diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index ce7954c57..07749ec61 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -8247,3 +8247,9 @@ Update 224 18/12/24 03:39:45 uniprotxml_downloader False Installed galaxyp 4ddc8 Update 224 18/12/24 03:40:28 volcanoplot False Installed iuc 99ace6c1ff57 99ace6c1ff57 Graph/Display Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_224/install_log.txt Install 1714 20/12/24 00:07:24 ncbi_fcs_gx True Tests failed iuc 32d058f3462a 32d058f3462a Staging Testing 1/2 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1714/install_log.txt Install 1716 20/12/24 03:02:03 ncbi_fcs_gx True Installed iuc 32d058f3462a 32d058f3462a FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1716/install_log.txt +Update 225 25/12/24 01:34:51 featurecounts False Tests failed iuc 5dbff3a5845a 5dbff3a5845a Staging Testing 6/7 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_225/install_log.txt +Update 225 25/12/24 01:43:30 infernal False Tests failed bgruening 3711f654044e 3711f654044e Staging Testing 7/12 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_225/install_log.txt +Update 225 25/12/24 01:49:10 krakentools_alpha_diversity False Tests failed iuc 78b69342c280 78b69342c280 Staging Testing 3/5 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_225/install_log.txt +Update 225 25/12/24 02:03:32 quast False Tests failed iuc a3b35edea53a a3b35edea53a Staging Testing 11/13 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_225/install_log.txt +Update 225 25/12/24 02:22:18 sistr_cmd False Installed nml cf767360ede1 cf767360ede1 2/2 Bacterial Typing toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_225/install_log.txt +Update 225 25/12/24 02:38:52 staramr False Installed nml 3548a93b39c1 3548a93b39c1 10/10 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_225/install_log.txt diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index 031f92832..1881282db 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,25 +2,25 @@ tools: - name: abricate owner: iuc revisions: + - 3f3e247c053d - 6e9aea89e388 + - 78c75f134c16 - 4efdca267d51 - c2ef298da409 - - 78c75f134c16 - - 3f3e247c053d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 owner: iuc revisions: - - 3f438bf5475d - c45c9dd066e2 + - 3f438bf5475d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_gaeval owner: iuc revisions: - - 8dc7512c9dc9 - 1dd7adc21b6d + - 8dc7512c9dc9 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: - - d6c074a93c51 - 1b52f0c8ad7f + - d6c074a93c51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - a79ee60b6926 - - 133f36c29579 + - 44018dd6b447 + - b5d8e5475247 - 3e1f6f6d557e + - cd2480f35935 - 1aae04680c4b + - fe3ca740a485 - 4f2967b27e67 + - a79ee60b6926 + - 133f36c29579 - f29602ae449e - - 44018dd6b447 - - fe3ca740a485 - - b5d8e5475247 - - cd2480f35935 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -63,36 +63,36 @@ tools: owner: bgruening revisions: - 6519ebe25019 - - f1e653756174 - aada0deea587 - dc027fa56d55 - 7be22100e5e1 + - f1e653756174 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 0fc0f9cf035a - - ca6d970d931c - 09855551d713 + - ca6d970d931c - bd0e53f3a891 + - 0fc0f9cf035a - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - d77802fe76f7 - - 728dacaf08a9 - 92eee5f31117 - da5f1924bb2e + - d77802fe76f7 + - 728dacaf08a9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - - 8fd427007e93 - 7355bbf5e05f + - 8fd427007e93 - fe48aa4ccd5e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -118,17 +118,17 @@ tools: - name: cpat owner: bgruening revisions: - - 7ccc6234b54e - - 8e9e228c54c4 - 1ac12c0cc7a0 + - 8e9e228c54c4 + - 7ccc6234b54e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - 63662ae295d6 - - d9c3016f7283 - 9d1fbff733cf + - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -158,61 +158,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 3bbe70fef6df - - 9f2455341fac - 9c15ca7e764e - - b6b5cd37f2a2 - - 582fd74dc2a1 - - 756376aeb1ae - 14f588312c56 + - 756376aeb1ae + - 582fd74dc2a1 + - 9f2455341fac + - b6b5cd37f2a2 + - 3bbe70fef6df tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 73428a792541 - - 989f7c061f35 - - a230ea445788 - - 0ffe5be70caf - 8e1ace8f77c6 + - 0ffe5be70caf + - 73428a792541 - 30fb23d4c31c - 1691af4a0d17 + - a230ea445788 + - 989f7c061f35 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 5a5ae61da69c - e94187d661df - 57c6718cbfcc + - 0418d28136de - 494f0bb4a993 - - 563a19373357 - 30f08d74024f - - 0418d28136de + - 5a5ae61da69c + - 563a19373357 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - d6c7106b7b2e - - 2bba2ff070d9 - - 1bc5a03faf2e - - 4b96ced19f75 - f31125bb85ea + - 2bba2ff070d9 - f77d7b685bb3 + - 4b96ced19f75 + - 1bc5a03faf2e + - d6c7106b7b2e - 7abc5f6dd595 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - b3cf4684e9c7 - - fed64e676186 - 54961e026fe4 - - 52af33194019 - d77fdcca400e - - d3af38b9c7e1 + - b3cf4684e9c7 + - 52af33194019 - 520e30695ec3 + - fed64e676186 + - d3af38b9c7e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -238,10 +238,10 @@ tools: - name: goseq owner: iuc revisions: - - 602de62d995b - ef2ad746b589 - 8b3e3657034e - 43798b4caee0 + - 602de62d995b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -265,8 +265,8 @@ tools: - name: infernal owner: bgruening revisions: - - c9e29ac5d099 - 477d829d3250 + - c9e29ac5d099 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan @@ -299,19 +299,19 @@ tools: - name: maker owner: iuc revisions: - - d46d803ca6cc - - 3c1a01127868 - 370c210d9541 + - 3c1a01127868 + - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - e95d52d295d7 + - 033755194fe9 - 624606f7c996 - c8ac28e8ac44 - - 033755194fe9 - b815ec682418 + - e95d52d295d7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -353,11 +353,11 @@ tools: - name: prokka owner: crs4 revisions: + - 8a22554cdde2 - d643e3b03500 + - bf68eb663bc3 - a17498c603ec - - 8a22554cdde2 - eaee459f3d69 - - bf68eb663bc3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -376,8 +376,8 @@ 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 @@ -401,23 +401,23 @@ tools: - name: snpeff owner: iuc revisions: - - 5c7b70713fb5 - 5a29ab10dba6 - - 68693743661e - - 8f92c2b26e6d - - c7275bd8b4d6 + - 5c7b70713fb5 - 6322be79bd8e - - 268d162b9c49 + - c7275bd8b4d6 + - 8f92c2b26e6d - 5b80f544c67f - cfcf33df7fc0 + - 68693743661e + - 268d162b9c49 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 09d6806c609e - - 2b3e65a4252f - 5fab4f81391d + - 2b3e65a4252f + - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -442,18 +442,18 @@ tools: - name: tbprofiler owner: iuc revisions: - - d03af1c7002c + - 4839e590cb26 + - 037a11682176 + - 8cb134b8c1a5 - 51dd22484644 + - 200c378d85f3 + - 37213cf56392 - 809dfc93d593 - e1a9d6fd258d - - 45083d070fb8 - - 4839e590cb26 - ac8250086ac3 - - 37213cf56392 - - 200c378d85f3 - - 037a11682176 + - d03af1c7002c - ba6f87115e13 - - 8cb134b8c1a5 + - 45083d070fb8 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 bae1618f0..21238f930 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,28 +2,28 @@ tools: - name: abyss owner: iuc revisions: - - 0124fce4654a - - 553bfe8bd0b5 - - 8f1b150a2487 - - db9b10824c61 - - 0e93176640ac - d6d5ccc2c581 - - 7547fcab5d19 - - fa5259cc561b + - a929ce596a34 + - db9b10824c61 - 890b794c997d + - 553bfe8bd0b5 - 841084c5fc46 - - a929ce596a34 + - 0e93176640ac + - fa5259cc561b + - 0124fce4654a + - 8f1b150a2487 + - 7547fcab5d19 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 067592b6b312 - b2860df42e16 - - ddddce450736 + - 067592b6b312 + - 21e491ad532a - b9e31c5c01c7 + - ddddce450736 - 94fe43e75ddc - - 21e491ad532a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -36,49 +36,49 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - faee8629b460 - - 3371c5bdc17a - - 22286dab5aa1 - a7f16f24e9a1 + - 22286dab5aa1 - 5258e18bbe23 + - faee8629b460 + - 3371c5bdc17a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - 53dd00a4ab68 - '392811378515' + - 53dd00a4ab68 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - cf13a1e03e5b - - f18f0b887c31 - - 602fb8e63aa7 + - e824f5d958d0 - 41030a6c03b7 - - 46ae58b1d792 - - 1440ae06552f + - e5c372c91e46 + - 0d243f458b53 - 5ecdeca79a0d + - 1e62c28ba91d + - 94170eee0ad8 + - 1440ae06552f - bb935709506a - - e824f5d958d0 - - 0d243f458b53 - - e4bd1e99bacf - - 2babe6d5c561 - 2dd755c1c6ff + - e4bd1e99bacf - 4048d82f0c88 - - 1e62c28ba91d - - e5c372c91e46 + - 46ae58b1d792 - ea8146ee148f - - 94170eee0ad8 + - 2babe6d5c561 + - 602fb8e63aa7 + - cf13a1e03e5b + - f18f0b887c31 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 86f150c8019d - c5b7390290b1 - 5732f959936a + - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -90,46 +90,46 @@ tools: - name: flye owner: bgruening revisions: + - cd11366d92cf - 276f5d8712d5 + - 291923e6f276 + - 3ee0ef312022 - 8d4f03b5fe9d + - cb8dfd28c16f + - 3e4f8642c77e - 1ce9b1d72ec3 - e27815e82dd4 - - 291923e6f276 - 1f0769f0b56b - - 3e4f8642c77e - - 3ee0ef312022 - - cd11366d92cf - - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 460fad600dce - - 01210c4e9144 - 3169a38c2656 + - 01210c4e9144 + - 460fad600dce - b2f674562a18 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 7348b69e5109 + - 06bcf65179fb - 8b330a577046 + - 7348b69e5109 - ba88bc5a6446 - - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 6ec1b853c8fd - f4a3eff8ab85 - - 5127a713de83 - 764f2516d837 - - 690c2caa367e - 3fba9c77550a - 3ef480892a9f + - 5127a713de83 + - 6ec1b853c8fd + - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -141,24 +141,24 @@ tools: - name: hifiasm owner: bgruening revisions: - - da9d8bf98802 - - 71740308d412 - - 366a11d316a7 - - 41cea2aa2dce - - 60024a528cbd - - 9ef6920c3089 - f3c89da3af16 - - ec9e21e9c71b - - 5f625c63b8bc - - 6505bd37670d - - 3f7be05a1597 - 284a1cb82b61 - - 045c7c3d8e59 - 5161f204ba63 - - df25d4fb79b7 - - 5bec28269d95 - 0ee0c3089254 + - 41cea2aa2dce + - 60024a528cbd + - df25d4fb79b7 + - ec9e21e9c71b + - da9d8bf98802 - 2061fb3b81b4 + - 71740308d412 + - 045c7c3d8e59 + - 3f7be05a1597 + - 6505bd37670d + - 9ef6920c3089 + - 5f625c63b8bc + - 366a11d316a7 + - 5bec28269d95 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -186,33 +186,33 @@ tools: owner: iuc revisions: - eb7b00ec347d - - d7edbc9c3a07 + - 39edec572bae - f8113c25bc6b - 09c589057ee8 - - 39edec572bae - 9d79beb19ac3 + - d7edbc9c3a07 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - 51c2360aa807 - - eadfd71dde37 - 29dabd8db6f2 + - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: + - 606b09cc9860 - fd128c111ab0 - e731ea24e48d + - 99ecfdafc64f - eb7a370f6588 - - 606b09cc9860 - f338e9942b27 + - 3ca2d2a9068c - 2ecf5a570907 - f369ef5f210b - - 99ecfdafc64f - - 3ca2d2a9068c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -224,10 +224,10 @@ tools: - name: miniasm owner: iuc revisions: - - a7b889b90140 - b799a615995d - - 73a3846701e1 + - a7b889b90140 - 8b6d0d85252b + - 73a3846701e1 - 8dee0218ac7d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -246,9 +246,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 7c2f5268d01c - - 15200570e926 - 64a1c751d99b + - 15200570e926 + - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -261,45 +261,45 @@ tools: owner: iuc revisions: - c6cec5ab35c1 - - bbe19ef04a74 - - dfb8a4497339 - 8fef980d48b5 - 02831bf9e95f - - d256a51a656b + - bbe19ef04a74 - 2b16ba799da9 + - d256a51a656b + - dfb8a4497339 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - a315c25dc813 - e9bd16ba5ebd + - a315c25dc813 - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 675488238c96 - - 6fcbee531de6 - - 875d0f36d66f - 3061c8b029e5 + - 675488238c96 - 342a1d1fed7b + - 6fcbee531de6 - 72472698a2df - - 59db8ea8c845 + - 875d0f36d66f - ebb0dcdb621a - 7594365c546b + - 59db8ea8c845 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - d865b62f501c - - a199cd7ac344 - 78c533842eeb - aa39b19ca11e - cd06929b224b - 39bed8de8017 + - d865b62f501c + - a199cd7ac344 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -317,31 +317,31 @@ tools: - name: raven owner: iuc revisions: - - f8564b2d7f63 - - 3edba9afc9bc - - f11b994b7eb2 - 33b7d8481a76 + - f8564b2d7f63 - 2b2a352488fa + - f11b994b7eb2 - 5c55448d0f33 + - 3edba9afc9bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast owner: iuc revisions: - - 8e66f695d859 - f73ab5187eed + - 8e66f695d859 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - 5fc94b3a4704 - - 1d06c8b38e77 - - 28189050e437 - - e122f9101584 - 53c2bc8c2ae3 - 378e55aeeb25 - ef69617ecb42 + - 1d06c8b38e77 + - 28189050e437 + - 5fc94b3a4704 + - e122f9101584 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -353,13 +353,13 @@ tools: - name: shovill owner: iuc revisions: + - f698c7604b3b + - 83ead2be47b2 + - ad80238462c1 - d9f6a00b6db7 - 865119fcb694 - - 83ead2be47b2 - ee17a294d3a3 - 196a599ec43d - - f698c7604b3b - - ad80238462c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot @@ -373,116 +373,116 @@ tools: - name: spades_biosyntheticspades owner: iuc revisions: + - 604782a8a53a + - c33a476f4001 - 051fd2db8a27 + - 1bb12736175c - 904bf932cf78 - - 604782a8a53a - - 1fc82fe7ebef - 7490b213baa9 - - 1bb12736175c - - c33a476f4001 + - 1fc82fe7ebef tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: + - 9678993ca5bd + - fee85957cebe - 34305b013402 + - ad8b536d1caa - 655fa188c3cc - - fee85957cebe - - 9678993ca5bd - 808b3a0a6716 - d6e617c4e338 - - ad8b536d1caa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - b8002c3f7141 - - e5a3b75a271f - - 6b5a5842531e - - 7e27faaad80e - - 037f9927c4ff - 8d4b90bf9caf - 21da31ed41a1 + - 037f9927c4ff + - 7e27faaad80e + - 6b5a5842531e + - b8002c3f7141 + - e5a3b75a271f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: + - 2a10645aeadd - 5b26685e5d3b - 328aa71f0f3c - f1532cb33c75 - - 2a10645aeadd - 9de69775f512 - - 7922870efcca - 86f66ab58e14 + - 7922870efcca tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: + - 340bc17f49cf - 8cc856b935ee - e41dcb0e913b - - 85fb02c43042 - - 340bc17f49cf - 1708851f8804 - 6aad515a5270 + - 85fb02c43042 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: + - 6357b127161e - b3490b036c5a + - 249f6a28c751 - d159735a6a9f - d5fb354f745d - de1260f8a300 - - 249f6a28c751 - - 6357b127161e - b65a43f70b99 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - dd7ad84f3943 - d2d1df21dfb9 - - d5887ace0dd4 - 9006e5836729 - a90db5dbaaf3 - 33368fec3b70 - - 7897763d14ec - b7829778729f + - 7897763d14ec + - dd7ad84f3943 + - d5887ace0dd4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - ced385aa976d + - 8f631679571f - 505a9833ab5d - - 6f4c8ad6ea01 - 189e837009c9 + - ced385aa976d + - 6f4c8ad6ea01 - 0368ac680e70 - - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 9ded6109434a - a7ed21de23fe + - d40ed4eb0c0e - 356afed970b4 + - 9ded6109434a - e59bee4565b3 - 19bdfd1e6fe3 - - d40ed4eb0c0e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - b23249f81bc4 - 4688ae3b49b5 - - ebd801e712bc - 7673a6c920b2 + - ebd801e712bc + - b23249f81bc4 - 6dd935e4984b - 80a17897564d tool_panel_section_label: Assembly @@ -490,54 +490,54 @@ tools: - name: trycycler_reconcile_msa owner: iuc revisions: - - ed312479d9eb - b64696992ee9 + - 59bd28f6265d + - ed312479d9eb + - 937ea677d437 - b5e35a2ca4f3 - cb1e3db43020 - - 937ea677d437 - - 59bd28f6265d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: + - 2628f6790eda + - cb4768eeca3b - 05bd7504fdb2 - b9b0246a2be3 - 383bb5ad32e2 - - cb4768eeca3b - - 2628f6790eda - 6015aa0303f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - e92675014ac9 + - 3e44ef016b45 - e022dff952df - 6e26c9afd301 - - 9e3e80cc4ad4 - - 3e44ef016b45 - - 0a3a602cd1e3 + - e92675014ac9 - 8f9f06995f98 + - 0a3a602cd1e3 + - 9e3e80cc4ad4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f - 5da9a0e2fb2d - - 920677cd220f - 8d09f8be269e + - 920677cd220f + - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - 82398ba86ba7 - - d81360ea69d8 - 4a53b89fa703 - - 0e2b4e3f9ca1 + - d81360ea69d8 - 37d88f41c810 + - 0e2b4e3f9ca1 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 05fc24e6e..b12649109 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,9 +2,9 @@ tools: - name: integron_finder owner: iuc revisions: + - 4768f7f8e93f - 392f100eebcd - 1ae00120dd24 - - 4768f7f8e93f - bfd290fe1588 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu @@ -17,17 +17,18 @@ tools: - name: mlst owner: iuc revisions: - - 1f5641a52664 - 8e8dc9a1e3e5 - - 31812e7a1315 - ded48b36f3b7 + - 31812e7a1315 + - 1f5641a52664 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 5c8ff92e38a9 - 24a7a95867b0 + - cf767360ede1 + - 5c8ff92e38a9 - 17fcac7ddf54 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 46b7e6773..29849fec7 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,21 +2,21 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - d1f62024a08b + - d58c27d2c5a7 + - 0840ba83860c - a9c9d768b751 - 1c427e24fb79 - - 0840ba83860c - - 7beb76ffbc0f + - d1f62024a08b - 204a131e47db - - d58c27d2c5a7 + - 7beb76ffbc0f - 159b04e36791 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge owner: iuc revisions: - - cab19c0452c4 - 1bb2b5b52030 + - cab19c0452c4 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_tadpole diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index d570d59d2..90f18e9ff 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: + - ce3c7f062223 + - 0a5c785ac6db - 589e7e57fd6d - - e19bebe96cd2 - - 07e8b80f278c - - a8eabd2838f6 - b28e0cfa7ba1 - - a1a923cd89e8 - - 0a5c785ac6db + - a68aa6c1204a + - 07e8b80f278c - 87ee588b3d45 + - a1a923cd89e8 + - e19bebe96cd2 - 64e2edfe7a2c + - a8eabd2838f6 - dde39ba9c031 - - a68aa6c1204a - - ce3c7f062223 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 eb6e18bb9..d8422b829 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -9,9 +9,9 @@ tools: owner: bgruening revisions: - f921014aba5a - - e8ac2b53f262 - 54f751e413f4 - 62c9df8382c2 + - e8ac2b53f262 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -24,14 +24,14 @@ tools: owner: devteam revisions: - 0e3cf9594bb7 - - e25d3acf6e68 - d999e774072a - - 5edc472ec434 - a52d2d93e595 - - cbf3f518b668 + - 5edc472ec434 - 2889433c7ae1 - acf4e47b734c + - e25d3acf6e68 - 6f386c5dc4fb + - cbf3f518b668 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index 055210f50..450f1fcd9 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: + - f4230f116196 + - 27ee142314a9 + - da6bd1975a71 - 095ad4d096d1 - - 710301bc46fa - 6ca543ec1bf8 - - da6bd1975a71 - - 27ee142314a9 - - f4230f116196 - c8cdde00b105 + - 710301bc46fa tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -111,8 +111,8 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - 67ee76f0e497 - 2a868592ebcb + - 67ee76f0e497 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -130,74 +130,74 @@ tools: - name: gmx_editconf owner: chemteam revisions: + - 79cfd9ead848 - 88076940fa94 - 3b8a9d5ced85 - - bfb65cb551d8 - - 79cfd9ead848 - 0fac8e2afc13 + - bfb65cb551d8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - 55918daa5651 - - 715cd0e87781 - - d532b7e5f64b - - f5d979cb4b54 - eb6564a60136 + - d532b7e5f64b - b46d4b4d995c + - f5d979cb4b54 + - 55918daa5651 + - 715cd0e87781 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - f26afd1b7104 + - d2f955aea23a - 5579659312e6 - fdf2cc80adb5 - - d2f955aea23a - 97872d87ba80 + - f26afd1b7104 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - d1d0efda35c0 - 319a28774da9 - bc31d02be922 + - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - 4da9ee404eab - - 070e3ecc3fda + - ed736e6eee39 - 2c349b027a01 - cac1886249a2 - - ed736e6eee39 + - 070e3ecc3fda tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: + - da8753545526 - 2e219a2d9327 - - c0c9a5024177 - - f197e34c33a9 - 73008ef1f487 - - 525ca7c8065f - - 807aa4c9293d - - da8753545526 - d1f803b5943c + - f197e34c33a9 + - c0c9a5024177 + - 807aa4c9293d + - 525ca7c8065f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: + - 7568ae18908a - 61094e01eff9 - - 1809414a9454 - - 2c8ed1b52bf7 - c4fbab8e03c5 - 27ea4e1a3f95 - - 7568ae18908a + - 1809414a9454 + - 2c8ed1b52bf7 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -209,11 +209,11 @@ tools: - name: md_converter owner: chemteam revisions: - - d7ec25187599 - - 730ef07b90ae - - ba83f0923369 - 79e8ab8f1e81 - ccfbd956a2d3 + - ba83f0923369 + - d7ec25187599 + - 730ef07b90ae 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: - - e6011617c748 - 1400d1977e7b - - 4242b4d68e9c - b59c91adeac1 + - e6011617c748 + - 4242b4d68e9c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -283,8 +283,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 75ee9c410951 - 7672039a0bb0 + - 75ee9c410951 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -339,10 +339,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 85fad59f8168 - - d4c67ced6abc - bf99565cec1f + - 85fad59f8168 - 9b48456a96fe + - d4c67ced6abc tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index 66f84f082..82b13dbc5 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -2,9 +2,9 @@ tools: - name: diffbind owner: bgruening revisions: - - fa56d93f7980 - - 163688bb8f73 - f907216064f6 + - 163688bb8f73 + - fa56d93f7980 - c97a786e8fb5 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -32,9 +32,9 @@ tools: revisions: - 86e2413cf3f8 - 495a4173006f - - f5d67c722d67 - 424aefbd7777 - 640d3af5d833 + - f5d67c722d67 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -46,16 +46,16 @@ tools: - name: rnachipintegrator owner: pjbriggs revisions: - - 087d9872fb0d - b695071de766 + - 087d9872fb0d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer owner: devteam revisions: - - 74c9214cc8e6 - 4a14714649b4 - 5c2cc3b58c7d + - 74c9214cc8e6 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 0780e0f99..31c948fa8 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -10,16 +10,16 @@ tools: owner: nml revisions: - 25136a2b0cfe - - 830961c48e42 - 33151a38533a - 90981f86000f + - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - dfde09461b1e - 3ddd99c7efee + - dfde09461b1e 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: - - 0046692724f9 - 6cbe2f30c2d7 - 2dae863c8f42 - baabc30154cd + - 0046692724f9 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 248e454ff..bc68fab6e 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -3,8 +3,8 @@ tools: owner: bgruening revisions: - e7449b2c14bf - - abba05ead5d7 - d6ede73082da + - abba05ead5d7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -16,32 +16,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 4a6ee918c13a - - ab9350a8ab4d - - 5e1240a87bcb - a3b86937ead6 + - ab9350a8ab4d - 6ef0b5664c69 - - 3b6f97e7094c - - f3a19509108a - 0b3c3ad92827 - - 367b1ed91207 + - 3b6f97e7094c - e3cbd2287f63 + - 4a6ee918c13a + - 367b1ed91207 + - 5e1240a87bcb + - f3a19509108a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - d4d4e9febf5c + - 1b5fc03380d4 + - e525f9ffb9ac + - 72ed72122deb - 584008e574b2 - - e177a8ea0bf1 - - bd46669113b9 - 54ccb7e1f49a - - 501c21cce614 + - d4d4e9febf5c - 091bb5922a82 + - e177a8ea0bf1 - 33c99804a32f - - 72ed72122deb - - 1b5fc03380d4 - - e525f9ffb9ac + - bd46669113b9 + - 501c21cce614 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -60,23 +60,23 @@ 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: - - 186b8d913e6c - 8979c288aefb - 77b41c89d856 + - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -102,9 +102,9 @@ tools: - name: gffread owner: devteam revisions: - - 4dea02886337 - 154d00cbbf2d - 3e436657dcd0 + - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -122,15 +122,15 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - 705821bf30d2 - f5c632894818 + - 705821bf30d2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -151,9 +151,9 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: - - 19e45916daf9 - - 26c6706bfb07 - 63769c4217a7 + - 26c6706bfb07 + - 19e45916daf9 - 92ac8e086317 - b9b385097f13 tool_panel_section_label: Convert Formats @@ -161,15 +161,15 @@ tools: - name: ucsc_fatovcf owner: iuc revisions: - - a40dd4fd3096 - 