + - d806504e96d9 - 6662b1a8d326 - a2d70c4fd406 - - aac8444d6681 - - d806504e96d9 - c361b12d207a - 10301d137111 + - aac8444d6681 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/dna_metabarcoding.yml b/usegalaxy.org.au/dna_metabarcoding.yml index bf3e8381d..652e65630 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -2,29 +2,29 @@ tools: - name: obi_annotate owner: iuc revisions: - - 3021b9f5809f - d50dc96e3ce9 + - 3021b9f5809f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_clean owner: iuc revisions: - - 08d873cdd5f6 - 7d16de45c021 + - 08d873cdd5f6 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert owner: iuc revisions: - - 4d705e3443a7 - e328ced6cf0a + - 4d705e3443a7 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep owner: iuc revisions: - - 02bab5ff7c37 - e9e49cf06b42 + - 02bab5ff7c37 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend @@ -37,8 +37,8 @@ tools: - name: obi_ngsfilter owner: iuc revisions: - - 91a1ed0b486f - 76e69de726b2 + - 91a1ed0b486f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort @@ -58,14 +58,14 @@ tools: - name: obi_tab owner: iuc revisions: - - 4cf47c504672 - 3299c7d5268f + - 4cf47c504672 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq owner: iuc revisions: - - d4bea99366f9 - c0f7b58b4ce4 + - d4bea99366f9 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index aaf7a1b11..3c40a1102 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: + - 832c20329690 - dba489bfcd62 - 63dd26468588 - ce385837c160 - - 832c20329690 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index b81e23d34..81a3b7c20 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - d82648ad25a3 - - 29bdbc353f20 - 6da3972210ee - - 62f5fab76dfb + - 29bdbc353f20 - cf1322aeb137 + - d82648ad25a3 + - 62f5fab76dfb tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -24,7 +24,7 @@ tools: - name: pileometh owner: bgruening revisions: - - d6787bab7b11 - 183cb55b1729 + - d6787bab7b11 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index b8d9fc476..08a78d208 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: - - c4b82dce8335 - - 64172f1c1202 - - 660cffd8d92a - - c5e2e5902201 + - 49370cb85f0f - fe74900d6dc7 - - 093678460093 - - 5915ea1ec9b1 - - 4e5056fefd88 - - c053d4cad713 - de6cebe3c043 + - 5915ea1ec9b1 + - 093678460093 - 288f97432497 - - 49370cb85f0f - - 5eb7e84243f2 - - 44e2cc14f75b - 135b80fb1ac2 + - 48f587c13075 + - b1c926deaa2d + - 44e2cc14f75b + - 64172f1c1202 - 8665bcc8b847 + - c053d4cad713 + - c4b82dce8335 - 8c0175e03cee - - 48f587c13075 + - 5eb7e84243f2 - e4691e1589d3 - - b1c926deaa2d + - 4e5056fefd88 + - 660cffd8d92a + - c5e2e5902201 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -41,9 +41,9 @@ tools: - name: fasta_compute_length owner: devteam revisions: - - de2db1bdfbf8 - 7d37cfda8e00 - 5cbde03c1103 + - de2db1bdfbf8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -77,91 +77,91 @@ tools: owner: devteam revisions: - f81d4362b6c1 - - ec0b5076173a - f773e98b26cf + - ec0b5076173a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: - - 0dbb995c7d35 - - 56022eb50bbd - 9c620a950d3a + - 0dbb995c7d35 - cd0874854f51 + - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - dbfc505896e9 - 1d8fe9bc4cb0 - c59d48774d03 + - dbfc505896e9 + - dbf9c561ef29 - d60c3f704da0 - 65b93b623c77 - - dbf9c561ef29 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - 9115b978ce10 - f1dc2a761c30 - b05e39b9c170 + - 9115b978ce10 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: - - 10b75444feae - - 81a9090d6df3 - '144275714590' + - 81a9090d6df3 + - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer owner: devteam revisions: - 47e5dbc3e790 - - e9f8633db0a2 - 8611b80a14d6 + - e9f8633db0a2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation owner: devteam revisions: - - 5b87038565bb - e30352e889fe - 7861f3b10c68 + - 5b87038565bb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality owner: devteam revisions: - - 9282652e7234 - 9dfda4e310ed - 4e1d64e6385f + - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - f3936d0632cb - 03d57fea6482 - 523c2aff0376 + - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer owner: devteam revisions: - b41c2c1bcfbf - - 2ccb8dcabddc - 3e396e702cea + - 2ccb8dcabddc tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner owner: devteam revisions: - - c885369b207b - 09a2199cd356 + - c885369b207b - 8d958759cf2a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -169,8 +169,8 @@ tools: owner: devteam revisions: - 35e38452bb3f - - e39cc71d3ed6 - 397dc333436b + - e39cc71d3ed6 - 249c8393f2d4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -185,16 +185,16 @@ tools: - name: fastq_stats owner: devteam revisions: - - f0e7deab6518 - f86c27295151 + - f0e7deab6518 - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer owner: devteam revisions: - - b63b2bfb3ea3 - 33794bdb7fe0 + - b63b2bfb3ea3 - f0b18efb97f1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -208,25 +208,25 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - d5e9e83cd3d8 - 567d5b3c52b1 - - 09070cacefd8 + - d5e9e83cd3d8 - 529bccd5e4a1 + - 09070cacefd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 4bedca26c133 - 8abdedf55101 + - 4bedca26c133 - 0b7ec11b3c7c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - - 90858c306551 - cb1e251cac37 + - 90858c306551 - bdf1ce174e39 - 736b8f6ee456 tool_panel_section_label: FASTA/FASTQ @@ -234,35 +234,35 @@ tools: - name: fastx_collapser owner: devteam revisions: - - 07497255281e - 7ce1891db6f5 - 421f0af4ee95 + - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - - b29d37ca9e41 + - f984bb114520 - 02f8a17a4ebd + - b29d37ca9e41 - 3599f5451ee2 - - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - 6027ef51ef91 - - 0c2907307ba4 - 177f0621c266 - e246088b6e34 + - 6027ef51ef91 + - 0c2907307ba4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - - 547e8d00f11c - 61b4cedc8934 - 73194cdd4f57 + - 547e8d00f11c - 377ac2829eac tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -275,10 +275,10 @@ tools: - name: pear owner: iuc revisions: - - 2f804526f5fd - b4c6f054210a - - 037f0acc7830 - f69501361cec + - 037f0acc7830 + - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id @@ -305,9 +305,9 @@ tools: - name: seqtk owner: iuc revisions: - - 4b494533146a - a019807f4e67 - 3da72230c066 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic @@ -320,40 +320,40 @@ tools: - name: ucsc_fasplit owner: iuc revisions: - - 71f649c23021 - bf04bd405d5b + - 71f649c23021 - d3f58a0dc09d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - b557acca0b56 - - e654095ab143 - a535cf1e5da4 + - 24013bf85a6f + - e654095ab143 - 71ad4a56c40c - 8250ea3a1501 - - 24013bf85a6f + - b557acca0b56 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup owner: iuc revisions: - - c5a2ee07c4e1 - f1d33e4c7bd8 + - c5a2ee07c4e1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract owner: iuc revisions: + - 27ac32a22ad2 - 6a675c3aa610 - - 7a7e33d28f62 - - f3759eec3018 + - 015cf18f4a15 + - 9fa7803d1c51 - 828dba98cdb4 - - 27ac32a22ad2 - 7accf7407811 - - 9fa7803d1c51 - - 015cf18f4a15 + - 7a7e33d28f62 + - f3759eec3018 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group diff --git a/usegalaxy.org.au/fastq_quality_control.yml b/usegalaxy.org.au/fastq_quality_control.yml index 6048409a7..43487bf40 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,38 +2,38 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 7b4468117008 - - ce9cd02d5b88 - 64e9a6afdd0c + - ce9cd02d5b88 + - 7b4468117008 - e41385662e5e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - 8050e091e99b - c64d534a763c + - 8050e091e99b tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - - e7b2202befea + - 2c64fded1286 + - 3d0c7bdf12f5 + - 5ec9f6bceaee + - ff9530579d1f - 2b0c9d9fc6ca + - e7b2202befea - 9da02be9c6cc - - 5ec9f6bceaee - f2e8552cf1d0 - - 3d0c7bdf12f5 - - 2c64fded1286 - - ff9530579d1f tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - a252d8415583 - 89d299153577 - c1a33f603da2 + - a252d8415583 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution @@ -47,39 +47,39 @@ tools: - name: fastx_quality_statistics owner: devteam revisions: - - 7306ec78632a - 59003d0543cd - cc0fd298cc17 + - 7306ec78632a tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: + - a72af9de6bf5 - 8880fb74ef56 - 1f296803dfa3 - - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 3d93dd18d9f8 + - 5e33b465d8d5 + - 75c93c70d094 - c1a4b5f3b432 - - f7e2f1eb3a16 - - b2f1f75d49c4 - - abfd8a6544d7 - 9a913cdee30e - 1c2db0054039 - bf675f34b056 - - 5e33b465d8d5 - - 75c93c70d094 + - b2f1f75d49c4 + - abfd8a6544d7 + - 3d93dd18d9f8 + - f7e2f1eb3a16 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 084bbd8ba7b8 - cd7e644cae1d + - 084bbd8ba7b8 - 949f01671246 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fetch_alignmentssequences.yml b/usegalaxy.org.au/fetch_alignmentssequences.yml index c01999d90..0dfc5355c 100644 --- a/usegalaxy.org.au/fetch_alignmentssequences.yml +++ b/usegalaxy.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 9e776e7fab4f - 19f42b3ea391 + - 9e776e7fab4f tool_panel_section_label: Fetch Alignments/Sequences tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index 3d83f6475..6e32629d8 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -9,8 +9,8 @@ tools: - name: gemini_amend owner: iuc revisions: - - 4bd4870ecd33 - be828b79bd4d + - 4bd4870ecd33 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate @@ -38,8 +38,8 @@ tools: - name: gemini_db_info owner: iuc revisions: - - 4c5f4e9b1931 - 7d75673f4d6f + - 4c5f4e9b1931 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo @@ -52,22 +52,22 @@ tools: - name: gemini_dump owner: iuc revisions: - - 40f85b45e472 - 96a2d270bf0f + - 40f85b45e472 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions owner: iuc revisions: - - 8151a5a0e4f6 - 91d53f89ca54 + - 8151a5a0e4f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -79,8 +79,8 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 184aa4e686e2 - 2550239feed5 + - 184aa4e686e2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load @@ -130,29 +130,29 @@ tools: - name: gemini_recessive_and_dominant owner: iuc revisions: - - 86f3aac4418d - 05124dc72dba + - 86f3aac4418d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region owner: iuc revisions: - - 33efe43c1dbb - 601b70d10d92 + - 33efe43c1dbb tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh owner: iuc revisions: - - 345d41f3f574 - 93967598e18e + - 345d41f3f574 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic owner: iuc revisions: - - ef9991a4a9a7 - e4e2128460e3 + - ef9991a4a9a7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats @@ -165,7 +165,7 @@ tools: - name: gemini_windower owner: iuc revisions: - - 8f04952b8882 - 0c58ba91d018 + - 8f04952b8882 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 18d33de94..f729cfa4c 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -2,15 +2,15 @@ tools: - name: mageck_count owner: iuc revisions: - - e329d44424d7 - 3edbd1ff5602 + - e329d44424d7 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea owner: iuc revisions: - - d46e36492bff - b946929d31c4 + - d46e36492bff tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle @@ -23,8 +23,8 @@ tools: - name: mageck_pathway owner: iuc revisions: - - 39a996d44e16 - 9744e1124d0f + - 39a996d44e16 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index 0c684b5ad..9a72c55c7 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: + - e9df53a75f3c - b39347891609 - - c1b437242fee - 983bf725dfc2 - - e9df53a75f3c + - c1b437242fee tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,54 +17,54 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - e063168e0a81 - 1c58de56d587 - 28587613264f + - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - f8054ea1c365 - - 8848455c0270 - - 7068f48d0ef9 - - e407b9da183a - - 653e89d73fc4 - - 6ea73833cf67 - 6591f049cf7e - ba931a59dd59 - - 69ebb7f46e45 + - aad3885b3216 + - f5ea3ce9b9b0 + - 1790dcf3c32d + - 516a54ddf218 - c441583adae5 - - 734abc7ac21d + - e407b9da183a - 1ec814014652 - - e08a7ad4378b + - 734abc7ac21d + - 6ea73833cf67 + - 9a776b080193 + - 69ebb7f46e45 - 83c7d564b128 - - 516a54ddf218 - 4df8de2d0e48 - - aad3885b3216 - - f5ea3ce9b9b0 - - 5e6237d58b0c - - 9a776b080193 + - 8848455c0270 - 4317d3cb6cba - - 1790dcf3c32d + - 5e6237d58b0c + - e08a7ad4378b + - 7068f48d0ef9 + - f8054ea1c365 + - 653e89d73fc4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 21a560af5913 - - 9aaa46d45472 - 75b3b3d0adbf - 34758ab8aaa4 + - 21a560af5913 + - 9aaa46d45472 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - bfdc6a7ffd3a + - 054483e27a35 + - af5eccf83605 - 95fb5712344f + - bfdc6a7ffd3a - 468c71dac78a - - af5eccf83605 - - 054483e27a35 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/graphdisplay_data.yml b/usegalaxy.org.au/graphdisplay_data.yml index 72cdda2e8..ccca7dd05 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - 290a11559985 - - 7f13dc906cb9 - - fd59d783248a + - 4b519282a05b + - ae9994cf526f - df7356989ac1 - c4bde687c846 - - ae9994cf526f - - a64dc31ab7f2 + - fd59d783248a - 740057a5126d - - 4b519282a05b + - 7f13dc906cb9 + - a64dc31ab7f2 + - 290a11559985 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -42,48 +42,48 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: + - ca7cb0eaad62 - 53460afd5115 - 374e9062d874 - - ca7cb0eaad62 - - 51c6ccaace7e - '566197475670' + - 51c6ccaace7e - 3b37b1b1c3a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - da4c086cff5b - 3d059e9c2fba - - 10515715c940 - 1a72f938213e - - d3a9e32672ec - 391a4cc45fea + - da4c086cff5b + - d3a9e32672ec + - 10515715c940 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram owner: iuc revisions: - - b0d96516e6a5 - 6fc8bab811da + - b0d96516e6a5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_pca owner: iuc revisions: - - ae344ccf9d62 - b1268b7544d3 + - ae344ccf9d62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - e3a675da7fd0 - - 299307abd804 - 5fe1dc76176e + - 1acf88921176 - d0fc8b746d57 - 5298e06f14f9 - - 1acf88921176 + - e3a675da7fd0 + - 299307abd804 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -102,8 +102,8 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - 97e3b735ed22 + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan @@ -128,17 +128,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 667e17248bfe - - 17359b808b01 + - 4542035c1075 - 836d1aa3e89a - - a6e57ff585c0 - - 2bb2e07a7a21 - - 112eb40ba6cf - ca2def38369c - 1cfc579079a6 + - 2bb2e07a7a21 + - a6e57ff585c0 - fd5dbf0f732e - - 4542035c1075 + - 112eb40ba6cf - 6cd09d7b5f37 + - 17359b808b01 + - 667e17248bfe tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -171,17 +171,17 @@ tools: - name: plot_ragtag_paf owner: galaxy-australia revisions: - - c1bed78b9ed5 - 501dcf66c0ce + - c1bed78b9ed5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: - - 1c5dcef5ce0f - - 62e3a4e8c54c - 85da91bbdbfb + - 1c5dcef5ce0f - f234e2e59d76 + - 62e3a4e8c54c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -201,8 +201,8 @@ tools: owner: iuc revisions: - 7c9417381ad5 - - 6c571966cfb9 - 44c66e8d21e6 + - 6c571966cfb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -214,23 +214,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 14e7c35f3d00 + - 4ac4e7083b7e - 36b848d5f3ec - 360df4999907 + - 326a3db8d9d1 + - 2824d77cd8f8 - a1abfa420d9d - 7dd841a32245 - - 2824d77cd8f8 - - 4ac4e7083b7e - - 326a3db8d9d1 + - 14e7c35f3d00 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 44608d0193ed - 83c573f2e73c - 73b8cb5bddcd - 2f557f6abbfb + - 44608d0193ed tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/usegalaxy.org.au/hca_single_cell.yml b/usegalaxy.org.au/hca_single_cell.yml index 9edd2be08..4c13e3be7 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -28,15 +28,15 @@ tools: - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 7779b9dcf040 - 22bd5861706d + - 7779b9dcf040 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells owner: ebi-gxa revisions: - - 361608369dda - bf1e0bdec1db + - 361608369dda tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes @@ -49,15 +49,15 @@ tools: - name: scanpy_find_cluster owner: ebi-gxa revisions: - - fc4b3b46dc9d - 36735850e461 + - fc4b3b46dc9d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers owner: ebi-gxa revisions: - - d8f5224005bb - 0a8e527d1517 + - d8f5224005bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes @@ -70,22 +70,22 @@ tools: - name: scanpy_integrate_bbknn owner: ebi-gxa revisions: - - c9da9192eee5 - 9d76c3d6dff6 + - c9da9192eee5 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 352cdf3b2f75 - 3c47bc560688 + - 352cdf3b2f75 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - 6903bc865d63 - c354af93f567 + - 6903bc865d63 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn @@ -99,8 +99,8 @@ tools: - name: scanpy_multiplet_scrublet owner: ebi-gxa revisions: - - 70cb0596ffef - 53ce0e336840 + - 70cb0596ffef tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalise_data @@ -113,8 +113,8 @@ tools: - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - 73d43034c860 - 0387a2179f88 + - 73d43034c860 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed @@ -127,36 +127,36 @@ tools: - name: scanpy_plot_scrublet owner: ebi-gxa revisions: - - 6f5509cf3176 - 4a74b45c1ce4 + - 6f5509cf3176 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory owner: ebi-gxa revisions: - - d3df472a21dc - cb1992d1804b + - d3df472a21dc tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x owner: ebi-gxa revisions: - - 287503c35cb4 - 078aa23c9374 + - 287503c35cb4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable owner: ebi-gxa revisions: - - 0bab2ae44e7a - d18ed15697bb + - 0bab2ae44e7a tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap owner: ebi-gxa revisions: - - 6a6364b488db - 79cc06a557b0 + - 6a6364b488db tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt @@ -183,29 +183,29 @@ tools: - name: scanpy_run_pca owner: ebi-gxa revisions: - - 0cf90e01d9f8 - 4428dba93375 + - 0cf90e01d9f8 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne owner: ebi-gxa revisions: - - 3fb53f5e46ea - abdb61e4afa3 + - 3fb53f5e46ea tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: - - 0f98603d0116 - - ea91cfd0444e - 767a675b5254 + - ea91cfd0444e + - 0f98603d0116 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - e2d0dc8a50ca - 4cc9362782b4 + - e2d0dc8a50ca tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index e2a1f6d20..6fecadf4c 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -3,50 +3,50 @@ tools: owner: bgruening revisions: - 921a2da49a0c - - a4c13ddcc8ee - 9edf8894a22d - - 29f66c353bcb - ed2cca6b5de4 + - a4c13ddcc8ee + - 29f66c353bcb tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - d404277cc87a - ec4b948dc6f0 - 78fb5e286609 - 5746d61f0a91 - 755df866ad0c + - d404277cc87a tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - 4d511437b1e5 - - 03dd3c16ae4e - 11fa44ee0603 - 9e357a8b2ec3 - 977dc15add20 + - 03dd3c16ae4e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - c3e5e2cf12b7 - - 41dbf4d162a2 - - 3b5b54ed6392 - 0ba4f56a3613 + - 3b5b54ed6392 + - 41dbf4d162a2 - 77919cc3618e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - b63363075c2e - - 9939786dd9c9 - - 5308ca68ef3d - 7babd8a46fe0 + - 9939786dd9c9 + - b63363075c2e - 12d51d7be66f + - 5308ca68ef3d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index 5b8ca01c8..d995e4f4c 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,21 +2,21 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 7db4fc31dbee + - 8bccb36e055a + - 3df9f0a4bf34 - 0c777d708acc - 81f0cbca04a7 - 699a5e9146b3 - - 8bccb36e055a - - 3df9f0a4bf34 + - 7db4fc31dbee tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: + - 0a53256b48c6 + - 5bc8cdc17fd0 - 5791a7f65275 - 2436a8807ad1 - - 5bc8cdc17fd0 - - 0a53256b48c6 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features @@ -30,9 +30,9 @@ tools: - name: 2d_histogram_equalization owner: imgteam revisions: - - 70316d792fc9 - - b1c2c210813c - 77f7159d775a + - b1c2c210813c + - 70316d792fc9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter @@ -52,11 +52,11 @@ tools: - name: bfconvert owner: imgteam revisions: - - 85edbb7a436b - - b07f4839ca77 - - 10eed33aa9b2 - fcadded98e61 - f3360fbeda64 + - 10eed33aa9b2 + - b07f4839ca77 + - 85edbb7a436b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -69,16 +69,16 @@ tools: - name: count_objects owner: imgteam revisions: - - 5bf8eb50b280 - b58447a2eed2 - 664232d2a3f7 + - 5bf8eb50b280 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - e917a2424690 - 0e4dccaafef5 + - e917a2424690 - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -100,9 +100,9 @@ tools: - name: cp_convert_objects_to_image owner: bgruening revisions: - - ef4aed1d34c4 - - cdf8e3c57dae - df3ad3ba5c6f + - cdf8e3c57dae + - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image @@ -116,56 +116,56 @@ tools: - name: cp_enhance_or_suppress_features owner: bgruening revisions: + - bace5a93a97c - 11f177b1a59e - f2ed92b011a9 - - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - d0178bdcd00e - f24c370e5ea4 - f8fa0f6718a3 + - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - ad271f78a87a - - 31d195bedf6d - 3245681b2f6d + - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - b6eec6087271 - - 87d4d92d7487 - 993faa34333b + - 87d4d92d7487 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - c09dcda1143f - - 6100a22bf4f2 - ff1a86a87364 + - 6100a22bf4f2 + - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - b178453ea8d1 - - 3a05117669cf - 667a513e67e4 + - 3a05117669cf + - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - a1a961c46d4b - ac5bea85a391 + - a1a961c46d4b - 2564f461de62 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -188,8 +188,8 @@ tools: - name: cp_measure_image_quality owner: bgruening revisions: - - e972e07c7845 - d3890df07463 + - e972e07c7845 - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -197,47 +197,47 @@ tools: owner: bgruening revisions: - e52c75a28c4b - - 407925835dd9 - 980aed9e8fd5 + - 407925835dd9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - d85f11570109 - - acf3aa487283 - 79e10d12d90a + - acf3aa487283 + - d85f11570109 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: + - 035a58c7f54a - b76841ee5560 - 80b200ae516b - - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines owner: bgruening revisions: - - b44b081bcf37 - 91560258e972 + - b44b081bcf37 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_relate_objects owner: bgruening revisions: + - 3a3033222f61 - 48102a685037 - 8083a87d2fdf - - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: + - 33f4fa1413fb - 27edbb90ab2b - 4ecf93628f97 - - 33f4fa1413fb tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -256,16 +256,16 @@ tools: - name: idr_download_by_ids owner: iuc revisions: - - 4b794652dcdc - f92941d1a85e + - 4b794652dcdc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info owner: imgteam revisions: - - 7b6d9412c7f8 - 236ec78b2e53 - f8b4eada923c + - 7b6d9412c7f8 