3c19c84fbce2 + - a40dd4fd3096 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_twobittofa owner: iuc revisions: - - e9bbe2f71784 - 8067dfa00ed2 + - e9bbe2f71784 - 3c6f9e8a4c17 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index fba917d78..e0e3c4169 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,205 +2,205 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: + - 5f6d123679f4 - e821645ef8fc - - de72ba3ed6f2 - c929a006727f - - 5f6d123679f4 + - 29451af70c52 - 268e91e540ee - a1ca9bccc7f2 - - 29451af70c52 + - de72ba3ed6f2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: + - 2d2cf5c1ea8a + - 0e49b109abc2 - 0e143b4c3987 + - 5d11599b8a7d - 7a7fd0f5f15d - - bb1e4f63e0e6 - - 0e49b109abc2 - - 2d2cf5c1ea8a - 12af64f93288 - - 5d11599b8a7d + - bb1e4f63e0e6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: + - 81b1e3e1fc6c + - dc059492a995 - c06951d10364 - - 1d848bc4585f - 195e98217334 - 7c1beb6d6eca - - 81b1e3e1fc6c - - dc059492a995 + - 1d848bc4585f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 26e7304d6737 - 93eb012d9eed - - bfff7454b59a + - 26e7304d6737 + - 71aa86af6762 - 3d211717a775 - 07418a30ed01 - a67ac707496a - - 71aa86af6762 + - bfff7454b59a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 26983857c91a - - dd0b7398bb96 + - 29fcfd36e90a - 56d5b797ce84 - - 2bc10a9ca58b + - 26983857c91a - 5be24eba848d - b8858746dc1f - - 29fcfd36e90a + - dd0b7398bb96 + - 2bc10a9ca58b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: + - 72bfafe3330b + - e6d0bff01239 + - c3e012dfe21f - ee3a1b0f45f1 - 7ef978dc1b8a - - e6d0bff01239 - 7e6bcd2e5128 - 9384cd033f30 - - c3e012dfe21f - - 72bfafe3330b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - 167788df3b46 - - b73e213add0c - 514fa53b5efb - - fd1275e01605 - - d9a637e83828 - fb9cf9c97ec4 - - a60c359ec43c - 9470f29702f8 + - d9a637e83828 + - a60c359ec43c + - 167788df3b46 + - fd1275e01605 + - b73e213add0c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - 5bffaa8354a1 + - 86febdcc4283 - a02cfa31e9cb + - c34d11ea4ba6 - 2c37ce318bc3 + - 5bffaa8354a1 - ca0616bb2cdf - e479c7ca5570 - - 86febdcc4283 - - c34d11ea4ba6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 78f405266706 - - 004aea905d4d - - 192ef85c0b0b + - 69a8621ca2f0 - 2d466b530754 - - 1fcb7adc39b8 + - 004aea905d4d + - 78f405266706 - 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: - - 2f9e4843f480 + - 137c4beed34b + - 459cfa861f0b - d9ce4897dbb2 - d580d6acd1df - - 9ecba5e225a6 - - 459cfa861f0b + - 2f9e4843f480 - 3c9f0c486cca + - 9ecba5e225a6 - db940c262830 - - 137c4beed34b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - fd408d755394 - fbe773640707 - - f264afa9fa6f - - 32e451def88c - bd7db9e2f2cb + - 32e451def88c + - fd408d755394 - bad3ca889618 + - f264afa9fa6f - 2c66e43f1c86 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 4e12ea27f788 - - 7e361d147872 + - 56bce3c82278 - 231994413f89 - 9368fbc49c8b - - 7fda5607e777 - 3b9d990a0a0e - - 56bce3c82278 + - 7fda5607e777 + - 4e12ea27f788 + - 7e361d147872 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - d9114ef1c8a5 - - 94ca68515826 - ce4ce3316f74 - - c03c3384cd81 + - d9114ef1c8a5 + - b1779366c8e9 - 4431f39ede55 - e65d16fb2724 - - b1779366c8e9 + - 94ca68515826 + - c03c3384cd81 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - 4ed32329e0ed - 793665fff0f8 - - 23f7c5f1fdaf + - d57251071381 + - b88ebb3672a1 - f8fc4e5aff9d + - 23f7c5f1fdaf - 2da482e408b8 - - 4ed32329e0ed - - b88ebb3672a1 - - d57251071381 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - ba6efa77fb79 - - 010e58e9d822 - - 25d830337d31 - - a4dfb122e52b - 512155688d98 + - a7849312d328 - e4c7985d4585 + - 25d830337d31 + - 010e58e9d822 + - a4dfb122e52b + - ba6efa77fb79 - c60570fa602f - - a7849312d328 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: + - 69264da0ce77 - 00d869ea03a1 + - aa200e4f3939 - 443d9a9d6d11 - - 38e3f226248b - - 69264da0ce77 - - 4d678170d29b - c899e0ccff8c - - aa200e4f3939 + - 4d678170d29b + - 38e3f226248b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: + - a2d70c4fd406 - 6662b1a8d326 - c361b12d207a - d806504e96d9 - - 10301d137111 - - a2d70c4fd406 - aac8444d6681 + - 10301d137111 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 c1e165269..d6bf8ce14 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -2,22 +2,22 @@ tools: - name: obi_annotate owner: iuc revisions: - - d50dc96e3ce9 - 3021b9f5809f + - d50dc96e3ce9 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - 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 owner: iuc revisions: - - 4d705e3443a7 - e328ced6cf0a + - 4d705e3443a7 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep @@ -37,8 +37,8 @@ tools: - name: obi_ngsfilter owner: iuc revisions: - - 76e69de726b2 - 91a1ed0b486f + - 76e69de726b2 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort @@ -51,8 +51,8 @@ tools: - name: obi_stat owner: iuc revisions: - - 5f4544915893 - 39320fee9d70 + - 5f4544915893 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab @@ -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 83e65c370..2bdbfb936 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -2,8 +2,8 @@ tools: - name: emboss_5 owner: devteam revisions: - - 832c20329690 - dba489bfcd62 + - 832c20329690 - ce385837c160 - 63dd26468588 tool_panel_section_label: EMBOSS diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index a3d84dd92..53cc6eea7 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - 6da3972210ee - cf1322aeb137 + - 29bdbc353f20 - 62f5fab76dfb - d82648ad25a3 - - 29bdbc353f20 + - 6da3972210ee 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/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index f4648155a..2e2a53d98 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: - - 135b80fb1ac2 - - 660cffd8d92a - - de6cebe3c043 - 49370cb85f0f - - c053d4cad713 - 8665bcc8b847 - - c5e2e5902201 - - c4b82dce8335 - - 5915ea1ec9b1 - - 8c0175e03cee - - e4691e1589d3 - - 44e2cc14f75b - fe74900d6dc7 - 5eb7e84243f2 - - b1c926deaa2d - - 64172f1c1202 - - 093678460093 - - 4e5056fefd88 - - 48f587c13075 + - 135b80fb1ac2 - 288f97432497 + - e4691e1589d3 + - c053d4cad713 + - 48f587c13075 + - c4b82dce8335 + - 4e5056fefd88 + - 44e2cc14f75b + - c5e2e5902201 + - 093678460093 + - de6cebe3c043 + - 8c0175e03cee + - 64172f1c1202 + - b1c926deaa2d + - 5915ea1ec9b1 + - 660cffd8d92a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -73,8 +73,8 @@ tools: - name: fasta_concatenate_by_species owner: devteam revisions: - - 25b8736c627a - 717aee069681 + - 25b8736c627a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_extract @@ -86,16 +86,16 @@ tools: - name: fasta_filter_by_length owner: devteam revisions: - - 8cacfcf96a52 - e626b3ff9922 + - 8cacfcf96a52 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: - - 516b97a23d7e - 859422bcb689 - 9457a20156db + - 516b97a23d7e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -114,9 +114,9 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - f81d4362b6c1 - - f773e98b26cf - ec0b5076173a + - f773e98b26cf + - f81d4362b6c1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -128,10 +128,10 @@ tools: - name: fasta_stats owner: iuc revisions: - - 9c620a950d3a - - 0dbb995c7d35 - cd0874854f51 - 56022eb50bbd + - 0dbb995c7d35 + - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -143,14 +143,14 @@ tools: - name: fastp owner: iuc revisions: - - dbfc505896e9 - - a626e8c0e1ba - - c59d48774d03 - - 65b93b623c77 - ecb9f4854617 + - 65b93b623c77 + - d60c3f704da0 - dbf9c561ef29 - 1d8fe9bc4cb0 - - d60c3f704da0 + - dbfc505896e9 + - a626e8c0e1ba + - c59d48774d03 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -162,8 +162,8 @@ tools: - name: fastq_combiner owner: devteam revisions: - - f1dc2a761c30 - 9115b978ce10 + - f1dc2a761c30 - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -176,9 +176,9 @@ tools: - name: fastq_filter owner: devteam revisions: - - 10b75444feae - - '144275714590' - 81a9090d6df3 + - '144275714590' + - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -204,9 +204,9 @@ tools: - name: fastq_manipulation owner: devteam revisions: + - e30352e889fe - 5b87038565bb - 7861f3b10c68 - - e30352e889fe tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation @@ -232,9 +232,9 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - 523c2aff0376 - 03d57fea6482 - f3936d0632cb + - 523c2aff0376 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -246,9 +246,9 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: + - 3e396e702cea - 2ccb8dcabddc - b41c2c1bcfbf - - 3e396e702cea tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -260,9 +260,9 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: - - 8d958759cf2a - - c885369b207b - 09a2199cd356 + - c885369b207b + - 8d958759cf2a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -274,9 +274,9 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - 397dc333436b - - e39cc71d3ed6 - 249c8393f2d4 + - e39cc71d3ed6 + - 397dc333436b - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -289,9 +289,9 @@ 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 @@ -303,9 +303,9 @@ tools: - name: fastq_stats owner: devteam revisions: - - f0e7deab6518 - - f86c27295151 - b1cea1b2fcd0 + - f86c27295151 + - f0e7deab6518 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats @@ -317,9 +317,9 @@ tools: - name: fastq_trimmer owner: devteam revisions: - - 33794bdb7fe0 - f0b18efb97f1 - b63b2bfb3ea3 + - 33794bdb7fe0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer @@ -331,16 +331,16 @@ tools: - name: fastqtofasta owner: devteam revisions: - - 297962e79f39 - ac3fed111eb6 + - 297962e79f39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter owner: devteam revisions: - 529bccd5e4a1 - - d5e9e83cd3d8 - 567d5b3c52b1 + - d5e9e83cd3d8 - 09070cacefd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -353,9 +353,9 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: - - 0b7ec11b3c7c - 4bedca26c133 - 8abdedf55101 + - 0b7ec11b3c7c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -368,9 +368,9 @@ tools: owner: devteam revisions: - cb1e251cac37 - - 736b8f6ee456 - - bdf1ce174e39 - 90858c306551 + - bdf1ce174e39 + - 736b8f6ee456 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -382,9 +382,9 @@ tools: - name: fastx_collapser owner: devteam revisions: - - 07497255281e - - 421f0af4ee95 - 7ce1891db6f5 + - 421f0af4ee95 + - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -396,10 +396,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - 3599f5451ee2 - - b29d37ca9e41 - - f984bb114520 - 02f8a17a4ebd + - f984bb114520 + - b29d37ca9e41 + - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -411,10 +411,10 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: - - 177f0621c266 + - e246088b6e34 - 6027ef51ef91 + - 177f0621c266 - 0c2907307ba4 - - e246088b6e34 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -426,10 +426,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: - - 61b4cedc8934 - - 377ac2829eac - 73194cdd4f57 - 547e8d00f11c + - 61b4cedc8934 + - 377ac2829eac tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -459,10 +459,10 @@ tools: - name: pear owner: iuc revisions: - - 037f0acc7830 - - f69501361cec - 2f804526f5fd + - f69501361cec - b4c6f054210a + - 037f0acc7830 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -481,25 +481,25 @@ tools: - name: seqkit_sort owner: iuc revisions: + - 61eb4cfc7313 - 29ef2c5ec205 - fdc21382376d - - 61eb4cfc7313 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: + - 795cd16de38f - fe1ae2ebf63d - 812705bcf39c - - 795cd16de38f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - 4b494533146a - 3da72230c066 - a019807f4e67 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -539,12 +539,12 @@ tools: - name: umi_tools_count owner: iuc revisions: - - 24013bf85a6f + - b557acca0b56 - 71ad4a56c40c + - a535cf1e5da4 - e654095ab143 - - b557acca0b56 + - 24013bf85a6f - 8250ea3a1501 - - a535cf1e5da4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -556,21 +556,21 @@ tools: - 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: - - 015cf18f4a15 - - 7a7e33d28f62 - 9fa7803d1c51 - - f3759eec3018 - 27ac32a22ad2 + - f3759eec3018 + - 015cf18f4a15 + - 828dba98cdb4 + - 7a7e33d28f62 - 7accf7407811 - 6a675c3aa610 - - 828dba98cdb4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract @@ -589,8 +589,8 @@ tools: - name: umi_tools_whitelist owner: iuc revisions: - - 4c8a1c7d3608 - - e4e12f0b3af1 - 953b4821b183 + - e4e12f0b3af1 + - 4c8a1c7d3608 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 530a0f8c1..6baa92eff 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -3,82 +3,82 @@ tools: owner: devteam revisions: - 64e9a6afdd0c - - ce9cd02d5b88 - - e41385662e5e - 7b4468117008 + - e41385662e5e + - ce9cd02d5b88 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - c64d534a763c - 8050e091e99b + - c64d534a763c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - - e7b2202befea - - 2c64fded1286 - 3d0c7bdf12f5 - - 2b0c9d9fc6ca - 9da02be9c6cc - - 5ec9f6bceaee - ff9530579d1f + - e7b2202befea + - 5ec9f6bceaee - f2e8552cf1d0 + - 2b0c9d9fc6ca + - 2c64fded1286 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - 89d299153577 - a252d8415583 + - 89d299153577 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - 18a51655db17 - b6b54ba71bd8 - ad116ae3f4d9 + - 18a51655db17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - cc0fd298cc17 - - 7306ec78632a - 59003d0543cd + - 7306ec78632a tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: + - 8880fb74ef56 - a72af9de6bf5 - 1f296803dfa3 - - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 9a913cdee30e - f7985e0479b9 - 1c2db0054039 - - abfd8a6544d7 + - 9a913cdee30e + - bf675f34b056 + - f7e2f1eb3a16 - 3d93dd18d9f8 - b2f1f75d49c4 - - 5e33b465d8d5 - - bf675f34b056 - 75c93c70d094 - - f7e2f1eb3a16 + - abfd8a6544d7 + - 5e33b465d8d5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - 949f01671246 - - 084bbd8ba7b8 - cd7e644cae1d + - 084bbd8ba7b8 tool_panel_section_label: FASTQ Quality Control 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 2fa9d9531..e76c0f8cb 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -2,23 +2,23 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 142d95ab942e - 3630a6e624d4 + - 142d95ab942e 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: - 0c8f7322f8fc - - f2f3bc622a16 - 8f53b238a360 + - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -31,15 +31,15 @@ tools: - name: gemini_comp_hets owner: iuc revisions: - - 62647e2637f6 - 7cf9bc210044 + - 62647e2637f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -52,8 +52,8 @@ 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 @@ -79,23 +79,23 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 2550239feed5 - 184aa4e686e2 + - 2550239feed5 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load owner: iuc revisions: - - cf61daf064fe - 45296e47d565 - b2c25142267e + - cf61daf064fe tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 2969a1f43b7d - 90021fffff70 + - 2969a1f43b7d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors @@ -108,8 +108,8 @@ tools: - name: gemini_pathways owner: iuc revisions: - - 9199331c3421 - 6b09debcfc49 + - 9199331c3421 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -122,8 +122,8 @@ tools: - name: gemini_query owner: iuc revisions: - - da74170c55c7 - 840fb4850be3 + - da74170c55c7 - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu @@ -137,8 +137,8 @@ tools: - 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 @@ -158,8 +158,8 @@ tools: - name: gemini_stats owner: iuc revisions: - - ee894347fcd6 - 5c9efee9cb1e + - ee894347fcd6 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 6e2bcd639..833a79c00 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -2,8 +2,8 @@ tools: - name: mageck_count owner: iuc revisions: - - 3edbd1ff5602 - e329d44424d7 + - 3edbd1ff5602 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea @@ -16,8 +16,8 @@ tools: - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index 45be047b2..e0afaf59f 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,9 +2,9 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - b39347891609 - - e9df53a75f3c - 983bf725dfc2 + - e9df53a75f3c + - b39347891609 - c1b437242fee tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -17,36 +17,36 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - 28587613264f - 1c58de56d587 - e063168e0a81 + - 28587613264f tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: + - 516a54ddf218 + - 4317d3cb6cba + - 734abc7ac21d - 1790dcf3c32d - - 69ebb7f46e45 - - 7068f48d0ef9 + - e407b9da183a - 653e89d73fc4 - - 8848455c0270 - - f8054ea1c365 - - 1ec814014652 - - 734abc7ac21d - - c441583adae5 - - 83c7d564b128 - - 9a776b080193 + - 4df8de2d0e48 + - 69ebb7f46e45 - 6591f049cf7e - - e407b9da183a - - f5ea3ce9b9b0 - - 6ea73833cf67 - e08a7ad4378b + - f5ea3ce9b9b0 + - 8848455c0270 + - 7068f48d0ef9 + - 83c7d564b128 - ba931a59dd59 - - 516a54ddf218 + - 1ec814014652 + - f8054ea1c365 + - 6ea73833cf67 - aad3885b3216 - - 4df8de2d0e48 - - 4317d3cb6cba - 5e6237d58b0c + - 9a776b080193 + - c441583adae5 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept @@ -62,8 +62,8 @@ tools: owner: bgruening revisions: - bfdc6a7ffd3a - - 054483e27a35 - - af5eccf83605 - 468c71dac78a + - af5eccf83605 + - 054483e27a35 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 c1a892875..ada97a912 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: + - 4b519282a05b + - 740057a5126d + - 7f13dc906cb9 - 290a11559985 - c4bde687c846 - - 7f13dc906cb9 - - 4b519282a05b - - fd59d783248a - ae9994cf526f - - df7356989ac1 + - fd59d783248a - a64dc31ab7f2 - - 740057a5126d + - df7356989ac1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -35,8 +35,8 @@ tools: owner: devteam revisions: - 867ab348287d - - f95284aa2946 - 7cf5b1d072b5 + - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -49,23 +49,23 @@ tools: owner: iuc revisions: - 53460afd5115 - - 3b37b1b1c3a7 - - ca7cb0eaad62 - 374e9062d874 - - 51c6ccaace7e + - 3b37b1b1c3a7 - '566197475670' + - ca7cb0eaad62 - 48b42ee61bc5 + - 51c6ccaace7e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 391a4cc45fea - - 10515715c940 - 1a72f938213e + - 10515715c940 - d3a9e32672ec - 3d059e9c2fba - da4c086cff5b + - 391a4cc45fea tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -85,19 +85,19 @@ tools: - name: ggplot2_point owner: iuc revisions: - - 299307abd804 - - 5fe1dc76176e + - e3a675da7fd0 - 1acf88921176 - 5298e06f14f9 + - 5fe1dc76176e - d0fc8b746d57 - - e3a675da7fd0 + - 299307abd804 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 @@ -136,16 +136,16 @@ tools: - name: jbrowse owner: iuc revisions: - - 112eb40ba6cf - - 1cfc579079a6 + - 836d1aa3e89a + - 17359b808b01 + - a6e57ff585c0 - ca2def38369c + - 1cfc579079a6 + - 667e17248bfe + - 2bb2e07a7a21 - 4542035c1075 - - a6e57ff585c0 - - 17359b808b01 + - 112eb40ba6cf - fd5dbf0f732e - - 2bb2e07a7a21 - - 836d1aa3e89a - - 667e17248bfe - 6cd09d7b5f37 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -164,40 +164,40 @@ tools: - name: pathview owner: iuc revisions: + - f1691de443a7 - 03c13085aecc - fe154a7af404 - - f1691de443a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram owner: iuc revisions: - - 594b85e4237a - bd1416eea1f0 + - 594b85e4237a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plot_ragtag_paf owner: galaxy-australia revisions: - - 94e0834ae4ed - 501dcf66c0ce - c1bed78b9ed5 + - 94e0834ae4ed tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: - - 85da91bbdbfb - - 1c5dcef5ce0f - 62e3a4e8c54c + - 1c5dcef5ce0f + - 85da91bbdbfb - f234e2e59d76 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 7b21a9b5922f - 9958188c6195 + - 7b21a9b5922f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -209,10 +209,10 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 26f2fe7e53a1 - - 7c9417381ad5 - - 44c66e8d21e6 - 6c571966cfb9 + - 44c66e8d21e6 + - 7c9417381ad5 + - 26f2fe7e53a1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -224,23 +224,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 360df4999907 - - 4ac4e7083b7e - 2824d77cd8f8 + - 36b848d5f3ec - 7dd841a32245 + - 4ac4e7083b7e - a1abfa420d9d - - 36b848d5f3ec - - 14e7c35f3d00 - 326a3db8d9d1 + - 14e7c35f3d00 + - 360df4999907 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 99ace6c1ff57 - 83c573f2e73c - 73b8cb5bddcd - 44608d0193ed + - 99ace6c1ff57 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 @@ -252,7 +252,7 @@ tools: - name: xy_plot owner: devteam revisions: - - 319fa5a9fc1b - ecb437f1d298 + - 319fa5a9fc1b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index a274a804e..9d18670a0 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 14b3f2a4523b - 1a642de6db01 + - 14b3f2a4523b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -28,55 +28,55 @@ tools: - name: scanpy_compute_graph owner: ebi-gxa revisions: + - bc9e8de21efb - 6417cccad133 - 7779b9dcf040 - - bc9e8de21efb - 22bd5861706d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells owner: ebi-gxa revisions: - - bf1e0bdec1db - e9283529cba1 - - 55ccc0a121bc + - bf1e0bdec1db - 361608369dda + - 55ccc0a121bc 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 - da611a744112 - 474a69c47184 - - cc64914b0cf4 - - 23d838d1569d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster owner: ebi-gxa revisions: + - 2ccd9f9e2cd0 - ad6995afd2e6 - 36735850e461 - fc4b3b46dc9d - - 2ccd9f9e2cd0 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers owner: ebi-gxa revisions: + - d8f5224005bb - 49653e680ea4 - 81c34e67f262 - - d8f5224005bb - 0a8e527d1517 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes owner: ebi-gxa revisions: + - 2861ca3bfe4d + - 64dd8bb151e1 - 79da59a0b180 - 4667fe07bd68 - - 64dd8bb151e1 - - 2861ca3bfe4d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn @@ -89,8 +89,8 @@ tools: - 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 @@ -103,25 +103,25 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 94697510d55f - - 9a2f72d7dbd2 - ff6decc0f432 + - 9a2f72d7dbd2 + - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet owner: ebi-gxa revisions: - - 53ce0e336840 - 70cb0596ffef + - 53ce0e336840 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalise_data owner: ebi-gxa revisions: - - 28b1546857b0 + - 6b97ffba31da - 8d9c22419c56 - 3027cb62adbd - - 6b97ffba31da + - 28b1546857b0 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator @@ -134,9 +134,9 @@ tools: - name: scanpy_plot_embed owner: ebi-gxa revisions: + - 7d5c97823f8b - 35f6611fb8c3 - 1be0fc4d8654 - - 7d5c97823f8b - 56d22aa6cb3b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -164,9 +164,9 @@ tools: - name: scanpy_regress_variable owner: ebi-gxa revisions: - - 36daab33aecf - - d18ed15697bb - 0bab2ae44e7a + - d18ed15697bb + - 36daab33aecf tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap @@ -186,8 +186,8 @@ tools: - name: scanpy_run_fdg owner: ebi-gxa revisions: - - be019b069e31 - 65c3ec07502b + - be019b069e31 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_paga @@ -200,37 +200,37 @@ tools: - name: scanpy_run_pca owner: ebi-gxa revisions: + - 0cf90e01d9f8 + - 3ee74b58c72d - 4428dba93375 - 59028945c857 - - 3ee74b58c72d - - 0cf90e01d9f8 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne owner: ebi-gxa revisions: - 8b0d6f6f44c8 - - abdb61e4afa3 - 181d61d2f3cd + - 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: - - fe562424a0a6 - - 767a675b5254 - - bd4a244faeb8 - ea91cfd0444e - 0f98603d0116 + - bd4a244faeb8 + - 767a675b5254 + - fe562424a0a6 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - 5605f8452eb3 - e2d0dc8a50ca - f86b2c3bc459 - 4cc9362782b4 + - 5605f8452eb3 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 b47a1b193..99b2148e2 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,60 +2,60 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 9edf8894a22d - - 29f66c353bcb - d9967770de96 + - 0f611e7d7858 + - 29f66c353bcb + - 9edf8894a22d - 921a2da49a0c - ed2cca6b5de4 - a4c13ddcc8ee - - 