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index 0ba9f5ca6..03afd9a7b 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 3e4f434a69c6 - - d6e72da3ec35 - - f362150bef41 - - 78bbd17d0703 - - a38934e303b9 - - 1069f6db0a0e + - 40737febe339 - e319b5b65879 + - 1069f6db0a0e + - a38934e303b9 - 3a72fede57ce - - 40737febe339 + - 78bbd17d0703 + - d6e72da3ec35 + - f362150bef41 + - 3e4f434a69c6 - e4ee04da1c19 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 72ddd32392cd - - 618297d23022 - 7fe36019c073 + - f91cfb73d369 + - 9537184d421f - fcbeda41d0ac - 0135f1d487a0 - - 9537184d421f + - c88553ec696e - 8f8df367470d - - f91cfb73d369 + - 618297d23022 + - 72ddd32392cd - 2b95d5c04908 - - c88553ec696e tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: + - d7e79eb3bcb3 - fafb3d685fa9 - 2cf4a1cafc16 - - d7e79eb3bcb3 - ad0dc9f4c9e2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - ee29337f905c - - 43aac8d29685 + - 8d36959b000d + - 8c05afb547fa + - bd2a7d1316b9 + - 94df24c6bc00 - 7f1cfa4c0e32 + - 6a1515bb0687 - 3d18f8c3c0f6 + - ee29337f905c + - 43aac8d29685 - a1c2aecd7a0d - - 5dc33613c288 - - bd2a7d1316b9 - 9eaadf03e0df - - 8d36959b000d - - 94df24c6bc00 + - 5dc33613c288 - 28a6f1908fcc - ee2beb764a7b - - 6a1515bb0687 - - 8c05afb547fa tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 364f4ffec275 - - e3bb03cf207a - 86a20ae274fc - - 5671e1d3d5ee - - cb903c9dc33d - 9f978da6528a - - 5d6ed46cc101 + - e3bb03cf207a + - a250929be21b - bcaa0d571ce2 - - d37ede8589b2 - c092052ed673 - db536ad45f28 + - 5d6ed46cc101 + - 5671e1d3d5ee + - cb903c9dc33d - 8858fa037a15 - - a250929be21b + - 364f4ffec275 + - d37ede8589b2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - e1a015876aa9 + - c5c9f02b6167 + - 584beffa972b + - ed28dd32141c + - 194e3ceee923 + - 49236b03e4fd - f95f403841ad - 38b91a3190cd - - 12d66d0d05ac - - 194e3ceee923 - - 584beffa972b - - 3b6a16d82c1b - - c5c9f02b6167 - abbc8041e8ec - - 49236b03e4fd + - 3b6a16d82c1b + - e1a015876aa9 - 230b05597996 - - ed28dd32141c + - 12d66d0d05ac tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/join_subtract_and_group.yml b/usegalaxy.org.au/join_subtract_and_group.yml index df9b213fd..dec9cfc4c 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: - - b8a457820315 - - 17e3b698dd52 - f198773344e4 + - 17e3b698dd52 + - b8a457820315 - 0f1724dd59d2 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - 374cb875d38a - a513e3fbb4c5 - ac092723240d - 22c2a1ac7ae3 - ba0c40780ecf + - 374cb875d38a tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index 2daca0628..b6619c8a9 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,17 +2,17 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 66d7efc06000 - 522137aaa9c4 - 772e0e89fc68 + - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - 4d81e3e2fb63 - - f22a9297440f - 8a794e6d3388 + - f22a9297440f + - 4d81e3e2fb63 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval @@ -28,10 +28,10 @@ tools: - name: ml_visualization_ex owner: bgruening revisions: - - 8334dc98c48e - - 947c2eacccb8 - 05143043ca13 - c80db5d6fd8c + - 8334dc98c48e + - 947c2eacccb8 - 1588f9076e32 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -39,62 +39,62 @@ tools: owner: bgruening revisions: - 25b46af53232 - - 1552b8cb4a94 + - 9991c4ddde14 - 83228baae3c5 - 29e4122c90de - - 9991c4ddde14 + - 1552b8cb4a94 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - f3dfa4bdf87e + - 841a6cc5fc58 - 53616c8b0865 + - f3dfa4bdf87e - 060ca94ac049 - - 841a6cc5fc58 - - 1a53edc4b438 - a07ab242b0b5 + - 1a53edc4b438 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - 927586a18553 - - 91c4e3331208 - 2fc89dcd41c8 + - 91c4e3331208 + - 40f4447733b2 - dc4b5fd604a6 - d4808d5b83da - - 40f4447733b2 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - c6ae57f774c6 - - e5a5ad882f1f + - 301e07345c93 - 25ab6b4e376e + - c6ae57f774c6 - 7626ea9c2e1b - 36e8d6d5d01b - - 301e07345c93 + - e5a5ad882f1f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: + - 4ed102b922cb + - b7c3e9a3b954 - 80852884053f - 02d2be90dedb - f9639b488779 - 0630258dcf35 - - b7c3e9a3b954 - - 4ed102b922cb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - 61634a87efc7 - - caeb57858702 - 14180f9c831e - ec69cbe34b73 + - caeb57858702 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index 4ca3e3854..e499570ed 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - f6877ad76b00 + - a6d65b0c67af - 0d4acadabb04 - - 937aa69e715f - - 3ba8d4563129 + - d5ceb9f3c25b - 03e9b2fbc005 - - cd659e8cc5fa - 749c918495f7 - - a6d65b0c67af - - d5ceb9f3c25b - 017aba02828d + - 3ba8d4563129 + - cd659e8cc5fa + - 937aa69e715f - 17062a0decb7 + - f6877ad76b00 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -24,19 +24,19 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - b4a22d90cce9 - bfaa0d22c2e4 + - b4a22d90cce9 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: + - 53646aaaafef - 2477830927ec - - 3fe632431b68 + - dfd8b7f78c37 - e188dc7a68e6 - - 53646aaaafef - 64f11cf59c6e - - dfd8b7f78c37 + - 3fe632431b68 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -49,45 +49,45 @@ tools: owner: devteam revisions: - 3e1ea2facca6 + - 60afcc2c1d05 + - 37b497aa133f - e7f19d6a9af8 - 2ff111fac1d7 - - 37b497aa133f - - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 11a0d50a54e6 - - b3eab4b67562 - - 037c6e54df11 - - 8c6cd2650d1f + - 53c0b7a1a0c3 + - 5cc34c3f440d - 77b2770508f6 + - 8c6cd2650d1f - 09b53c1d4ab1 - - be1d967337e4 + - 037c6e54df11 + - f54f5baedfdd - c0c2d0941de8 - - 6b1e195506a3 - 3f4d6399997b - - 5cc34c3f440d - - 53c0b7a1a0c3 - - f54f5baedfdd + - 6b1e195506a3 + - 11a0d50a54e6 + - b3eab4b67562 + - be1d967337e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 5ef7ec16b04f - - 9ee34ba73ebf - - 178bdbdb6d24 - - 42ce70172b72 - - b8f5f6e87f5c - - 45795f582ae9 - 1cd2511a396e - 79b885ce78d7 + - b8f5f6e87f5c + - 45795f582ae9 + - ec9cbd6b9a49 - 13022c3d3076 + - 178bdbdb6d24 + - 42ce70172b72 - e403d27e8f24 - 00fbfac99d39 - - ec9cbd6b9a49 + - 5ef7ec16b04f + - 9ee34ba73ebf tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/usegalaxy.org.au/metabolomics.yml b/usegalaxy.org.au/metabolomics.yml index 5e7a1b288..459d70120 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -75,8 +75,8 @@ tools: - name: matchms_convert owner: recetox revisions: - - c990df6afc24 - b9cc12600553 + - c990df6afc24 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering @@ -96,15 +96,15 @@ tools: - name: matchms_formatter owner: recetox revisions: - - 1b09315a3f87 - 9e3c83d2afc3 + - 1b09315a3f87 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export owner: recetox revisions: - - b576ed720711 - f04610d25411 + - b576ed720711 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match @@ -123,8 +123,8 @@ tools: - name: matchms_networking owner: recetox revisions: - - 1d74ae228df3 - 8147d93d372d + - 1d74ae228df3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key @@ -155,8 +155,8 @@ tools: - name: matchms_split owner: recetox revisions: - - 0cf68b536cd1 - 500f473df7e4 + - 0cf68b536cd1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting @@ -168,8 +168,8 @@ tools: - name: msmetaenhancer owner: recetox revisions: - - 90745ecc5e9f - b5467dead5b1 + - 90745ecc5e9f tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msnbase_readmsdata @@ -231,8 +231,8 @@ tools: - name: recetox_aplcms_align_features owner: recetox revisions: - - 7b42ee54d757 - c53a97599181 + - 7b42ee54d757 - 79ad928a0dae tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -240,48 +240,48 @@ tools: owner: recetox revisions: - 149b9cc7499b - - f3a18e020cdd - 18ec7635bac6 + - f3a18e020cdd tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - - dfebc82ba1f0 - 481d769e2f7a - 134be5abb208 + - dfebc82ba1f0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - - 51332c2520c7 - - 9064aecc78a7 - - 02c772a49998 - 501a232f3cd5 + - 02c772a49998 + - 9064aecc78a7 + - 51332c2520c7 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - b3413f335327 - b341cfd4baf8 - e7305ba0dd38 + - b3413f335327 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - cf061712a184 - 17a48d0a80f4 + - cf061712a184 - dd7bbc2b99d1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - 99d118321d5f - 24278c6b6d1c + - 99d118321d5f - d7f5878a98c3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index cfe9ea358..4beb2d146 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -2,23 +2,23 @@ tools: - name: bracken owner: iuc revisions: - - 1d4bd12f01cf - 0c7b6eb7e752 + - 1d4bd12f01cf tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_bins owner: iuc revisions: - - 0094893f5001 - 18676df0cb3a + - 0094893f5001 - 0e63d03c8790 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise owner: iuc revisions: - - a8216def322b - 7f1aaa1932d8 + - a8216def322b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -90,128 +90,128 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 65db807336bc - - 63f86089423e - - 76d3d2b10738 - - 7c2100246a2f - 5b5a7af9fbb4 + - 7c2100246a2f + - 76d3d2b10738 + - 63f86089423e + - 65db807336bc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - 84fd33a60b35 - - 96336c6a2bb7 - 1c35dadbe76f - - 18a502a9d287 - 00f5005840fa + - 96336c6a2bb7 + - 18a502a9d287 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - e8fba04706d3 - - 34e55239e68b - - f732237754fc - a9f4a217dcd6 - addaf9d22850 + - 34e55239e68b + - f732237754fc + - e8fba04706d3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 75403243703a - 0776d824d896 + - 8c202e741d68 - 04c15826a0b8 + - 75403243703a - 5fe3edf19b9c - - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 1c9b3bcd4261 - 43c99742158b - e96bbb9e24ea - - 75c8945b0da2 + - 1c9b3bcd4261 - 8470de786d47 + - 75c8945b0da2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 84743da21318 - - 5c865a382933 - - 1d75bd0595e2 - 306a40d4bb8f - 35176674168c + - 5c865a382933 + - 84743da21318 + - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 555ccac8a4c5 + - ac72310b038a + - 8daf4564ccda - 78faebd0879c - 32c9ea835770 - - 8daf4564ccda - - ac72310b038a + - 555ccac8a4c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - a58e4a43f49c - 7b8cb2b02978 - f947b4bb5107 - - d60df8727f59 + - a58e4a43f49c - cae017b76acb + - d60df8727f59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - 04144473e59e - - 1bc3657cd694 + - 7f3b59dee073 - 073608a50ac3 + - 1bc3657cd694 - 7136e9ab70db - - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 0a1224c4b781 - - 9058d8943303 - - a7817705348e - d943081510da + - 9058d8943303 + - 0a1224c4b781 - 19299bb1c6af + - a7817705348e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - e005e659ae21 - c7e73acfa3eb + - e005e659ae21 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: - - dbf1798c0dcc - 4d9445dff47b + - a68b985913ab - c4db8c4de66f + - b907a3c0434f + - 65d52c693b8e - f8f56dd6449f - - a68b985913ab + - dbf1798c0dcc - 5c7ba3d85a01 - - 65d52c693b8e - - b907a3c0434f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 15dbb444df71 - 213df31ba341 + - 15dbb444df71 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level @@ -231,8 +231,8 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - e66ab198ec15 - bd7a9c6efb10 + - e66ab198ec15 - 6aad8ca3918b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -247,9 +247,9 @@ tools: - name: humann2_unpack_pathways owner: iuc revisions: - - 9704f1a3b32d - cad93abecac9 - 7f208f1eb64f + - 9704f1a3b32d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -274,8 +274,8 @@ tools: - name: humann_join_tables owner: iuc revisions: - - f01ca38fb6c5 - 6bf703133209 + - f01ca38fb6c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_reduce_table @@ -289,32 +289,32 @@ tools: owner: iuc revisions: - 79706f10d680 - - 31c6d107e7a5 - e88b731dad59 - - c409a495841f + - 31c6d107e7a5 - 8237a0f225db + - c409a495841f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 172920f67a84 - - 094ad9c068af - - 714d5a28cc5c - d24841f5c3d2 - - 71ea608ddfa3 - aabf8cfb8fef + - 71ea608ddfa3 + - 714d5a28cc5c + - 094ad9c068af + - 172920f67a84 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: + - a4d7148ccee4 + - 4137b492233e + - 2bdd84912a2b - d7e9a3c41657 - - 12fb63b5f63f - a293a742194f - - 2bdd84912a2b - - 4137b492233e - - a4d7148ccee4 + - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -326,20 +326,20 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - a92c06a3afa7 - - 64bc7acc22a9 - - e2c71b852aba - 6fcb8ac37a3e - - 75bedfb2078b - cf87759761eb + - 75bedfb2078b - 97f7bb0851e7 + - a92c06a3afa7 + - e2c71b852aba + - 64bc7acc22a9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - 81c5dd1c777f - e9d12c223a80 + - 81c5dd1c777f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler @@ -351,22 +351,22 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 4e5e73d03f0d - - 4033827c76b8 - - 080ea153677c - 5e5a999ffaa9 - c82508e76ad1 + - 080ea153677c - 2d35528d2141 + - 4e5e73d03f0d + - 4033827c76b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - 6b7622dda516 + - fc6c328c292f + - 2cd76b089570 - c2803012bbb3 - 95bf7479d53c - - 2cd76b089570 - - fc6c328c292f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: jellyfish @@ -379,8 +379,8 @@ tools: - name: khmer_abundance_distribution_single owner: iuc revisions: - - 385a965c6f87 - 65b382bf9b7c + - 385a965c6f87 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution @@ -400,8 +400,8 @@ tools: - name: khmer_extract_partitions owner: iuc revisions: - - adb3dd5a899f - 1061711538c6 + - adb3dd5a899f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance @@ -414,22 +414,22 @@ tools: - name: khmer_filter_below_abundance_cutoff owner: iuc revisions: - - 19607c740d19 - 00f7064c564b + - 19607c740d19 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_normalize_by_median owner: iuc revisions: - - 4d23ab83ea29 - b1fe2ef3d244 + - 4d23ab83ea29 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition owner: iuc revisions: - - 8388fe31d604 - 5a0fa29951ae + - 8388fe31d604 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kmc @@ -441,17 +441,17 @@ tools: - name: kraken2 owner: iuc revisions: - - 328c607150ff - 4a9da2b6c2e3 - - cdee7158adf3 - 20e2f64aa1fe + - 328c607150ff + - cdee7158adf3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax owner: devteam revisions: - - f03c7ba8d8bc - 50bd98b3ae5a + - f03c7ba8d8bc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -490,8 +490,8 @@ tools: - name: kraken owner: devteam revisions: - - 766d5f63b0f4 - 8ba2174315aa + - 766d5f63b0f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_alpha_diversity @@ -509,8 +509,8 @@ tools: - name: krakentools_combine_kreports owner: iuc revisions: - - 073c867c5244 - 4960abe31b4d + - 073c867c5244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -559,22 +559,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 27250f92a01a - - 327d9f4cc95f - - 0270541aaf46 - 3cc4a60615c0 - - 4fd3b5d8706b - 2cff76cf35c6 + - 0270541aaf46 + - 27250f92a01a - e073891b2afc + - 4fd3b5d8706b + - 327d9f4cc95f - 7f5d7b0e9884 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: + - 76bc4efa1aeb - eb50e7eca3dc - 708abf08a626 - - 76bc4efa1aeb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -647,26 +647,26 @@ tools: - name: metaphlan owner: iuc revisions: - - 1a6cdf55390f - - ec368db926f4 - - 1a037928504c - - 2131d7dca455 - - a92a632c4d9b - - ef65b083bd0c - - 740fd2d16a28 + - b89b0765695d + - ff8f55893e7d - 289b3807e80c - a16313517e55 - - ff8f55893e7d + - ef65b083bd0c + - 1a037928504c - fd69c607b43f - - b89b0765695d + - 2131d7dca455 + - a92a632c4d9b + - ec368db926f4 - 6dee4abadccb + - 1a6cdf55390f + - 740fd2d16a28 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning owner: galaxy-australia revisions: - - e3a64a1d2a6e - 2a8bc1d26d06 + - e3a64a1d2a6e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -697,22 +697,22 @@ tools: - name: picrust2_hsp owner: iuc revisions: - - 3b133b8d578a - 6eafc1e01a8c + - 3b133b8d578a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 415cb5d91168 - 709adbfcf308 + - 415cb5d91168 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline owner: iuc revisions: - - 6077821e8ae7 - f53beb324696 + - 6077821e8ae7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline @@ -725,15 +725,15 @@ tools: - name: picrust2_place_seqs owner: iuc revisions: - - 680fb3eb574c - 73b56418e7f4 + - 680fb3eb574c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions owner: iuc revisions: - - 881f2faa5fe7 - 677f3c8db525 + - 881f2faa5fe7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -764,8 +764,8 @@ tools: - name: picrust_normalize_by_copy_number owner: iuc revisions: - - 2e62e32d4f33 - 65e5f9caefcc + - 2e62e32d4f33 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_predict_metagenomes @@ -789,20 +789,20 @@ tools: - name: recentrifuge owner: iuc revisions: - - d4fbfd31696c - 591175c0f051 + - d4fbfd31696c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: staramr owner: nml revisions: - - aeaa20b96ef2 - - 4b9a8031ab74 - - 3b22de20bd4b - 4d83eccf5f81 - 2fd4d4c9c5c2 - - be818ae858e4 - 141afacabcfa + - 3b22de20bd4b + - be818ae858e4 + - 4b9a8031ab74 + - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index d28bbc559..5a2d3a8fe 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - ab12df91b47f - 7238968f58f7 + - ab12df91b47f tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 2344ed181ae6 - 72be09dfd803 + - 2344ed181ae6 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index a5116c32d..ffdb09828 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 80f03df2e2ce - - a74dbfee5a86 - - bdfbaf0c10aa + - 2263989660f5 + - 94b8c6013083 + - 098506c54016 - cd07731e4434 + - 8b67dd48fec1 - 6ae5a7b5a0a2 - - 098506c54016 - - 9baa871cb1d1 - - 2263989660f5 - - 48c13389050d + - 80f03df2e2ce - 9422c5a87ee2 - - 94b8c6013083 + - 48c13389050d - 9eeb13a92d79 - - 8b67dd48fec1 + - a74dbfee5a86 + - 9baa871cb1d1 + - bdfbaf0c10aa tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - c44f824c051a - - 2e093badc689 + - f14193ec1f50 - d7ce0ec78e51 - - be78f13134e2 - - 3ff17bad4006 - - aaa0d6a8b808 - - bc3831dd65c1 + - fc2e49f91e52 + - f0af8936ed41 - 5abf2c2249aa - - '764845535798' - d390fe1567dc + - bc3831dd65c1 + - 2e093badc689 + - be78f13134e2 - 4a60927aaca5 - c18157c68134 - - f14193ec1f50 - - f0af8936ed41 - - fc2e49f91e52 + - aaa0d6a8b808 + - c44f824c051a + - '764845535798' + - 3ff17bad4006 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -67,30 +67,30 @@ tools: - name: mafft owner: rnateam revisions: - - a65296ffb4a0 - - c5908940967d + - 15974dd17515 - bf28a8cff401 + - a65296ffb4a0 - 6f28e90db932 - 8e649f27aa0d - f1a5908ea2cb - - 15974dd17515 + - c5908940967d - f0d493f8f84f tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - fbca557a4847 - - e8fdceffea4c - b3acbb3a6af0 + - e8fdceffea4c + - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 60698466facd - - 5561a1193611 - c9685bc0407c + - 5561a1193611 + - 60698466facd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer @@ -104,24 +104,24 @@ tools: - name: mummer_mummerplot owner: iuc revisions: + - ebe3b0f84de9 - fb43e8887350 - 4fc0cb2ac8ae - - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - e18267f90096 - - 636b049e6141 - 7cd7a55a678d + - 636b049e6141 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: + - cf3c9489c088 - 959c1f8dae95 - b4124df98b26 - - cf3c9489c088 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index 2d9e90193..ea558a411 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -9,35 +9,35 @@ tools: owner: galaxy-australia revisions: - 1145758d2f0b - - 18a8d140ec6f - 7c47b3c9e493 - 28928576e1ea + - 18a8d140ec6f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado owner: galaxy-australia revisions: - - 63d8ecfcfab1 - fc5b6491cf78 + - 63d8ecfcfab1 - 99c9427219d3 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus_pipeline owner: iuc revisions: - - 72b5e9dda577 - - cb34f00cc10f - - fc8804320156 - a7228a7ea146 - - 79e9a869f40e - 0e9e7fcdd543 + - 72b5e9dda577 + - 79e9a869f40e + - fc8804320156 + - cb34f00cc10f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - db25ec99c3ea - fa11aa8103b2 + - db25ec99c3ea - d6cddc06aeae - 18505fe2bdb1 tool_panel_section_label: Nanopore @@ -51,14 +51,14 @@ tools: - name: medaka_variant owner: iuc revisions: - - eb746fa6f514 - 0f5f4a208660 + - 2bf63b38ee9b - 43815fa60f3a + - eb746fa6f514 + - ec699520444c + - 222669c4afb6 - cc36773a3681 - - 2bf63b38ee9b - 19f3b583a9b3 - - 222669c4afb6 - - ec699520444c - edf6d4003fad tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -78,60 +78,60 @@ tools: - name: nanoplot owner: iuc revisions: + - a38bdcec9e4c + - a3c4fe6f49ab - 7b379e98b9a9 + - 0f1c34698076 + - edbb6c5028f5 - a02b8b3f5a0c - - a3c4fe6f49ab - 645159bcee2d - - edbb6c5028f5 - - 0f1c34698076 - - a38bdcec9e4c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - d219b6d8158a - - 85a394edc247 - 3b6f94fc7e1d + - 85a394edc247 + - d219b6d8158a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - a8d4be409446 - be95355fef8d - 90a922f32523 + - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - d376944466bf - - 4857d5bcce52 - 449e9aeded2d + - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - a3afc5f0a96c - bec636361cfd + - a3afc5f0a96c - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 5f76b20953e5 - 93d623d9979c - 543cbeef3949 + - 5f76b20953e5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 1d835c691480 - daf8518d243a + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -143,8 +143,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - d1805f9c4c82 - 47936349f3e9 + - d1805f9c4c82 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -176,8 +176,8 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - 26e6c9362b7b - ce8af9373061 + - 26e6c9362b7b tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index 8bc7291e3..24939b806 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -2,8 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - a5921c09b7b7 - 592ef3959907 + - a5921c09b7b7 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -27,19 +27,19 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - 3e73c97f025d - adfd6bf710bd + - d74850cf4e42 - 97b1b5ad1cda - baceff842902 - - d74850cf4e42 + - 3e73c97f025d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 9dd107db92c2 - - 83da94c0e4a6 - 1586b111d2a3 + - 83da94c0e4a6 + - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -52,18 +52,18 @@ tools: owner: iuc revisions: - 13851aefa67a - - 1e34d2e3d285 + - 19b6a2f0dbe2 - ed1518ce2237 - e4b4837f06f5 - - 19b6a2f0dbe2 - 2f27f3b86827 + - 1e34d2e3d285 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -75,23 +75,23 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 472dabcb03bf - 74af283d8ebd + - 472dabcb03bf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_dada2 owner: iuc revisions: - - 38ccd4589990 - - 48a42ca61006 - 5711fc06a63e + - 48a42ca61006 + - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 5a0d0bee4f8d - 4a08b7b76b78 + - 5a0d0bee4f8d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -132,9 +132,9 @@ tools: owner: iuc revisions: - 52b6a4d98009 - - 27a6a256cd23 - b4b2b284230a - 172815da3d41 + - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -160,8 +160,8 @@ tools: owner: iuc revisions: - fea85c467896 - - 19bbd19b74b3 - 87febc68b45b + - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -174,8 +174,8 @@ tools: - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 15c2fc266540 - 4c7ebbad42cf + - 15c2fc266540 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -193,12 +193,12 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 5fe20c915fa6 - - d8dc037e3c13 - - 0cb27ea69dc1 - 4ba60cb14cb0 + - 0cb27ea69dc1 - 2c61c30a57e7 + - d8dc037e3c13 - 9c43baa60906 + - 5fe20c915fa6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -211,18 +211,18 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - 9d09724f2bf1 - 0db22932bc39 - aec831b54a5b + - 9d09724f2bf1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - 6e24e79d3d69 - - 29c738066906 - - ed7a967cb11b - df30a2f1db55 + - ed7a967cb11b + - 29c738066906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -240,16 +240,16 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - ad90c2da4f38 - - 3e4d45aca422 - 1865e693d8b2 + - 3e4d45aca422 + - ad90c2da4f38 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - d107d20dc6bd - def511e8e005 + - d107d20dc6bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -261,17 +261,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: + - d63c1442407f - 64deddb6a8ec - c520a52b5174 - - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: + - 625fd9476402 - 94a50db37d1a - 9946bc39c834 - - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -782,8 +782,8 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - d64562a4ebb3 - 544f6d2329ac + - d64562a4ebb3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index a43440f87..e2728841f 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -20,8 +20,8 @@ tools: - name: gubbins owner: iuc revisions: - - 96e6283e4745 - 637ec5d5368c + - 96e6283e4745 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -34,64 +34,64 @@ tools: owner: iuc revisions: - b89cac5156ec - - f04a1264e2a2 - - 26de3a7b1cb9 - - '841557158611' - - d7c7ef3353fe + - c78f3d7dd1db + - f73435dc282b + - a6619171428e + - 81e66674859e - 6a457678efcb - - 8834daeb9892 - - 3b8b5bde0bd9 - cce7b18495e4 - - c78f3d7dd1db + - 8834daeb9892 + - 3f59ebfbfe3d + - f04a1264e2a2 - 107d3ba7024a - - a6619171428e + - 3b8b5bde0bd9 + - d7c7ef3353fe + - 26de3a7b1cb9 - d033ffc1c161 - 5a7c56a5cc08 - - 81e66674859e - - 3f59ebfbfe3d - - f73435dc282b + - '841557158611' tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 6a726db04d4b - - 5b777002c2de - - 3b96e92e8ec3 - - 02b8758214b0 - 4755f52427c4 - - aa8cc71438cf - - e75442c7f4da - - a185b079b095 - - 659517798cc4 - - 6223845127ea - - 6283babe736e + - 02b8758214b0 + - 5b777002c2de - b0af57c1a968 - 5fcd1ece3a6e - - 7a2092844346 + - 659517798cc4 - df47d4845b62 - 88c4aa435ded + - 7a2092844346 + - a185b079b095 + - 6a726db04d4b + - 6223845127ea + - aa8cc71438cf + - e75442c7f4da + - 3b96e92e8ec3 + - 6283babe736e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 24d024316465 - - d1c340a5664b - - b8476e82ac20 + - 70acec670c30 - 111bd54f6bc4 - - c1d53e95327f + - b8476e82ac20 - f97743d52b87 + - c1d53e95327f - f87ac61981f0 - - 70acec670c30 + - d1c340a5664b + - 24d024316465 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: + - 4f6349228462 - feb40665d7cd - 9e10ba792be2 - - 4f6349228462 - daddf188c13f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -104,26 +104,26 @@ tools: - name: pangolin owner: iuc revisions: - - abf6dbe8c9d7 - - ca337cce3888 + - 9d61d3fa046c + - 14ae456b8cc5 + - 83a69484cb87 + - 42a174224817 + - 3a43c3982401 - 7bb8726be37c - - b7e297c2ede6 - b6abccb1f25b - - 42a174224817 + - 36912871ccdc - 81804a978fc0 - ca0d8cf80567 + - 437e28791761 - 8ad84c5753ea - - 9d61d3fa046c - - 14ae456b8cc5 - - 3a43c3982401 - - 36912871ccdc + - 03ed9524dcd1 + - 2f1019071464 + - ca337cce3888 + - b7e297c2ede6 - 5f8727ff21e7 - 2fa9d4f1b48f - - 437e28791761 - - 03ed9524dcd1 - - 83a69484cb87 + - abf6dbe8c9d7 - a2099fb98cdb - - 2f1019071464 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -144,18 +144,18 @@ tools: revisions: - ba29b5e2a4be - ea30d3089354 - - 73a469f7dc96 + - b1e68bbe4cef - 29ff6a849eac + - 73a469f7dc96 - a4b71be30c3c - - b1e68bbe4cef tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - 91887494eb97 - - dbe2b2204555 - f1ccc8a6eb05 + - dbe2b2204555 - 809e42326fc2 - 15ac71df11a0 - 9b2b122d0415 diff --git a/usegalaxy.org.au/picard.yml b/usegalaxy.org.au/picard.yml index c88cc2ccf..977a4ee93 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - 3f254c5ced1d - - fc288950c3b7 - 881d7645d1bf - - b502c227b5e6 + - f6ced08779c4 - 7d34178f2812 - - 1aac2a13842a - f9242e01365a + - b502c227b5e6 - a1f0b3f4b781 - - f6ced08779c4 + - 3f254c5ced1d + - 1aac2a13842a + - fc288950c3b7 tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomic_ai.yml b/usegalaxy.org.au/proteomic_ai.yml index 31d0f4a43..67c1a94a3 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,17 +2,17 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - a58f7eb0df2c - - e4a053d67e24 + - 3bd420ec162d + - 7fbec959cf2b - c0e71cb2bd1b - - d00e15139065 - - 2f7702fd0a4c - - 5b85006245f3 - e7f1b552a695 - eb085b3dbaf8 - - 7fbec959cf2b - - 3bd420ec162d - - ca90d17ff51b + - 5b85006245f3 + - e4a053d67e24 + - a58f7eb0df2c + - 2f7702fd0a4c + - d00e15139065 - 6ab1a261520a + - ca90d17ff51b tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomics.yml b/usegalaxy.org.au/proteomics.yml index 57632e7a4..843a0a1a6 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,65 +2,65 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - b574b84afc4d - - 0a18ac48ac53 - 4c177985028a + - ece627528a78 + - 0a18ac48ac53 - f28ad96b76dc - - b18329a8ac14 + - b574b84afc4d - 277dc652246e - - ece627528a78 + - b18329a8ac14 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - bf06d196e23d - 525f201b86c1 + - b41107d8fe89 + - bf06d196e23d + - a9a28e46d54a - e215f71d7983 - e988563cc6e5 - - a9a28e46d54a - - b41107d8fe89 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 8da3511c9467 - - bb6397b94018 - 56da27be956a + - bb6397b94018 - 4fbffddde8cd + - 8da3511c9467 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - 890845926d4b + - a8157342d9a3 + - 528fb09022be - f23d67e28cc8 - b8c79e70516d - - 528fb09022be - - a8157342d9a3 + - 890845926d4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - 80600735685d - - 25b83cbd596a - - ae304a72db7b + - a69865da6f80 - 59e85306eae5 + - ae304a72db7b - a95a82eb4d50 - - a69865da6f80 + - 25b83cbd596a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: + - e0669b1854b1 + - f1897eb07081 - 798da6bdff3d + - 611d80c0e29d - 83aac7741200 - ed9ed1e6cca2 - - e0669b1854b1 - - 611d80c0e29d - - f1897eb07081 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report @@ -75,21 +75,21 @@ tools: - name: cardinal_segmentations owner: galaxyp revisions: - - 91f0f5922011 - 82f6c2f4332d - - df2187f9013b - cc430977c8ff + - df2187f9013b + - 91f0f5922011 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - c5aa9fca18c6 + - 1693b2126f30 - d2483487e077 - - 10566783d718 - 043f9c91f686 - - 1693b2126f30 - ba92b59cd529 + - 10566783d718 + - c5aa9fca18c6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -107,9 +107,9 @@ tools: - name: diann owner: galaxyp revisions: + - 9fa3dbf06f17 - ff8c9e0e8a7b - bf0728e000cd - - 9fa3dbf06f17 - ae4dc0c041f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -122,24 +122,24 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: + - eac99effe86f - d263296cd73e - d0ea7589e95f - - eac99effe86f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: - - 4081e4faa4ab - - 1c5cbf8f79ce - 0fa397f4f40b + - 1c5cbf8f79ce + - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib owner: galaxyp revisions: - - 36880dfd9fa7 - fb192dd6658a + - 36880dfd9fa7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut @@ -160,8 +160,8 @@ tools: owner: galaxyp revisions: - 160538a890a6 - - d286ff4600dd - e66f552a3c47 + - d286ff4600dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing @@ -181,16 +181,16 @@ tools: - name: maxquant owner: galaxyp revisions: + - 37d669de2828 + - e42225f8a659 + - 4d17fcdeb8ff - 837224ad1694 + - 97a7f34fcb6a - 9c52362ae7bb - - f522c08e900c - - 7f432d87c82c - 1f39c833f65f - - 37d669de2828 - 2133b0be850a - - 97a7f34fcb6a - - e42225f8a659 - - 4d17fcdeb8ff + - f522c08e900c + - 7f432d87c82c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -202,46 +202,46 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - e63db1aa82ee - - 0ed07016d668 - - 85b8866f06d7 - a72ac2c7cc5b + - 85b8866f06d7 + - 0ed07016d668 + - e63db1aa82ee tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - 1974224d63c2 - - 990b4560ead7 - - 352b37c66d97 - 767c1d761aaf + - 352b37c66d97 + - 990b4560ead7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - 4f359549383c - - deaf035bbe9f - 35cc7ca0bdc7 - 99450519d727 + - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - 06f6826d380c - - c7745841de24 - c1343e3389ca - e79958768a2c + - 06f6826d380c + - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - d46d64e7964d + - da986f83631b - d2eac53666f0 + - d46d64e7964d - b9d453dca8d3 - - da986f83631b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz @@ -256,24 +256,24 @@ tools: - name: morpheus owner: galaxyp revisions: - - 8295d959ca28 - e0104a9f20f0 + - 8295d959ca28 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert owner: galaxyp revisions: - - 6153e8ada1ee - ab6c14374bc0 + - 6153e8ada1ee tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstats owner: galaxyp revisions: - - 8212e342e482 - - 28434abe6c5c - 593839e1f2c3 + - 28434abe6c5c - de7593c29499 + - 8212e342e482 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -288,80 +288,80 @@ tools: revisions: - f4be248c3d47 - 4e77b8f12cd3 - - 01dbaf6a57e0 - 8960fb791701 + - 01dbaf6a57e0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 370141bc0da3 - 06cca574e337 + - 370141bc0da3 - 25529df60a81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - - f7fef900f5b2 - - 9cdf15d3cfc8 - - 518b1730cf2a - 6ccbf9a2072c + - 518b1730cf2a + - f7fef900f5b2 - c9eff69a7c62 + - 9cdf15d3cfc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - ca88bd28f116 + - 9876bda3ec53 - 5e948629bc73 - dff6c756eee5 - - 9876bda3ec53 + - ca88bd28f116 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - 1595601708ec - - 41859bbdc16e - - 890025d6e426 - 658494a2cb00 + - 890025d6e426 + - 41859bbdc16e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: + - 9b7977080f6d + - 2a93a25f0599 - 5ad0b5bf1deb - 6634cad7d797 - - 2a93a25f0599 - - 9b7977080f6d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - fe4e4587d265 + - d6878d27f051 - 0bb5056cb775 - 05d5e1ddc985 - - d6878d27f051 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 5ad830edc021 - - 52ba9695e752 - - febd569ad26f - 4af67edd5aef + - febd569ad26f + - 52ba9695e752 + - 5ad830edc021 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - b2fc8da99bcc - - 27cba4c5fc42 - 39e8fde08881 + - b2fc8da99bcc - 92352a475eed + - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector @@ -377,19 +377,19 @@ tools: owner: galaxyp revisions: - ca1740533b59 - - c28f13cab67a - 3720e349ba2a + - c28f13cab67a - 8a04ed1c1d1b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: + - c427a8628cbe - a5d785af0ad8 - - ca799a7246e7 - c55dddc5844a - 382cde407f81 - - c427a8628cbe + - ca799a7246e7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper @@ -397,8 +397,8 @@ tools: revisions: - b5d0905419da - 8ddb7bab1138 - - 39caaa778d2e - adca857b4884 + - 39caaa778d2e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger @@ -406,69 +406,69 @@ tools: revisions: - 18f93351f8b6 - f817513840a9 - - 1c5f31b8d632 - - 34e7afee141d - 8d4db262964c + - 34e7afee141d + - 1c5f31b8d632 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 5d9f175dff81 - - 986e03d3201e - 111c3a00136d + - 986e03d3201e - c69f69d7867a + - 5d9f175dff81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: + - 476b5e296979 - 0e52c85f3b15 - - be74a8cd7d66 - 4204882495f2 - - 476b5e296979 + - be74a8cd7d66 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: + - 2b2a7551a857 - f5ec766d80cf - a407b6790342 - c18d8efa4474 - - 2b2a7551a857 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - 021fdb80f204 - d0304fb829c0 - 4e66c4e73909 + - 021fdb80f204 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: + - ee860980edc6 - 2735db4dd8d9 - - 8098330f6d91 - bf32e0bcf554 - - ee860980edc6 + - 8098330f6d91 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - - a2a6e9551046 - 08488066d588 - 0ced5bc9f4dd + - a2a6e9551046 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - 8c01da82292c - - 2a9ff56cb279 - de7a553552a6 + - 2a9ff56cb279 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring @@ -482,32 +482,32 @@ tools: - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 9f505cd4428f - f861ec9fbe59 - 496cf619e311 + - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: - 0bddef8d144e - - d4396637b9f5 - c99d5004b74f + - d4396637b9f5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 4bb198c0bd3e - 89254095cbf6 + - 4bb198c0bd3e - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - f82b320ceb90 - 05ec9fb05ed1 + - f82b320ceb90 - f9ed7e074900 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -515,75 +515,75 @@ tools: owner: galaxyp revisions: - d31426ef20f6 - - 18826fb8e5db - 6e8cc5ed2a9b + - 18826fb8e5db tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - - 4a7b96835140 - 2aebe58de46e - bc63b4d12779 + - 4a7b96835140 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - 6b01678ec2fc - - 5ae104d0da6e - decc397c3b7e - 3d8d4ada5405 + - 5ae104d0da6e + - 6b01678ec2fc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - 539a3a4dcc9e - - d6aca689dd48 - - 5182338d5e7c - e039cc5c7aed + - 5182338d5e7c - dd173849c3d8 + - d6aca689dd48 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: + - 16026cdb1330 - d426affe977c - 8a45fd5a608a - - 16026cdb1330 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - dd71e020e2aa - - 9c70a651a53e - 43b9ed22e8ce + - 9c70a651a53e + - dd71e020e2aa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: + - d063e2fe4ba4 - 1b03536aa3c9 - 9020199dba0a - - d063e2fe4ba4 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - ad2ba3a95a02 - - 78c080d36945 - f036e8cf1a55 + - 78c080d36945 + - ad2ba3a95a02 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - fb52e95a370c - 5c2a97a234d6 - 7f6a1f27553e + - fb52e95a370c - c8b225c69a7f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -610,14 +610,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - a72c48001f7c + - 07ff622ec007 + - da885ca16cb2 + - 3ec27b4cee7c - 1beff3ddce58 + - 943a34df6047 - 3634c90301af - - 3ec27b4cee7c + - a72c48001f7c - 7fdd9119cc4f - - da885ca16cb2 - - 07ff622ec007 - - 943a34df6047 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -677,10 +677,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: + - 12692567c7f9 + - a371252a2cf6 - 265c35540faa - 1a5690a5eedc - - a371252a2cf6 - - 12692567c7f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index 31f532f03..5df6dd20e 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,45 +2,45 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 110a346daf36 - - 289b7d6b69a4 - 2f1d464ebfd2 + - 110a346daf36 + - e345aadf914f - cd5f98911089 - 42201b90e3f4 - - e345aadf914f + - 289b7d6b69a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - 42d9087b4789 + - 8501601a118d - 0345dbaaa79b + - 0cd2df8af811 + - 42d9087b4789 - fcce77c09289 - c207119ba5f6 - - 8501601a118d - - 0cd2df8af811 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: + - 421c33b8bf17 - 04db7fd6b238 - ad5ab22ffe24 - - 405a212b32ab - 33486216eec0 + - 405a212b32ab - 89eb29319bf4 - - 421c33b8bf17 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - 7b72fde3d27e - eb784fa07f80 - - 1d839ead7ad3 + - 7370bb65bad4 - f6e91108b7b1 + - 7b72fde3d27e - fa51dc5e8386 - - 7370bb65bad4 + - 1d839ead7ad3 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -48,86 +48,86 @@ tools: revisions: - d30e36c48c93 - c9b77ced9a78 + - 3d70c2996730 - 8a55d29c8fcf - a3e86cd9cac7 - 1544278c272e - - 3d70c2996730 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - a5969aa9347e - 887cf585cafc - 7b881f5f5ad5 - - b242deb58952 + - a5969aa9347e - 564c33e5c3e3 - e2db212d64ad + - b242deb58952 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - e897c74a48bb - 8cff84759bf6 - - 9a171f9a450b - bd5ff77e2036 + - e897c74a48bb - b4bab607eb05 + - 9a171f9a450b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - 6dafad990086 - - 887e0991eb24 - - 33f0793edf93 - 4f65e343ecdf + - 887e0991eb24 - adc7a7610d4f + - 33f0793edf93 - 5e10f396979e + - 6dafad990086 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - 17d39bf0a63a - - 43e3eeb2e0ec - - c5d7050e4ad7 - 4e280b27a831 - - c287418eb288 - 97575d01f06b + - c5d7050e4ad7 + - 17d39bf0a63a + - c287418eb288 + - 43e3eeb2e0ec tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - 0b8c84a7fdb5 + - 9586f08634c0 + - 09b8edb56d80 + - d9bf483266a1 - cd034465d4a4 + - 0b8c84a7fdb5 - a819ec3b362d - - d9bf483266a1 - - 09b8edb56d80 - - 9586f08634c0 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - - a9c34a289493 - bf0e43ab0416 - - 2645575d1bf2 - 95351dd0fd3f - - 69842dd5aa48 - a4b4bd84f69e + - 69842dd5aa48 + - a9c34a289493 + - 2645575d1bf2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - d1fda11e602f - - cfb504394ae1 - bb0475c884ff - - 8a35a3bc6752 - - 912f904a6e1e - d033e1ccb386 + - cfb504394ae1 + - 912f904a6e1e + - 8a35a3bc6752 + - d1fda11e602f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -195,8 +195,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 96de7538bf0c - 563af4497055 + - 96de7538bf0c tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 90abe7b42..6a43c3bdf 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -3,26 +3,26 @@ tools: owner: iuc revisions: - 7acb00fc980a - - cf01dd6c6b1f - - 31f8063eedea - 2d4e3aff9dc7 + - 31f8063eedea + - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 703a2cb3fb38 - 125d20cb23d7 - - 7a5a2d28c539 - 32e542c2a773 + - 703a2cb3fb38 + - 7a5a2d28c539 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - 01ccd366690d - - 45c2ec061cf9 - 3d61a698e5e1 + - 45c2ec061cf9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -89,34 +89,34 @@ tools: - name: cuffcompare owner: devteam revisions: - - ad5d061fbdf2 - e66b9b5b8580 - f648e5180e40 + - ad5d061fbdf2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: - 6926716bbfb5 - - e04dbae2abe0 - d080005cffe1 + - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - - cf747d1bd79a - - 6a6717a5f421 - 22cf48ad7b16 + - 6a6717a5f421 - 86285ddd4512 + - cf747d1bd79a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - 9a854107dbb2 - 28b94cfbfdb9 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -141,9 +141,9 @@ tools: - name: describe_samples owner: iuc revisions: - - 3b36efd62b3e - - e3b16fd7dd08 - 0693ccd171c4 + - e3b16fd7dd08 + - 3b36efd62b3e - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -151,39 +151,39 @@ tools: owner: iuc revisions: - 6a3a025714d3 - - 9a882d108833 - - cd9874cb9019 - 0696db066a5b - d027d1f4984e - 8fe98f7094de + - cd9874cb9019 + - 9a882d108833 - 24a09ca67621 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: + - b47c006d90c5 - 2872c633f07e - - df929f257179 - 9a7c5b6d8f1e - - b47c006d90c5 + - df929f257179 - 62adf13b86ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 3d89af8a44f0 - - ae2aad0a6d50 + - 334ce9b1bac5 + - df0c8d0a5992 + - f2843df56434 - 070900306913 + - a8305cf0c951 + - 6e53e565fc6a - 555659de7321 + - 9bdff28ae1b1 + - ae2aad0a6d50 - 0cb907a2a810 - - 6e53e565fc6a + - 3d89af8a44f0 - 5bf899c13979 - - 334ce9b1bac5 - - f2843df56434 - - df0c8d0a5992 - - 9bdff28ae1b1 - - a8305cf0c951 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -202,17 +202,17 @@ tools: - name: featurecounts owner: iuc revisions: - - a56fbe2d6ba7 - - ea04b737afa0 + - 7db9d3ea71c9 - 90d16db017d7 - 38b6d12edc68 - - e6a2a912677a - - 6f66ae7c5f7a - - af814359d244 - f3a5f075498f - a37612abf7f9 + - 6f66ae7c5f7a + - e6a2a912677a + - ea04b737afa0 - f9d49f5cb597 - - 7db9d3ea71c9 + - af814359d244 + - a56fbe2d6ba7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -236,9 +236,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 3c97c841a443 - - 0f710191a66d - 3c5e024a18cf + - 0f710191a66d + - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -250,21 +250,21 @@ tools: - name: hisat2 owner: iuc revisions: - - 26371a1df031 - - 3fb01a8c902d - 6c19daec423d - - a86e80d3c09c - 6ab42baa56e9 + - 26371a1df031 + - 3fb01a8c902d - f4af63aaf57a + - a86e80d3c09c - d4b55e2beb12 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - - 916cb26bd9d3 - 67b0b160903a - 4418229c501e + - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -276,31 +276,31 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 87c11c05d238 - 1c75aa5de15e - 01247aaf0a10 - - 5ae5c312d718 - ce5d418183c5 + - 5ae5c312d718 + - 87c11c05d238 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - 4f9c4e6566e5 - - c971db6f0fe5 - 40985510cd98 + - c971db6f0fe5 + - 4f9c4e6566e5 - 10c98fab6c5a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 0921444c832d + - 32511f586472 - 58c35179ebf0 - 119b069fc845 - 708348a17fa1 - - 32511f586472 - 97e06a4c7c75 + - 0921444c832d - e827f9aae031 - d6f5fa4ee473 tool_panel_section_label: RNA-seq @@ -339,8 +339,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - 72927fc9e9ed - d696cf0a9622 + - 72927fc9e9ed tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -358,21 +358,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - c7c55b694974 - - c772497b2c32 - - 5ec75f5dae3c - - e132e7d02a3e - 7ed2edc1337f - 3ea5a2a63fa2 - - b9e04854e2bb + - c772497b2c32 - 980d2a2e1180 - - 99b17b74a8cd - - 4074fc1940e2 - - 0a563fd2f22e - b0f2be869d6d - - 79de45b5069b + - 4074fc1940e2 + - b9e04854e2bb + - 5ec75f5dae3c - 4014de1b6daf + - c7c55b694974 - 4df95e2d7f61 + - 0a563fd2f22e + - 99b17b74a8cd + - e132e7d02a3e + - 79de45b5069b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -384,36 +384,36 @@ tools: - name: salmon owner: bgruening revisions: - - 49121db48873 - - e3d32471da11 - 2c0ca397d302 - 15cd64d7c58b + - 49121db48873 - f4d5237a84f6 - - 53e9709776a0 + - e3d32471da11 - cc05793bb896 - ebab418107f5 + - 53e9709776a0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - - 8c28affc7c48 - 56242ff81c84 - - c0fd285eb553 - fab6ff46e019 + - 8c28affc7c48 + - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - cbf488da3b2c - - 76d290331481 - - ae618321f34a + - 258d696dbd7e - dd4df992d93d - cef79931dda5 + - ae618321f34a + - cbf488da3b2c + - 76d290331481 - 1ebd14235b92 - 914cfcba0ec8 - - 258d696dbd7e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -443,28 +443,28 @@ tools: - name: transdecoder owner: iuc revisions: + - c6334cb383ff + - d0d4cef4f967 - 0db979fead3a - ffd1300599a1 - - d0d4cef4f967 - - c6334cb383ff tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - bcc5f03f1900 - - ba3720d7e68b - d6a479fd4281 - 74217fbfba4d + - bcc5f03f1900 + - ba3720d7e68b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: + - 2fb4ee002432 - c2b82a94493e - 