0f611e7d7858 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 11de0d28ab30 - - 78fb5e286609 + - d404277cc87a - ec4b948dc6f0 - - 755df866ad0c - 478aacfbaa37 - - d404277cc87a + - 11de0d28ab30 + - 78fb5e286609 - 5746d61f0a91 + - 755df866ad0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 11fa44ee0603 - - 9d93c8fbe0a6 + - 03dd3c16ae4e + - f72063d9426b - 9e357a8b2ec3 - 4d511437b1e5 - 977dc15add20 - - 03dd3c16ae4e - - f72063d9426b + - 11fa44ee0603 + - 9d93c8fbe0a6 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - f86ca478c6af + - 1da5f169b491 + - 3b5b54ed6392 - 0ba4f56a3613 + - c3e5e2cf12b7 - 41dbf4d162a2 - - 1da5f169b491 + - f86ca478c6af - 77919cc3618e - - c3e5e2cf12b7 - - 3b5b54ed6392 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - 7babd8a46fe0 - - 9939786dd9c9 - 025a128652dc + - 5308ca68ef3d + - 9939786dd9c9 - b63363075c2e - f741330d4a71 - - 5308ca68ef3d - 12d51d7be66f tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index 0df8eb1be..136301228 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -3,18 +3,18 @@ tools: owner: imgteam revisions: - 81f0cbca04a7 - - 0c777d708acc - - 699a5e9146b3 - - 7db4fc31dbee - 8bccb36e055a - 3df9f0a4bf34 + - 7db4fc31dbee + - 699a5e9146b3 + - 0c777d708acc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5bc8cdc17fd0 - 0a53256b48c6 + - 5bc8cdc17fd0 - 2436a8807ad1 - 5791a7f65275 tool_panel_section_label: Imaging @@ -22,24 +22,24 @@ tools: - 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 owner: imgteam revisions: + - 77f7159d775a - 70316d792fc9 - b1c2c210813c - - 77f7159d775a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - f70b215d155c - dba87c4b32d3 + - f70b215d155c - d51310ab328a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -47,17 +47,17 @@ tools: owner: imgteam revisions: - fcadded98e61 + - b07f4839ca77 + - f3360fbeda64 - 85edbb7a436b - 10eed33aa9b2 - - f3360fbeda64 - - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 984358e43242 - 6e65fd971e13 + - 984358e43242 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects @@ -71,9 +71,9 @@ tools: - name: cp_cellprofiler owner: bgruening revisions: + - eb6c08714244 - 0e4dccaafef5 - e917a2424690 - - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -87,24 +87,24 @@ tools: owner: bgruening revisions: - e7273daa5ae2 - - 6070780813d9 - 670975e92458 + - 6070780813d9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - ef4aed1d34c4 - - df3ad3ba5c6f - cdf8e3c57dae + - df3ad3ba5c6f + - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - 5d28ac336861 - - 2484086dee41 - 6a7da2e5f696 + - 2484086dee41 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features @@ -119,96 +119,96 @@ tools: owner: bgruening revisions: - d0178bdcd00e - - f8fa0f6718a3 - f24c370e5ea4 + - f8fa0f6718a3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - - 31d195bedf6d - 3245681b2f6d - ad271f78a87a + - 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: + - ff1a86a87364 - c09dcda1143f - 6100a22bf4f2 - - ff1a86a87364 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - 3a05117669cf - b178453ea8d1 - 667a513e67e4 + - 3a05117669cf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - ac5bea85a391 - a1a961c46d4b - 2564f461de62 + - ac5bea85a391 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - a32c3f810ade - - 91e03287f285 - 20dbb1f7ec7b + - 91e03287f285 + - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - b64af54c5c09 - 8536b1ae0254 - 5499dc6f8ac1 + - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - d3890df07463 - e972e07c7845 + - d3890df07463 - 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 - 79e10d12d90a + - acf3aa487283 + - d85f11570109 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - 80b200ae516b - - b76841ee5560 - 035a58c7f54a + - b76841ee5560 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -220,17 +220,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 8083a87d2fdf - 3a3033222f61 - 48102a685037 + - 8083a87d2fdf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 4ecf93628f97 - 27edbb90ab2b - 33f4fa1413fb + - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -242,22 +242,22 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 1fd453cd757b - 972d2c365739 + - 1fd453cd757b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 236ec78b2e53 - 7b6d9412c7f8 + - 236ec78b2e53 - f8b4eada923c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -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 ab1f40c8b..8ba6016e2 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: - - 3e4f434a69c6 - - e319b5b65879 - - a38934e303b9 + - 78bbd17d0703 - 3a72fede57ce - - f362150bef41 - d6e72da3ec35 - - 40737febe339 - - 1069f6db0a0e - - 78bbd17d0703 - e4ee04da1c19 + - 1069f6db0a0e + - 40737febe339 + - f362150bef41 + - e319b5b65879 + - 3e4f434a69c6 + - a38934e303b9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 0135f1d487a0 - c88553ec696e - - 2b95d5c04908 - - 72ddd32392cd - - 9537184d421f + - fcbeda41d0ac + - 618297d23022 - 8f8df367470d + - 0135f1d487a0 - f91cfb73d369 + - 2b95d5c04908 + - 9537184d421f - 7fe36019c073 - - 618297d23022 - - fcbeda41d0ac + - 72ddd32392cd tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - ad0dc9f4c9e2 + - d7e79eb3bcb3 - 2cf4a1cafc16 - fafb3d685fa9 - - d7e79eb3bcb3 + - ad0dc9f4c9e2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: + - 28a6f1908fcc - 3d18f8c3c0f6 - - 7f1cfa4c0e32 - - 8c05afb547fa - - 6a1515bb0687 - - ee29337f905c - - a1c2aecd7a0d - - 43aac8d29685 - 94df24c6bc00 - - 8d36959b000d - - bd2a7d1316b9 - 9eaadf03e0df + - a1c2aecd7a0d - ee2beb764a7b - - 28a6f1908fcc + - 8c05afb547fa + - 43aac8d29685 + - bd2a7d1316b9 + - ee29337f905c + - 7f1cfa4c0e32 - 5dc33613c288 + - 6a1515bb0687 + - 8d36959b000d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 5671e1d3d5ee - - 364f4ffec275 + - db536ad45f28 - bcaa0d571ce2 - - a250929be21b - - 86a20ae274fc - - 5d6ed46cc101 - - e3bb03cf207a - - d37ede8589b2 + - 364f4ffec275 - 9f978da6528a - cb903c9dc33d - - db536ad45f28 - 8858fa037a15 - c092052ed673 + - 5d6ed46cc101 + - a250929be21b + - 5671e1d3d5ee + - e3bb03cf207a + - d37ede8589b2 + - 86a20ae274fc tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - abbc8041e8ec + - 194e3ceee923 + - 3b6a16d82c1b + - ed28dd32141c + - c5c9f02b6167 + - 12d66d0d05ac - e1a015876aa9 - - f95f403841ad - 230b05597996 - - 12d66d0d05ac - - 38b91a3190cd - - c5c9f02b6167 - - 3b6a16d82c1b - - 194e3ceee923 - 584beffa972b - - ed28dd32141c + - f95f403841ad + - 38b91a3190cd + - abbc8041e8ec - 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 e3e2207e4..857bfe3da 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -3,18 +3,18 @@ tools: owner: iuc revisions: - b8a457820315 - - f198773344e4 - 17e3b698dd52 - 0f1724dd59d2 + - f198773344e4 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: + - 22c2a1ac7ae3 - 374cb875d38a - ba0c40780ecf - a513e3fbb4c5 - ac092723240d - - 22c2a1ac7ae3 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 e23469ca7..3d5146ec8 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -10,19 +10,19 @@ tools: - name: keras_model_config owner: bgruening revisions: - - f22a9297440f - 4d81e3e2fb63 - 8a794e6d3388 + - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - 2af1346e68c9 - - 818f9b69d8a0 - - f1b9a42d6809 - e1317b5502fa + - f1b9a42d6809 - b6ef6d0cb6b7 + - 818f9b69d8a0 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex @@ -38,9 +38,9 @@ tools: - name: model_prediction owner: bgruening revisions: - - 1552b8cb4a94 - - 9991c4ddde14 - 83228baae3c5 + - 9991c4ddde14 + - 1552b8cb4a94 - 25b46af53232 - 29e4122c90de tool_panel_section_label: Machine Learning @@ -48,45 +48,45 @@ tools: - name: sklearn_ensemble owner: bgruening revisions: - - 841a6cc5fc58 + - 53616c8b0865 - f3dfa4bdf87e - 1a53edc4b438 - - 060ca94ac049 - - 53616c8b0865 - a07ab242b0b5 + - 841a6cc5fc58 + - 060ca94ac049 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - d4808d5b83da + - 40f4447733b2 - 2fc89dcd41c8 - dc4b5fd604a6 - - 91c4e3331208 - - 40f4447733b2 - 927586a18553 + - 91c4e3331208 + - d4808d5b83da tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 301e07345c93 - - e5a5ad882f1f - 25ab6b4e376e - c6ae57f774c6 - 7626ea9c2e1b - 36e8d6d5d01b + - e5a5ad882f1f + - 301e07345c93 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - b7c3e9a3b954 - - 80852884053f - - 4ed102b922cb - - 02d2be90dedb - f9639b488779 + - 4ed102b922cb + - 80852884053f - 0630258dcf35 + - 02d2be90dedb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index d32f833ab..77fe56e2c 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: + - f6877ad76b00 + - 937aa69e715f + - 03e9b2fbc005 + - 017aba02828d - 749c918495f7 - - 17062a0decb7 - 3ba8d4563129 - d5ceb9f3c25b - - 0d4acadabb04 - - 03e9b2fbc005 - - f6877ad76b00 - - 017aba02828d - - 937aa69e715f - - a6d65b0c67af + - 17062a0decb7 - cd659e8cc5fa + - a6d65b0c67af + - 0d4acadabb04 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -31,12 +31,12 @@ tools: - name: bwa owner: devteam revisions: + - 53646aaaafef - 3fe632431b68 - dfd8b7f78c37 - - 53646aaaafef - - e188dc7a68e6 - - 2477830927ec - 64f11cf59c6e + - 2477830927ec + - e188dc7a68e6 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: - - e7f19d6a9af8 - 2ff111fac1d7 + - e7f19d6a9af8 - 60afcc2c1d05 - - 3e1ea2facca6 - 37b497aa133f + - 3e1ea2facca6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 77b2770508f6 - b3eab4b67562 - - 11a0d50a54e6 - c0c2d0941de8 - - 53c0b7a1a0c3 + - 77b2770508f6 + - 6b1e195506a3 - 09b53c1d4ab1 + - 8c6cd2650d1f - 037c6e54df11 - - 6b1e195506a3 - - be1d967337e4 - - f54f5baedfdd - 5cc34c3f440d - - 8c6cd2650d1f + - 11a0d50a54e6 + - f54f5baedfdd + - be1d967337e4 - 3f4d6399997b + - 53c0b7a1a0c3 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - b8f5f6e87f5c - - 1cd2511a396e - - e403d27e8f24 - - 42ce70172b72 - - 9ee34ba73ebf - - 79b885ce78d7 - 5ef7ec16b04f + - 13022c3d3076 + - 9ee34ba73ebf - 00fbfac99d39 + - 42ce70172b72 + - 1cd2511a396e + - e403d27e8f24 - 381a32c51141 + - b8f5f6e87f5c - ec9cbd6b9a49 - - 13022c3d3076 - 178bdbdb6d24 + - 79b885ce78d7 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 4c72ed3cc..e40c53b2d 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 @@ -63,8 +63,8 @@ tools: - name: isolib owner: recetox revisions: - - 6b0fef8a77c0 - 2b1118bce0b1 + - 6b0fef8a77c0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: lcmsmatching @@ -94,29 +94,29 @@ tools: - name: matchms_convert owner: recetox revisions: - - b9cc12600553 - 9e83636da9d3 + - b9cc12600553 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering owner: recetox revisions: - - a177ac3c752c - 83c4b4359ac4 + - a177ac3c752c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity owner: recetox revisions: - - 84af792d3a78 - fd890f162ce6 + - 84af792d3a78 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter owner: recetox revisions: - - a5a5b147da70 - 1b09315a3f87 + - a5a5b147da70 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export @@ -142,8 +142,8 @@ tools: - name: matchms_networking owner: recetox revisions: - - 8147d93d372d - f04b378325e5 + - 8147d93d372d tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key @@ -167,8 +167,8 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: - - 7ba589b01dbc - 9ff95a1a2705 + - 7ba589b01dbc tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split @@ -193,8 +193,8 @@ 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 @@ -242,8 +242,8 @@ tools: - name: ramclustr_define_experiment owner: recetox revisions: - - f2c1d0bbb074 - 5f2b58dadb39 + - f2c1d0bbb074 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr @@ -256,18 +256,18 @@ tools: - name: recetox_aplcms_align_features owner: recetox revisions: + - ec196e27a61a - c53a97599181 - 7b42ee54d757 - 79ad928a0dae - - ec196e27a61a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - - 59c393d35e0e - f3a18e020cdd - 149b9cc7499b + - 59c393d35e0e - 18ec7635bac6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -275,56 +275,56 @@ tools: owner: recetox revisions: - dfebc82ba1f0 - - 134be5abb208 - 481d769e2f7a + - 134be5abb208 - 50b9918aeff2 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: + - 30bf4e35da3e + - 51332c2520c7 - a82db010c53e - 501a232f3cd5 - - 51332c2520c7 - - 02c772a49998 - - 30bf4e35da3e - 9064aecc78a7 + - 02c772a49998 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - b3413f335327 - - 89178a72388a - - b341cfd4baf8 - e7305ba0dd38 + - b341cfd4baf8 + - 89178a72388a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - dd7bbc2b99d1 + - cf061712a184 - 17a48d0a80f4 + - dd7bbc2b99d1 - b7c8a44b9cc1 - - cf061712a184 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - d7f5878a98c3 - 99d118321d5f - - 24278c6b6d1c - f92b1b64da93 + - d7f5878a98c3 + - 24278c6b6d1c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - ea0758b41473 - - 7acd11ddc061 - ffbabefbd2e2 + - ea0758b41473 - d90187b0f247 + - 7acd11ddc061 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -336,8 +336,8 @@ 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 diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index a4800bf32..07e2ed413 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -9,8 +9,8 @@ tools: owner: iuc revisions: - 0094893f5001 - - 18676df0cb3a - 0e63d03c8790 + - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -22,8 +22,8 @@ tools: - name: cat_summarise owner: iuc revisions: - - 7f1aaa1932d8 - a8216def322b + - 7f1aaa1932d8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -95,60 +95,60 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: + - 3a89c3f99f3d - 5b5a7af9fbb4 + - 63f86089423e - 7c2100246a2f - 76d3d2b10738 - - 3a89c3f99f3d - - 63f86089423e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - 00f5005840fa - - 1c35dadbe76f + - 18a502a9d287 - 96336c6a2bb7 - 84fd33a60b35 - - 18a502a9d287 + - 1c35dadbe76f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - a9f4a217dcd6 - - f732237754fc - 34e55239e68b - - addaf9d22850 - e8fba04706d3 + - addaf9d22850 + - f732237754fc + - a9f4a217dcd6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 04c15826a0b8 - - 75403243703a + - 8c202e741d68 - 0776d824d896 - 5fe3edf19b9c - - 8c202e741d68 + - 04c15826a0b8 + - 75403243703a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 8470de786d47 - - e96bbb9e24ea - 43c99742158b - 1c9b3bcd4261 - 75c8945b0da2 + - e96bbb9e24ea + - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: + - 84743da21318 - 5c865a382933 - 1d75bd0595e2 - 35176674168c - - 84743da21318 - 306a40d4bb8f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -156,19 +156,19 @@ tools: owner: iuc revisions: - 32c9ea835770 - - 555ccac8a4c5 - - ac72310b038a - 8daf4564ccda - 78faebd0879c + - ac72310b038a + - 555ccac8a4c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: + - 7b8cb2b02978 + - f947b4bb5107 - cae017b76acb - a58e4a43f49c - - f947b4bb5107 - - 7b8cb2b02978 - d60df8727f59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -176,10 +176,10 @@ tools: owner: iuc revisions: - 04144473e59e - - 7f3b59dee073 - 1bc3657cd694 - - 1770d188f72d + - 7f3b59dee073 - 7136e9ab70db + - 1770d188f72d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts @@ -187,44 +187,44 @@ tools: revisions: - d943081510da - 9058d8943303 - - 0a1224c4b781 - - a7817705348e - 19299bb1c6af + - a7817705348e + - 0a1224c4b781 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - bc939965ce41 - c7e73acfa3eb + - bc939965ce41 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: - - b907a3c0434f + - f8f56dd6449f + - a68b985913ab - c4db8c4de66f - 4d9445dff47b - - 65d52c693b8e - - a68b985913ab - - f8f56dd6449f - - 5c7ba3d85a01 - dbf1798c0dcc + - 5c7ba3d85a01 + - b907a3c0434f + - 65d52c693b8e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 213df31ba341 - 15dbb444df71 + - 213df31ba341 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 6d364c65c946 - 654548ae1357 - 6c84982ee6f7 + - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -245,16 +245,16 @@ tools: owner: iuc revisions: - b084117133af - - c6676a890f50 - d77397f09da1 + - c6676a890f50 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - 9704f1a3b32d - - 7f208f1eb64f - cad93abecac9 + - 7f208f1eb64f + - 9704f1a3b32d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -279,8 +279,8 @@ tools: - name: humann_join_tables owner: iuc revisions: - - 6bf703133209 - f01ca38fb6c5 + - 6bf703133209 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_reduce_table @@ -293,33 +293,33 @@ tools: - name: humann_regroup_table owner: iuc revisions: + - e88b731dad59 + - 8237a0f225db - 79706f10d680 - c409a495841f - 31c6d107e7a5 - - 8237a0f225db - - e88b731dad59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - d24841f5c3d2 + - 094ad9c068af - aabf8cfb8fef - 172920f67a84 - - 094ad9c068af - 71ea608ddfa3 - 714d5a28cc5c + - d24841f5c3d2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - 12fb63b5f63f - - 2bdd84912a2b - - d7e9a3c41657 - - 4137b492233e - a4d7148ccee4 + - 2bdd84912a2b - a293a742194f + - 12fb63b5f63f + - 4137b492233e + - d7e9a3c41657 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -331,13 +331,13 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - 97f7bb0851e7 - 75bedfb2078b + - cf87759761eb - 6fcb8ac37a3e - a92c06a3afa7 + - 97f7bb0851e7 - 64bc7acc22a9 - e2c71b852aba - - cf87759761eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -356,22 +356,22 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - c82508e76ad1 - 2d35528d2141 + - 4033827c76b8 - 4e5e73d03f0d - 5e5a999ffaa9 - - 4033827c76b8 - 080ea153677c + - c82508e76ad1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 2cd76b089570 - - c2803012bbb3 - 6b7622dda516 - - fc6c328c292f - 95bf7479d53c + - 2cd76b089570 + - fc6c328c292f + - c2803012bbb3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -396,29 +396,29 @@ tools: - name: khmer_abundance_distribution_single owner: iuc revisions: - - 65b382bf9b7c - 385a965c6f87 + - 65b382bf9b7c 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 owner: iuc revisions: - - adb3dd5a899f - 1061711538c6 + - adb3dd5a899f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance @@ -438,8 +438,8 @@ tools: - name: khmer_normalize_by_median owner: iuc revisions: - - b1fe2ef3d244 - 4d23ab83ea29 + - b1fe2ef3d244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition @@ -458,17 +458,17 @@ tools: - name: kraken2 owner: iuc revisions: + - cdee7158adf3 - 4a9da2b6c2e3 - - 328c607150ff - 20e2f64aa1fe - - cdee7158adf3 + - 328c607150ff 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 @@ -534,16 +534,16 @@ tools: - name: krakentools_extract_kraken_reads owner: iuc revisions: - - f329328da134 - 4bf1e2701504 + - f329328da134 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2krona owner: iuc revisions: - - 88d274322340 - 02bbace216f2 - 2deaada69b14 + - 88d274322340 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa @@ -580,22 +580,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - e073891b2afc + - 327d9f4cc95f - 3cc4a60615c0 - 4fd3b5d8706b - - 27250f92a01a - - 2cff76cf35c6 - - 327d9f4cc95f - 7f5d7b0e9884 + - 27250f92a01a - 0270541aaf46 + - 2cff76cf35c6 + - 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 @@ -661,26 +661,26 @@ 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: - - ec368db926f4 - 1a037928504c - ef65b083bd0c - - 740fd2d16a28 - - a92a632c4d9b - - 289b3807e80c - ff8f55893e7d - - 2131d7dca455 - b89b0765695d - - 1a6cdf55390f + - ec368db926f4 + - 289b3807e80c - a16313517e55 - - 6dee4abadccb - fd69c607b43f + - 740fd2d16a28 + - a92a632c4d9b + - 6dee4abadccb + - 1a6cdf55390f + - 2131d7dca455 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -732,8 +732,8 @@ tools: - 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 @@ -785,8 +785,8 @@ 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 @@ -831,12 +831,13 @@ tools: owner: nml revisions: - 3b22de20bd4b - - 4d83eccf5f81 - - 4b9a8031ab74 + - 3548a93b39c1 - aeaa20b96ef2 - - be818ae858e4 - - 141afacabcfa + - 4d83eccf5f81 - 2fd4d4c9c5c2 + - 141afacabcfa + - be818ae858e4 + - 4b9a8031ab74 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index a43ddad63..0551c3018 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - f4d7d5755f01 - 63b74bfc8052 + - f4d7d5755f01 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -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 559fcd7c1..5bd4c74e2 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: - - 94b8c6013083 + - 098506c54016 - 6ae5a7b5a0a2 + - 48c13389050d - bdfbaf0c10aa - - 9eeb13a92d79 - - 098506c54016 - - 8b67dd48fec1 - 2263989660f5 - - 48c13389050d - cd07731e4434 + - 8b67dd48fec1 + - 9eeb13a92d79 - 80f03df2e2ce - 9baa871cb1d1 - a74dbfee5a86 + - 94b8c6013083 - 9422c5a87ee2 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: + - fc2e49f91e52 + - bc3831dd65c1 - 2e093badc689 - d7ce0ec78e51 - - bc3831dd65c1 - - fc2e49f91e52 + - f14193ec1f50 + - c18157c68134 + - 3ff17bad4006 - aaa0d6a8b808 - - d390fe1567dc - - be78f13134e2 - - c44f824c051a - 5abf2c2249aa - - '764845535798' - - 3ff17bad4006 - f0af8936ed41 - - f14193ec1f50 + - d390fe1567dc - 4a60927aaca5 - - c18157c68134 + - '764845535798' + - c44f824c051a + - be78f13134e2 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -60,21 +60,21 @@ tools: - name: gecko owner: iuc revisions: - - 1de657a3198d - 5efbd15675ca + - 1de657a3198d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mafft owner: rnateam revisions: - - a65296ffb4a0 - - 15974dd17515 - f1a5908ea2cb + - bf28a8cff401 - 6f28e90db932 - f0d493f8f84f - - c5908940967d - - bf28a8cff401 + - a65296ffb4a0 - 8e649f27aa0d + - 15974dd17515 + - c5908940967d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter @@ -96,32 +96,32 @@ tools: - name: mummer_mummer owner: iuc revisions: - - bcd65de9725b - 57f042937ba7 + - bcd65de9725b - 48823c9635a4 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - ebe3b0f84de9 - 4fc0cb2ac8ae + - ebe3b0f84de9 - fb43e8887350 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - e18267f90096 - 636b049e6141 + - e18267f90096 - 7cd7a55a678d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - cf3c9489c088 - b4124df98b26 - 959c1f8dae95 + - cf3c9489c088 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index d1a9f63d1..695230dfa 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,10 +8,10 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 9aa9d92c3c51 - - 7c47b3c9e493 - - 18a8d140ec6f - 28928576e1ea + - 18a8d140ec6f + - 7c47b3c9e493 + - 9aa9d92c3c51 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado_trimming @@ -24,8 +24,8 @@ tools: owner: galaxy-australia revisions: - 63d8ecfcfab1 - - fc5b6491cf78 - 6942f170cc43 + - fc5b6491cf78 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: guppy_basecaller @@ -37,12 +37,12 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - fc8804320156 + - cb34f00cc10f - 72b5e9dda577 - a7228a7ea146 - - 79e9a869f40e - - cb34f00cc10f - 0e9e7fcdd543 + - fc8804320156 + - 79e9a869f40e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus @@ -63,15 +63,15 @@ tools: - name: medaka_variant owner: iuc revisions: - - 0f5f4a208660 - edf6d4003fad - - 2bf63b38ee9b - - 43815fa60f3a - 19f3b583a9b3 - - eb746fa6f514 + - 43815fa60f3a - 222669c4afb6 - - ec699520444c + - eb746fa6f514 + - 2bf63b38ee9b - cc36773a3681 + - ec699520444c + - 0f5f4a208660 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -90,13 +90,13 @@ tools: - name: nanoplot owner: iuc revisions: - - 7b379e98b9a9 - a38bdcec9e4c - - a02b8b3f5a0c + - edbb6c5028f5 - 0f1c34698076 - - a3c4fe6f49ab - 645159bcee2d - - edbb6c5028f5 + - a02b8b3f5a0c + - 7b379e98b9a9 + - a3c4fe6f49ab tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign @@ -110,40 +110,40 @@ tools: - 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: - - 449e9aeded2d - d376944466bf - 4857d5bcce52 + - 449e9aeded2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: + - de5b3d8f5b90 - a3afc5f0a96c - bec636361cfd - - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - 5f76b20953e5 - - 543cbeef3949 - 93d623d9979c + - 543cbeef3949 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 @@ -155,8 +155,8 @@ 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 @@ -188,8 +188,8 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - ce8af9373061 - 26e6c9362b7b + - ce8af9373061 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -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 5a37a7982..539ac3fe4 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -66,18 +66,18 @@ tools: owner: iuc revisions: - 97b1b5ad1cda - - 3e73c97f025d - - adfd6bf710bd - d74850cf4e42 + - adfd6bf710bd + - 3e73c97f025d - baceff842902 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: + - 83da94c0e4a6 - 1586b111d2a3 - 9dd107db92c2 - - 83da94c0e4a6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -90,12 +90,12 @@ tools: owner: iuc revisions: - e4b4837f06f5 - - 1e34d2e3d285 - e9ee4d074d5d - - 8c533e19b697 - 2f27f3b86827 - - ed1518ce2237 + - 8c533e19b697 + - 1e34d2e3d285 - edacc4bcd3cb + - ed1518ce2237 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -121,16 +121,16 @@ tools: - 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 @@ -143,8 +143,8 @@ tools: - name: data_manager_fetch_busco owner: iuc revisions: - - 15b97817550a - 2b4526fdf7fb + - 15b97817550a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta @@ -163,15 +163,15 @@ 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: - - 5bcf0e24f42c - 27a6a256cd23 + - 5bcf0e24f42c - 172815da3d41 - b4b2b284230a tool_panel_section_label: None @@ -179,15 +179,15 @@ tools: - name: data_manager_gtdbtk_database_installer owner: iuc revisions: - - 10232d2b5062 - df84aaed4769 + - 10232d2b5062 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d74c740bdb25 - d210e1f185bd + - d74c740bdb25 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -199,16 +199,16 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - fea85c467896 - 19bbd19b74b3 - 87febc68b45b + - fea85c467896 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 7776cb18fdf8 - 0df47f8552f6 + - 7776cb18fdf8 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder @@ -233,19 +233,19 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 4ba60cb14cb0 - 5fe20c915fa6 - - 0cb27ea69dc1 - 9c43baa60906 - - 2c61c30a57e7 + - 0cb27ea69dc1 - d8dc037e3c13 + - 2c61c30a57e7 + - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - 14785f8a3725 - d9339bb8127e + - 14785f8a3725 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite @@ -259,8 +259,8 @@ tools: - name: data_manager_pangolearn owner: iuc revisions: - - 29c738066906 - df30a2f1db55 + - 29c738066906 - ed7a967cb11b - 6e24e79d3d69 tool_panel_section_label: None @@ -280,17 +280,17 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - ad90c2da4f38 - - 1865e693d8b2 - - 3e4d45aca422 - defd3e9ddd2d + - 3e4d45aca422 + - 1865e693d8b2 + - 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 @@ -302,18 +302,18 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - 64deddb6a8ec - 71c994a11f71 - - c520a52b5174 + - 64deddb6a8ec - d63c1442407f + - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 94a50db37d1a - - 9946bc39c834 - 625fd9476402 + - 9946bc39c834 + - 94a50db37d1a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1070,16 +1070,16 @@ 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 owner: bgruening revisions: - c362398df83b - - a22969b08177 - e4b7d1507a75 + - a22969b08177 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes @@ -1091,11 +1091,11 @@ tools: - name: salsa owner: iuc revisions: + - 58a870ef434c - ab5b7f6b7198 - 9a22227bb6d0 - - ba7b0f11e470 - f77f7a7f3b83 - - 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 98db1f432..37d5ae39a 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 @@ -39,65 +39,65 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - d033ffc1c161 - - 3b8b5bde0bd9 - - 3f59ebfbfe3d + - 5a7c56a5cc08 - 107d3ba7024a - - b89cac5156ec - - 26de3a7b1cb9 - 8834daeb9892 - - f73435dc282b - - 5a7c56a5cc08 - - 6a457678efcb + - d7c7ef3353fe - f04a1264e2a2 - 81e66674859e - - c78f3d7dd1db - - cce7b18495e4 + - 26de3a7b1cb9 - a6619171428e - - d7c7ef3353fe + - 3f59ebfbfe3d + - c78f3d7dd1db + - f73435dc282b + - 3b8b5bde0bd9 + - b89cac5156ec + - 6a457678efcb - '841557158611' + - d033ffc1c161 + - cce7b18495e4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 6223845127ea + - 3b96e92e8ec3 + - 02b8758214b0 + - 6a726db04d4b - 5b777002c2de - b0af57c1a968 - 88c4aa435ded - - 7a2092844346 - - 02b8758214b0 - - a185b079b095 - - 6a726db04d4b + - 6223845127ea - df47d4845b62 - - e75442c7f4da + - 4755f52427c4 + - a185b079b095 + - 5fcd1ece3a6e + - 659517798cc4 + - 7a2092844346 - aa8cc71438cf + - e75442c7f4da - 6283babe736e - - 659517798cc4 - - 5fcd1ece3a6e - - 3b96e92e8ec3 - - 4755f52427c4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 70acec670c30 + - f87ac61981f0 - f97743d52b87 + - d1c340a5664b + - 70acec670c30 - 524d31add34a + - 111bd54f6bc4 - b8476e82ac20 - - d1c340a5664b - 24d024316465 - - f87ac61981f0 - - 111bd54f6bc4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: + - feb40665d7cd - daddf188c13f - 4f6349228462 - - feb40665d7cd - 9e10ba792be2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -110,33 +110,33 @@ tools: - name: pangolin owner: iuc revisions: - - 2f1019071464 - - 7bb8726be37c - - 81804a978fc0 - - ca0d8cf80567 - 9d61d3fa046c - - a2099fb98cdb - b6abccb1f25b - - abf6dbe8c9d7 - - 14ae456b8cc5 - - 2fa9d4f1b48f - - ca337cce3888 - - 83a69484cb87 - - 437e28791761 - - 36912871ccdc + - 8ad84c5753ea + - 7bb8726be37c - b7e297c2ede6 - 42a174224817 + - ca337cce3888 - 5f8727ff21e7 + - abf6dbe8c9d7 + - ca0d8cf80567 + - 2f1019071464 - 3a43c3982401 - - 8ad84c5753ea + - 81804a978fc0 + - 437e28791761 + - 2fa9d4f1b48f + - 83a69484cb87 + - a2099fb98cdb + - 14ae456b8cc5 - 03ed9524dcd1 + - 36912871ccdc tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 7157a5b34a68 - 2bf47d57ebb5 + - 7157a5b34a68 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -148,23 +148,23 @@ tools: - name: raxml owner: iuc revisions: + - a4b71be30c3c - 29ff6a849eac + - ba29b5e2a4be - b1e68bbe4cef - 73a469f7dc96 - - a4b71be30c3c - - ba29b5e2a4be - ea30d3089354 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - e88a7de55d6e - dbe2b2204555 - 9b2b122d0415 - f1ccc8a6eb05 - - 809e42326fc2 - - 91887494eb97 + - e88a7de55d6e - 15ac71df11a0 + - 91887494eb97 + - 809e42326fc2 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 3287e1d83..8dac0d77d 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - b502c227b5e6 - - 881d7645d1bf - 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name: cardinal_mz_images owner: galaxyp revisions: - - ae304a72db7b - 80600735685d - a69865da6f80 - 25b83cbd596a - 59e85306eae5 - a95a82eb4d50 + - ae304a72db7b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - e0669b1854b1 - - 611d80c0e29d + - f1897eb07081 - 83aac7741200 - - ed9ed1e6cca2 + - e0669b1854b1 - 798da6bdff3d - - f1897eb07081 + - ed9ed1e6cca2 + - 611d80c0e29d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 74b61bf5bc4b - - d426a9107a6c - a7fb9b395ddf + - d426a9107a6c - 5a35e3a8d013 + - 74b61bf5bc4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - cc430977c8ff - 91f0f5922011 - 82f6c2f4332d + - cc430977c8ff - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - 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7f6a1f27553e - fb52e95a370c - - c8b225c69a7f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -616,14 +616,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: + - 07ff622ec007 + - 3ec27b4cee7c - 3634c90301af - 1beff3ddce58 - - a72c48001f7c - - 3ec27b4cee7c - 7fdd9119cc4f - 943a34df6047 - - 07ff622ec007 - da885ca16cb2 + - a72c48001f7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -683,11 +683,11 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 265c35540faa - - a371252a2cf6 - 4ddc8da62671 - 1a5690a5eedc - 12692567c7f9 + - a371252a2cf6 + - 265c35540faa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/staging.gvl.org.au/qiime_2.yml b/staging.gvl.org.au/qiime_2.yml index bf015d3f9..52697721b 100644 --- a/staging.gvl.org.au/qiime_2.yml +++ b/staging.gvl.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 10447a4b0cc3 - 18c6b2b6740f + - 10447a4b0cc3 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index a140a5a55..8ccb5de09 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 289b7d6b69a4 - - 2f1d464ebfd2 - - cd5f98911089 - 110a346daf36 - - 42201b90e3f4 + - 2f1d464ebfd2 - e345aadf914f + - 42201b90e3f4 + - cd5f98911089 + - 289b7d6b69a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -19,12 +19,12 @@ tools: - name: stacks2_cstacks owner: iuc revisions: + - 0345dbaaa79b + - c207119ba5f6 + - fcce77c09289 - 42d9087b4789 - 0cd2df8af811 - - fcce77c09289 - 8501601a118d - - 0345dbaaa79b - - c207119ba5f6 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: - - 405a212b32ab - - 33486216eec0 - 421c33b8bf17 - - 89eb29319bf4 - - 04db7fd6b238 - ad5ab22ffe24 + - 04db7fd6b238 + - 33486216eec0 + - 405a212b32ab + - 89eb29319bf4 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: - - 7b72fde3d27e - - 1d839ead7ad3 - - eb784fa07f80 - - f6e91108b7b1 - fa51dc5e8386 + - f6e91108b7b1 + - eb784fa07f80 - 7370bb65bad4 + - 1d839ead7ad3 + - 7b72fde3d27e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -71,11 +71,11 @@ tools: owner: iuc revisions: - 3d70c2996730 - - d30e36c48c93 - - 8a55d29c8fcf - - c9b77ced9a78 - a3e86cd9cac7 + - 8a55d29c8fcf - 1544278c272e + - 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: - - 887cf585cafc + - a5969aa9347e - 7b881f5f5ad5 - - e2db212d64ad - b242deb58952 + - 887cf585cafc + - e2db212d64ad - 564c33e5c3e3 - - 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 - 8cff84759bf6 - - e897c74a48bb - b4bab607eb05 - 9a171f9a450b - - bd5ff77e2036 + - e897c74a48bb tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad @@ -120,11 +120,11 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 887e0991eb24 - - 5e10f396979e - 6dafad990086 - - adc7a7610d4f - 33f0793edf93 + - adc7a7610d4f + - 5e10f396979e + - 887e0991eb24 - 4f65e343ecdf tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -138,11 +138,11 @@ tools: owner: iuc revisions: - 4e280b27a831 - - 43e3eeb2e0ec - c287418eb288 - - 97575d01f06b + - 43e3eeb2e0ec - 17d39bf0a63a - c5d7050e4ad7 + - 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: - - 0b8c84a7fdb5 - - a819ec3b362d - 09b8edb56d80 + - cd034465d4a4 - d9bf483266a1 + - a819ec3b362d - 9586f08634c0 - - cd034465d4a4 + - 0b8c84a7fdb5 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: - - 69842dd5aa48 - - 2645575d1bf2 + - bf0e43ab0416 - 95351dd0fd3f - - a4b4bd84f69e - a9c34a289493 - - bf0e43ab0416 + - a4b4bd84f69e + - 2645575d1bf2 + - 69842dd5aa48 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - d1fda11e602f - - bb0475c884ff - 8a35a3bc6752 - d033e1ccb386 - - cfb504394ae1 + - bb0475c884ff - 912f904a6e1e + - d1fda11e602f + - cfb504394ae1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -236,8 +236,8 @@ tools: owner: iuc revisions: - d504d945a655 - - 95286af4139b - d1fad35bdb4a + - 95286af4139b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -267,8 +267,8 @@ 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/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 997be0706..6c70e7f6c 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,26 +2,26 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 2d4e3aff9dc7 - cf01dd6c6b1f - - 31f8063eedea - 7acb00fc980a + - 2d4e3aff9dc7 + - 31f8063eedea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 7a5a2d28c539 - - 32e542c2a773 - 703a2cb3fb38 + - 32e542c2a773 - 125d20cb23d7 + - 7a5a2d28c539 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 3d61a698e5e1 - 45c2ec061cf9 + - 3d61a698e5e1 - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -34,8 +34,8 @@ tools: - name: blockclust owner: rnateam revisions: - - dbb6ee3179bc - aab6cf87b40a + - dbb6ee3179bc tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockclust @@ -77,8 +77,8 @@ tools: - name: cuffcompare owner: devteam revisions: - - f648e5180e40 - ad5d061fbdf2 + - f648e5180e40 - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -106,10 +106,10 @@ tools: owner: devteam revisions: - 86285ddd4512 - - cf747d1bd79a - - 6a6717a5f421 - 22cf48ad7b16 - 04adc9db1581 + - 6a6717a5f421 + - cf747d1bd79a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -121,9 +121,9 @@ tools: - name: cuffnorm owner: devteam revisions: - - 28b94cfbfdb9 - 9a854107dbb2 - 6cbfede05833 + - 28b94cfbfdb9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -161,9 +161,9 @@ tools: owner: iuc revisions: - 8f0181aacb7a + - 0693ccd171c4 - e3b16fd7dd08 - 3b36efd62b3e - - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -179,9 +179,9 @@ tools: - 0696db066a5b - cd9874cb9019 - 9a882d108833 - - d027d1f4984e - - 8fe98f7094de - 24a09ca67621 + - 8fe98f7094de + - d027d1f4984e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -193,11 +193,11 @@ tools: - name: dexseq owner: iuc revisions: - - b47c006d90c5 + - df929f257179 - 62adf13b86ea + - b47c006d90c5 - 2872c633f07e - 9a7c5b6d8f1e - - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -209,18 +209,18 @@ tools: - name: edger owner: iuc revisions: - - 334ce9b1bac5 - - 9bdff28ae1b1 - - a8305cf0c951 - - 555659de7321 - - 0cb907a2a810 - - 070900306913 - df0c8d0a5992 - 3d89af8a44f0 - - 6e53e565fc6a + - ae2aad0a6d50 + - 334ce9b1bac5 - f2843df56434 - 5bf899c13979 - - ae2aad0a6d50 + - 555659de7321 + - 6e53e565fc6a + - 0cb907a2a810 + - a8305cf0c951 + - 070900306913 + - 9bdff28ae1b1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -232,8 +232,8 @@ tools: - name: egsea owner: iuc revisions: - - fba1660fb717 - 31ea4992b948 + - fba1660fb717 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -251,18 +251,18 @@ tools: - name: featurecounts owner: iuc revisions: - - 1b851f87fbe0 - a56fbe2d6ba7 - 7db9d3ea71c9 + - 90d16db017d7 - 6f66ae7c5f7a - - af814359d244 - - f3a5f075498f - e6a2a912677a + - af814359d244 - f9d49f5cb597 + - 1b851f87fbe0 - a37612abf7f9 - - 38b6d12edc68 - ea04b737afa0 - - 90d16db017d7 + - f3a5f075498f + - 38b6d12edc68 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -292,9 +292,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 3c97c841a443 - 0f710191a66d - 3c5e024a18cf + - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -312,13 +312,13 @@ tools: - name: hisat2 owner: iuc revisions: - - 26371a1df031 - - 6ab42baa56e9 + - d4b55e2beb12 - 3fb01a8c902d + - 6ab42baa56e9 + - f4af63aaf57a + - 26371a1df031 - 6c19daec423d - - d4b55e2beb12 - a86e80d3c09c - - f4af63aaf57a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -337,8 +337,8 @@ tools: owner: lparsons revisions: - 4418229c501e - - 67b0b160903a - 916cb26bd9d3 + - 67b0b160903a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -357,8 +357,8 @@ tools: owner: iuc revisions: - 5ae5c312d718 - - ce5d418183c5 - 87c11c05d238 + - ce5d418183c5 - 01247aaf0a10 - 1c75aa5de15e tool_panel_section_label: RNA-seq @@ -373,8 +373,8 @@ tools: owner: iuc revisions: - 4f9c4e6566e5 - - 10c98fab6c5a - c971db6f0fe5 + - 10c98fab6c5a - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -387,14 +387,14 @@ tools: - name: limma_voom owner: iuc revisions: - - 708348a17fa1 - - 32511f586472 - 58c35179ebf0 + - 32511f586472 + - 0921444c832d + - 708348a17fa1 - 119b069fc845 + - 97e06a4c7c75 - e827f9aae031 - d6f5fa4ee473 - - 97e06a4c7c75 - - 0921444c832d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -443,8 +443,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - d696cf0a9622 - 72927fc9e9ed + - d696cf0a9622 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -462,21 +462,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 3ea5a2a63fa2 - - b0f2be869d6d - - e132e7d02a3e - - c7c55b694974 - - 4df95e2d7f61 - - 980d2a2e1180 - 5ec75f5dae3c - - c772497b2c32 - - 79de45b5069b - 0a563fd2f22e - - 99b17b74a8cd + - e132e7d02a3e + - 79de45b5069b + - b0f2be869d6d + - 3ea5a2a63fa2 - 53255f6eecfc - - 7ed2edc1337f + - c7c55b694974 + - 4df95e2d7f61 - 4074fc1940e2 + - 7ed2edc1337f + - 99b17b74a8cd + - c772497b2c32 - b9e04854e2bb + - 980d2a2e1180 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -500,13 +500,13 @@ tools: - name: salmon owner: bgruening revisions: - - f4d5237a84f6 + - 15cd64d7c58b + - 49121db48873 - 2c0ca397d302 - ebab418107f5 - - 15cd64d7c58b + - f4d5237a84f6 - e3d32471da11 - 53e9709776a0 - - 49121db48873 - cc05793bb896 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -519,23 +519,23 @@ tools: - name: seurat owner: iuc revisions: - - 56242ff81c84 - - 8c28affc7c48 - - c0fd285eb553 - fab6ff46e019 + - c0fd285eb553 + - 8c28affc7c48 + - 56242ff81c84 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 258d696dbd7e - - cef79931dda5 + - 1ebd14235b92 + - ae618321f34a + - 76d290331481 - 914cfcba0ec8 + - cef79931dda5 + - 258d696dbd7e - cbf488da3b2c - dd4df992d93d - - ae618321f34a - - 76d290331481 - - 1ebd14235b92 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -571,10 +571,10 @@ tools: - name: transdecoder owner: iuc revisions: - - d0d4cef4f967 - - c6334cb383ff - - ffd1300599a1 - 0db979fead3a + - ffd1300599a1 + - c6334cb383ff + - d0d4cef4f967 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -586,9 +586,9 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - d6a479fd4281 - - ba3720d7e68b - 74217fbfba4d + - ba3720d7e68b + - d6a479fd4281 - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -601,9 +601,9 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 2fb4ee002432 - c2b82a94493e - 56162e446004 + - 2fb4ee002432 - 478f36effca1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -616,9 +616,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: + - 3f4094b6a565 - fab23c3b5258 - 9ff3765e7172 - - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -630,9 +630,9 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: + - 4687ecf0eb2d - 870ac06dff8e - 34a018cbee9c - - 4687ecf0eb2d - be3f26533209 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -645,10 +645,10 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - c5fbddcac63a - - 65e7dea767ea - 5192f657f305 - 33406f5a445c + - c5fbddcac63a + - 65e7dea767ea - 05ab8d5e04a2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -661,10 +661,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d + - 6f0fb35b799c - a35cba31d904 - e406ac71165d - - 6f0fb35b799c + - 1fdb25a8384d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -676,8 +676,8 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - c2c039e421af - 964b7efe2639 + - c2c039e421af - 37a1129c89d2 - 7c7fbf13aadd tool_panel_section_label: RNA-seq @@ -691,10 +691,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 1d689e4e1caf - - eafea3083352 - 047c22569787 + - 1d689e4e1caf - 24e94d84adc9 + - eafea3083352 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -706,9 +706,9 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 9871104ea630 - - 1812dbc5bb7b - 04bb8bb7c198 + - 1812dbc5bb7b + - 9871104ea630 - 3a4ac03d1266 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -733,15 +733,15 @@ tools: - name: trinity owner: iuc revisions: + - 9fa24d5aac68 - 8f1c3df4dd49 - 48636f857c4b - d84caa5a98ad + - d2bc35f3d1c5 - 32b86cd8eb50 + - db1f362cca3e - c9cfec002f71 - cee61b3fcf78 - - d2bc35f3d1c5 - - 9fa24d5aac68 - - db1f362cca3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -753,10 +753,10 @@ tools: - name: trinotate owner: iuc revisions: - - 2b093007fab9 - 6fd16fad465d - 4383070d29ed - 9e61bc67866f + - 2b093007fab9 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 a0868c72e..e03e93b4c 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: - - 1a052c827e88 - 080fd5739bb4 + - 1a052c827e88 - 473382134e56 - 27e16a30667a tool_panel_section_label: RSeQC diff --git a/staging.gvl.org.au/sambam.yml b/staging.gvl.org.au/sambam.yml index a5c4bcebc..5c3f724a7 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 @@ -16,10 +16,10 @@ tools: - name: bamtools_filter owner: devteam revisions: - - 993b19f20c76 - 1dfd95ee241e - - 108db6635177 - cb20f99fd45b + - 993b19f20c76 + - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -63,8 +63,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - ef11139d4545 - 9c1c0b947e46 + - ef11139d4545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -82,8 +82,8 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 30a201c9c310 - e7fd6754d093 + - 30a201c9c310 - 5f8e69cc4c6e - 19ece8afbaab tool_panel_section_label: SAM/BAM @@ -97,8 +97,8 @@ tools: - name: qualimap_multi_bamqc owner: iuc revisions: - - e38af83df163 - 17b35d23731f + - e38af83df163 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -149,9 +149,9 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - dc6ff68ea5e8 - - 56c31114ad4a - 649a225999a5 + - 56c31114ad4a + - dc6ff68ea5e8 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip @@ -163,9 +163,9 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 9149ad20699a - 6856f8a01905 - 46c6639921f1 + - 9149ad20699a - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -178,10 +178,10 @@ tools: - name: samtools_calmd owner: devteam revisions: - - 33208952b99d - - 26b4f9f98aca - 92ec40abcdcf + - 26b4f9f98aca - 06dc50b7b711 + - 33208952b99d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -205,11 +205,11 @@ tools: - name: samtools_fastx owner: iuc revisions: - - a8d69aee190e - - 720217c23995 + - b906586a6596 - b3d99709fe1a + - 720217c23995 + - a8d69aee190e - 66e23b11feae - - b906586a6596 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -221,17 +221,17 @@ 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 owner: devteam revisions: - - db17d5321bad - - cc61ade70eb8 - 22970df7a40e + - db17d5321bad - fe34990e5ce7 + - cc61ade70eb8 - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -244,11 +244,11 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - fa5d3e61e429 - 7a6034296ae9 - - 88b8c2916784 - 7def34e6cf4d + - 88b8c2916784 - 811fc2d75ad4 + - fa5d3e61e429 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -267,21 +267,21 @@ tools: - name: samtools_merge owner: iuc revisions: + - 65a38e8c8e2a + - cae2794d2deb - b40e2d865d52 - 36677f429310 - 740ce0a18f0d - - 65a38e8c8e2a - - cae2794d2deb tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 583abf29fc8e - - fa7ad9b89f4a - b61f5d6a7f25 - - 9da0311ab1dd + - fa7ad9b89f4a - 329deb17a9f7 + - 583abf29fc8e + - 9da0311ab1dd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -293,8 +293,8 @@ tools: - name: samtools_phase owner: devteam revisions: - - 1e5880498f52 - b5c3b1856370 + - 1e5880498f52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -306,9 +306,9 @@ tools: - name: samtools_reheader owner: devteam revisions: - - db000c6007a0 - bb8cfc6f6e0c - 30388d878f81 + - db000c6007a0 - 85e38b31e8b3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -341,10 +341,10 @@ tools: - name: samtools_sort owner: devteam revisions: - - 6c2c1836728b - cab3f8d35989 - d54a4df48867 - e613c1ad4c4c + - 6c2c1836728b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -356,12 +356,12 @@ tools: - name: samtools_split owner: devteam revisions: - - 5d9ae78f34d3 - - 135c85f4cfaf + - bcedabb53ddf - bd850490c7f1 - b7f7826ef1cd - 818030fa6bbf - - bcedabb53ddf + - 135c85f4cfaf + - 5d9ae78f34d3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -373,12 +373,12 @@ tools: - name: samtools_stats owner: devteam revisions: - - 3a0efe14891f - - 5a08c09b9311 - 541082d03bef - - 24c5d43cb545 + - 5a08c09b9311 - 1cc79f49b8d5 - 145f6d74ff5e + - 3a0efe14891f + - 24c5d43cb545 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: - - 6be888be75f9 - - 350bbc5c2ffd - - b01db2684fa5 - 2dce91e11ca7 - - 32dc5f781059 + - c370440f901e - bf328cec6a42 - b72793637686 - - 5826298f6a73 - 0dbf49c414ae - - c370440f901e + - 5826298f6a73 + - b01db2684fa5 + - 6be888be75f9 + - 350bbc5c2ffd + - 32dc5f781059 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 b070fb4fc..b443f9d44 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -8,13 +8,13 @@ tools: - name: ena_upload owner: iuc revisions: - - a62c4a11a67d - - ea5e944f447d + - 59bb6d34fca6 