56162e446004 - 478f36effca1 - - 2fb4ee002432 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -478,19 +478,19 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - be3f26533209 - - 4687ecf0eb2d - 870ac06dff8e - 34a018cbee9c + - be3f26533209 + - 4687ecf0eb2d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 5192f657f305 - 33406f5a445c - - c5fbddcac63a + - 5192f657f305 - 05ab8d5e04a2 + - c5fbddcac63a - 65e7dea767ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -498,36 +498,36 @@ tools: owner: iuc revisions: - 1fdb25a8384d - - a35cba31d904 - - 6f0fb35b799c - e406ac71165d + - 6f0fb35b799c + - a35cba31d904 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - - c2c039e421af - - 37a1129c89d2 - 964b7efe2639 + - 37a1129c89d2 - 7c7fbf13aadd + - c2c039e421af tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - eafea3083352 - - 1d689e4e1caf - - 047c22569787 - 24e94d84adc9 + - 047c22569787 + - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: - - 9871104ea630 - 3a4ac03d1266 - 04bb8bb7c198 - 1812dbc5bb7b + - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_stats @@ -545,15 +545,15 @@ tools: - name: trinity owner: iuc revisions: - - d2bc35f3d1c5 - - db1f362cca3e - - d84caa5a98ad - - 8f1c3df4dd49 - - 32b86cd8eb50 - - 9fa24d5aac68 - cee61b3fcf78 - - 48636f857c4b - c9cfec002f71 + - 48636f857c4b + - 9fa24d5aac68 + - 8f1c3df4dd49 + - 32b86cd8eb50 + - db1f362cca3e + - d84caa5a98ad + - d2bc35f3d1c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/usegalaxy.org.au/rseqc.yml b/usegalaxy.org.au/rseqc.yml index 5c8b52871..a0868c72e 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: - - 473382134e56 - 1a052c827e88 - 080fd5739bb4 + - 473382134e56 - 27e16a30667a tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/sambam.yml b/usegalaxy.org.au/sambam.yml index 87770bf3d..926e224af 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -10,10 +10,10 @@ tools: - name: bamtools_filter owner: devteam revisions: + - 108db6635177 - cb20f99fd45b - 1dfd95ee241e - 993b19f20c76 - - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_mapped @@ -75,10 +75,10 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 19ece8afbaab + - 30a201c9c310 - e7fd6754d093 - 5f8e69cc4c6e - - 30a201c9c310 + - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -103,15 +103,15 @@ tools: - name: sam_pileup owner: devteam revisions: - - a3b4ad6858ff - 890d97772e2a + - a3b4ad6858ff tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam owner: devteam revisions: - - cf1ffd88f895 - 0e60e2dd20af + - cf1ffd88f895 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sambamba @@ -130,19 +130,19 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 9149ad20699a - 46c6639921f1 - - 6856f8a01905 + - 9149ad20699a - 12749212f61b + - 6856f8a01905 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - 33208952b99d - - 92ec40abcdcf - 06dc50b7b711 - 26b4f9f98aca + - 33208952b99d + - 92ec40abcdcf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_coverage @@ -161,80 +161,80 @@ tools: owner: iuc revisions: - b3d99709fe1a + - 66e23b11feae - 720217c23995 - b906586a6596 - a8d69aee190e - - 66e23b11feae tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fixmate owner: iuc revisions: - - e5ece8fa99de - d2df79922531 + - e5ece8fa99de tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - fe34990e5ce7 + - cc61ade70eb8 - fefd89ab563c + - fe34990e5ce7 - db17d5321bad - - cc61ade70eb8 - 22970df7a40e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - 811fc2d75ad4 - - 88b8c2916784 + - fa5d3e61e429 - 7a6034296ae9 + - 811fc2d75ad4 - 7def34e6cf4d - - fa5d3e61e429 + - 88b8c2916784 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_markdup owner: iuc revisions: - - 40fa6c240105 - a389f74c3630 + - 40fa6c240105 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: + - cae2794d2deb - 740ce0a18f0d - - 36677f429310 - - 65a38e8c8e2a - b40e2d865d52 - - cae2794d2deb + - 65a38e8c8e2a + - 36677f429310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 329deb17a9f7 - - b61f5d6a7f25 + - 583abf29fc8e - 8da515fbc1bf + - b61f5d6a7f25 + - 329deb17a9f7 - 9da0311ab1dd - - 583abf29fc8e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase owner: devteam revisions: - - b5c3b1856370 - 1e5880498f52 + - b5c3b1856370 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader owner: devteam revisions: - - 30388d878f81 + - bb8cfc6f6e0c - 85e38b31e8b3 + - 30388d878f81 - db000c6007a0 - - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -246,16 +246,16 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - b8beef827165 - - a4a10c7924d1 - 344fc91e1bfd + - a4a10c7924d1 + - b8beef827165 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - cab3f8d35989 - d54a4df48867 + - cab3f8d35989 - e613c1ad4c4c - 6c2c1836728b tool_panel_section_label: SAM/BAM @@ -264,36 +264,36 @@ tools: owner: devteam revisions: - 818030fa6bbf - - bcedabb53ddf - 135c85f4cfaf + - b7f7826ef1cd + - bcedabb53ddf - 5d9ae78f34d3 - bd850490c7f1 - - b7f7826ef1cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 5a08c09b9311 - - 3a0efe14891f - - 145f6d74ff5e - - 541082d03bef - 24c5d43cb545 - 1cc79f49b8d5 + - 145f6d74ff5e + - 3a0efe14891f + - 541082d03bef + - 5a08c09b9311 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - bf328cec6a42 + - 2dce91e11ca7 + - c370440f901e + - 350bbc5c2ffd - 32dc5f781059 + - 6be888be75f9 - b01db2684fa5 - - 5826298f6a73 - b72793637686 - - 2dce91e11ca7 - 0dbf49c414ae - - 350bbc5c2ffd - - c370440f901e - - 6be888be75f9 + - bf328cec6a42 + - 5826298f6a73 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/send_data.yml b/usegalaxy.org.au/send_data.yml index 413deed33..39e7ebe01 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -8,13 +8,13 @@ tools: - name: ena_upload owner: iuc revisions: + - ea5e944f447d - 59bb6d34fca6 - - d147d6455873 - - 4aab5ae907b6 - a62c4a11a67d - - ea5e944f447d - 480d9e9d156b - - 5cb6146337d8 + - d147d6455873 - 6f6537780379 + - 5cb6146337d8 + - 4aab5ae907b6 tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/single_cell.yml b/usegalaxy.org.au/single_cell.yml index 29b68160f..f2565c908 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -8,63 +8,64 @@ tools: - name: alevin owner: bgruening revisions: - - e32b215b7c04 - f2000bc73102 + - b0fe3e482cb7 + - e32b215b7c04 - e4c01dcece8b - - c9944a2600f1 - ecb9ea6269ee + - c9944a2600f1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - 707023fa62fe - - e1c3c2f2a834 - c0b037b12765 + - e1c3c2f2a834 + - 707023fa62fe - cfaf5a405371 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 32e547223c9e - - cfc3f5a57dc6 - fb9e030ffae4 + - cfc3f5a57dc6 + - 32e547223c9e - 55e35e9203cf + - d330b3082107 - 00712416fdaa - 93dd15e13e6a - - d330b3082107 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 0bf7fddf90c7 - - 6f0d0c784f09 + - 39e945f0b2c1 - 688357ad5e61 - - ee98d611afc6 - b9fac48532eb - - 39e945f0b2c1 + - 0bf7fddf90c7 + - ee98d611afc6 + - 6f0d0c784f09 - 038e32885fec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - ed4996a16f7f - 7e8c677a7b71 - - 43cb7b5a6fe7 - - 9bd945a03d7b + - ed4996a16f7f - 3d748954434b + - 43cb7b5a6fe7 - b85871dd69f9 + - 9bd945a03d7b - d4af736e7b83 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - - fe75d2414dc0 - a4774b7b2e85 + - fe75d2414dc0 - 2e8022f1923c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -72,36 +73,36 @@ tools: owner: iuc revisions: - 769d815e4b0d - - 4fff5a293013 - 02b1fe7aed76 + - 4fff5a293013 - 0e70b2dfe4be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - a90f8efe08b4 - - c29e7bb492bf - aa4a6f0916b4 - 344c2af50552 + - a90f8efe08b4 + - c29e7bb492bf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - 5b7c81b35b89 - - c32347702e12 - 050cf43887d3 - b13d3e4c48e1 + - 5b7c81b35b89 + - c32347702e12 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 02fc39c8610d - ae969fdb8442 - - 1d77986f9ddc + - 02fc39c8610d - 239193b96d72 + - 1d77986f9ddc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -137,11 +138,11 @@ tools: - name: dropletutils owner: iuc revisions: - - 2c1200fba922 - a9caad671439 - - cdf4443d5625 - 8855361fcfc5 - cfe1e6c28d95 + - cdf4443d5625 + - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: episcanpy_build_matrix @@ -178,8 +179,8 @@ tools: - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - 9d42a6133690 - 57aeaf6b237d + - 9d42a6133690 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata @@ -192,15 +193,15 @@ tools: - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - 013e53ccc7ac - f47ac4a0b337 + - 013e53ccc7ac tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - - a63e9713c39d - b892fa1fcaec + - a63e9713c39d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions @@ -213,29 +214,29 @@ tools: - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: - - 9d02f1819e81 - f963c251ac77 + - 9d02f1819e81 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - f881c94fb3b3 - 40fee49bc6c3 + - f881c94fb3b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - - e06265d204f6 - 2dccb6bb0add + - e06265d204f6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - f0216498a666 - b05f662f9f35 + - f0216498a666 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions @@ -248,15 +249,15 @@ tools: - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - e03780179ee5 - 3ee5332bf57c + - e03780179ee5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 3a6a5381db36 - 4401ed529d2c + - 3a6a5381db36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat @@ -269,8 +270,8 @@ tools: - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - 62b720dceb56 - ea19190ce5e0 + - 62b720dceb56 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate @@ -304,15 +305,15 @@ tools: - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 7f7c6ead2d0d - 409396ea5cf0 + - 7f7c6ead2d0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo owner: bgruening revisions: - - e4f8fceab96a - 51e40e9b6c3c + - e4f8fceab96a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad @@ -353,36 +354,36 @@ tools: - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - - 11f39d7f6c64 - 6326cd29c1c3 + - 11f39d7f6c64 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - 337705015ee8 - b4e780e93c91 + - 337705015ee8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: - - 8d203e74869b - 58de3c7c8e89 + - 8d203e74869b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicquickqc owner: bgruening revisions: - - 21d859ad4502 - ea8fb5e899e8 + - 21d859ad4502 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - 1d6af10874d5 - 36dfa2825a59 + - 1d6af10874d5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -407,19 +408,19 @@ tools: - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 1d201e8378b3 - 11a3385e03b5 + - 1d201e8378b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: - - e98619de2776 - - 59be31ac9dc3 + - 4b0adaa31c95 - 0f1aaff9b22d + - e98619de2776 - 7784821452ac - - 4b0adaa31c95 - eeab712b0b99 + - 59be31ac9dc3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -432,22 +433,22 @@ tools: owner: bgruening revisions: - 282819d09a4f - - 7ffaa0968da3 - 2cfd0db49bbc + - 7ffaa0968da3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 56371b5a2da9 - 2ba99a52bd44 + - 56371b5a2da9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset owner: bgruening revisions: - - 8c64a2da3869 - 7705cc75ac18 + - 8c64a2da3869 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -465,20 +466,20 @@ tools: - name: raceid_clustering owner: iuc revisions: - - f911a64454fb - - 7e014059a88d - - 0bff0ee0683a - a4b734cd253b + - 7e014059a88d - c4f39bf4a068 + - 0bff0ee0683a + - f911a64454fb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: - b83fbc90161e + - 43c146e25a43 - d45f092caf24 - 7608d5faee41 - - 43c146e25a43 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -492,19 +493,19 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - 69018f285aa3 - df8e4e54d367 - a6821f856a1e + - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - - 44b935f2271b - - 2af7c5086a96 - e93b008c637a - 72979cac22b2 + - 2af7c5086a96 - c92d0f9338c5 + - 44b935f2271b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: run_sccaf @@ -522,102 +523,102 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: + - 6acb08931836 - 4d8f983cd751 - - 8983e7a04ba7 - - f9353ee6a0d4 - - aaa5da8e73a9 - - b2df381a6004 - 77b91b9bdf52 + - f9353ee6a0d4 - cb43c5d3acd3 - 38db3fef7aad + - 8983e7a04ba7 - 6f83f8fd381f - - 6acb08931836 + - aaa5da8e73a9 + - b2df381a6004 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - a03ff8633507 - - a97abb8cd15b - - d636ce5cde16 - - 3c86f71498bc - 64388be6d510 - - 72a6bebab2a5 + - d636ce5cde16 + - a03ff8633507 - 8cb783c81905 - - fc0321c000a3 + - a97abb8cd15b - 277313130da5 + - 3c86f71498bc - b409c2486353 + - fc0321c000a3 + - 72a6bebab2a5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - 5c3ebe2adc77 - 6c145a6868cc - - c0a80a16560f + - c5d3684f7c4c - 18262103fa61 - - f54f0f0598ad + - 6bd82ed14acd + - 3081ff5c84a3 - 5e9171dc8244 - - c5d3684f7c4c + - f54f0f0598ad + - 5c3ebe2adc77 + - c0a80a16560f - d86cb2ce311b - - 3081ff5c84a3 - - 6bd82ed14acd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - 146ae5d70b47 + - 3bcd5445cd7a - c9cb76cf8d6c + - 9f354c7c8c92 - ab55fe8030b6 - - 3bcd5445cd7a - - 4bda4412b8c2 - - d844935c906c + - 146ae5d70b47 - 7b9fafe32c86 - 94c19fb1281c - - 56c0d4acef02 + - d844935c906c - a407e7f8bdc1 - - 9f354c7c8c92 + - 4bda4412b8c2 + - 56c0d4acef02 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: + - 0185bd174ea0 + - 62acdd96d4a0 + - 1072ce66b426 + - dbbe1ea8ecb1 + - f7446fd8d5e7 - 95777145cb92 - - 40812a65a78b + - 9b0cdb8cf6be - 6adf98e782f3 - - 1072ce66b426 - - 6f5349dd5c49 - 7647e5cd1b8b - - dbbe1ea8ecb1 - aa0c474463c2 - - 62acdd96d4a0 - - 9b0cdb8cf6be - - f7446fd8d5e7 - - 0185bd174ea0 + - 40812a65a78b + - 6f5349dd5c49 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - a39040ae0a38 - 73ab2ac53d06 - - bf2017df9837 - - fe8f16c594ec + - 974bb00b2f43 + - d18e7a6e5cd4 - f2f6c703da06 + - 215733a383f2 + - fe8f16c594ec + - bf2017df9837 + - a39040ae0a38 + - c65fce500915 - 9fb627495ec2 - - d18e7a6e5cd4 - 458e8f43a775 - - c65fce500915 - - 974bb00b2f43 - - 215733a383f2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - 8f333f90d8d6 - b834074a9aff + - 8f333f90d8d6 - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -625,8 +626,8 @@ tools: owner: iuc revisions: - 652923ce664f - - 7a365ec81b52 - b7ea9f09c02f + - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_normalize @@ -638,9 +639,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 2e41b35b5bdd - 81e5bdff4853 - ef4c80837bc5 + - 2e41b35b5bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_exprs_freq @@ -653,8 +654,8 @@ tools: owner: iuc revisions: - 9e5c0bb18d08 - - 46fc6751d746 - c99ba278dfa9 + - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_tsne @@ -896,29 +897,29 @@ tools: - name: snapatac2_clustering owner: iuc revisions: - - 8f8bef61fd0b - afb90d3485df + - 8f8bef61fd0b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 588c811fdd48 - 88192fe25375 + - 588c811fdd48 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting owner: iuc revisions: - - 370d45e0d1a8 - fecf9664c885 + - 370d45e0d1a8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing owner: iuc revisions: - - cec3e76eaf05 - fef8f61cb34c + - cec3e76eaf05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: squidpy diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index 99a45d8eb..642475c67 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,11 +32,11 @@ tools: - name: datamash_ops owner: iuc revisions: - - 2f3c6f2dcf39 - - 4c07ddedc198 - 562f3c677828 - - 746e8e4bf929 - 419027d822d6 + - 4c07ddedc198 + - 746e8e4bf929 + - 2f3c6f2dcf39 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass @@ -49,15 +49,15 @@ tools: - name: dwt_cor_avb_all owner: devteam revisions: - - 8564f6927b87 - e01e8a9a82f4 + - 8564f6927b87 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all owner: devteam revisions: - - 506ae7b0d85d - 0b89b03ad760 + - 506ae7b0d85d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass @@ -70,8 +70,8 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: - - cb1c59d69557 - 6c29c7e347e8 + - cb1c59d69557 - 7a15159140d1 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -114,43 +114,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 7442b94d6a1e - - 4c4ec859c31a + - 840f29aad145 - aef56d0e7a61 - 9c3e1d3235c8 + - 7442b94d6a1e + - 4c4ec859c31a - b1eda492f063 - - 840f29aad145 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - d0352e8b4c10 - - 9fda0b82f419 - 30d21a6041f6 - 375bbd555f4a - 07843f917990 + - d0352e8b4c10 + - 9fda0b82f419 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - cd02bf168d23 - - 7ae443e6217d - - 2c58b83c9bad - 4cc980df6265 - 8b1b2b91f8d0 + - 7ae443e6217d + - cd02bf168d23 + - 2c58b83c9bad tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - bb9fc9d46ea4 - - 4bbaf77573ef - - e10e776f2109 - 7dd3fb35904f - - ad7e0b4291ee - 1dd433d2c92c + - 4bbaf77573ef + - ad7e0b4291ee + - e10e776f2109 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index 84e678a7e..923bbc310 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -14,8 +14,8 @@ tools: - name: add_value owner: devteam revisions: - - 745871c0b055 - 023f0a3760b3 + - 745871c0b055 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -27,8 +27,8 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - 6c6d26ff01ff - f18f67056946 + - 6c6d26ff01ff tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker @@ -36,12 +36,12 @@ tools: revisions: - be25c075ed54 - 02026300aa45 - - aff5135563c6 - 6e8d94597139 - - 6595517c2dd8 - - 13b6f0007d9e - 464b9305180e + - 6595517c2dd8 - 9cd341095afd + - 13b6f0007d9e + - aff5135563c6 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -53,8 +53,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 3a4694d4354f - 6f54dc6b37da + - 3a4694d4354f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -78,11 +78,11 @@ tools: - name: filter_tabular owner: iuc revisions: + - 557ec8d7087d - 34d29339abab - 37cde8134c6a - - 557ec8d7087d - - 9cc411a62277 - 90f657745fea + - 9cc411a62277 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -113,22 +113,22 @@ tools: - name: query_tabular owner: iuc revisions: - - 33d61c89fb8d + - 623f3eb7aa48 - 1ea4e668bf73 - - 83069b38aa85 - - cf4397560712 + - cf34c344508d - 3a6b78c39dca + - cf4397560712 - 2e8f945f7285 - - 623f3eb7aa48 - - cf34c344508d + - 83069b38aa85 + - 33d61c89fb8d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - 503bcd6ebe4b - - 399da6b5ec21 - ae8c4b2488e7 + - 399da6b5ec21 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -140,10 +140,10 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - b722161a845a + - f768f6183386 - bce29ec10b78 - c4d18aa4ec4a - - f768f6183386 + - b722161a845a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -156,14 +156,14 @@ tools: - name: text_processing owner: bgruening revisions: + - d698c222f354 - 9ff72e942410 - - 86755160afbf - - 74a8bef53a00 - - ddf54b12c295 - - 12615d397df7 - - f46f0e4f75c4 - fbf99087e067 + - f46f0e4f75c4 + - ddf54b12c295 + - 74a8bef53a00 + - 86755160afbf - a6f147a050a2 - - d698c222f354 + - 12615d397df7 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/variant_calling.yml b/usegalaxy.org.au/variant_calling.yml index bed08173f..e704bb070 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -14,9 +14,9 @@ tools: - name: breseq owner: iuc revisions: + - 0d18a3ba2d1c - 85c57cc9b558 - 82fb5e3bb93e - - 0d18a3ba2d1c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -35,50 +35,50 @@ tools: - name: freebayes owner: devteam revisions: - - a5937157062f + - 156b60c1530f + - ef2c525bd8cd - 04fa42777df9 + - a5937157062f - 57def2d7c093 - - ef2c525bd8cd - - 156b60c1530f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - 791f73caa0c8 - - 09d6e4693887 - e61c9ac190ad + - 09d6e4693887 - 435b157bed6d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 4805fe3d8fda - - b11e8e9c23bf - 3b4b2121842f + - b11e8e9c23bf + - dfadc322b065 - 65432c3abf6c - - 074d44697036 + - 4805fe3d8fda - 03627f24605f - - dfadc322b065 + - 074d44697036 - e1461b5c52a0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: + - 7dfca164d2e3 - 9cb929f21cfa - 701d134358ad - - 7dfca164d2e3 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - 426d707dfc47 - - f4473557ffc7 - c27549b9aa1f + - f4473557ffc7 - 971e07ca4456 + - 426d707dfc47 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi @@ -98,16 +98,16 @@ tools: - name: sniffles owner: iuc revisions: - - 43fffeed243f - 93c4b04a0769 + - 43fffeed243f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: + - fa016f1eea1a - 5bbf9eada9c2 - d220115f882b - - fa016f1eea1a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -143,21 +143,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - ee4a90760848 - - 40f0591deda0 - 3b1e7c170b10 + - ee4a90760848 - e7aff4a85df5 - 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+421,15 @@ tools: - name: vcfannotategenotypes owner: devteam revisions: - - 70bc6ced57f7 - 84959112d9a6 + - 70bc6ced57f7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect owner: devteam revisions: - - 9edfe5145ba8 - aea8e90ad788 + - 9edfe5145ba8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbreakcreatemulti @@ -442,8 +442,8 @@ tools: - name: vcfcheck owner: devteam revisions: - - aa8e8c96ca06 - 5e850c85ba32 + - aa8e8c96ca06 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -456,8 +456,8 @@ tools: - name: vcfcommonsamples owner: devteam revisions: - - 254f285dbaaa - f1852ecef841 + - 254f285dbaaa tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance @@ -470,9 +470,9 @@ tools: - name: vcffilter owner: devteam revisions: - - eae7c08ebb6f - 4bdc111b2470 - 6b935ab36d7b + - eae7c08ebb6f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup @@ -492,8 +492,8 @@ tools: - name: vcfgeno2haplo owner: devteam revisions: - - b890055e07bd - a3dea556218d + - b890055e07bd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes @@ -506,15 +506,15 @@ tools: - name: vcfhethom owner: devteam revisions: - - b07ef36cf7e6 - 8254e0fe7358 + - b07ef36cf7e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfleftalign owner: devteam revisions: - - 29f9b782727e - d2406f98a782 + - 29f9b782727e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfprimers @@ -527,15 +527,15 @@ tools: - name: vcfrandomsample owner: devteam revisions: - - 12b570dd0bc5 - 6257ee3b50d3 + - 12b570dd0bc5 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfselectsamples owner: devteam revisions: - - 2ba3b87f904f - 958b6484a7f1 + - 2ba3b87f904f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfsort @@ -554,7 +554,7 @@ tools: - name: vcfvcfintersect owner: devteam revisions: - - 166c4f50525f - 6f6bf10618d7 + - 166c4f50525f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/viral_tools.yml b/usegalaxy.org.au/viral_tools.yml index 15250eab7..06370d956 100644 --- a/usegalaxy.org.au/viral_tools.yml +++ b/usegalaxy.org.au/viral_tools.yml @@ -2,7 +2,7 @@ tools: - name: quasitools owner: nml revisions: - - 9def47f3c1e4 - 18aad692772a + - 9def47f3c1e4 tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu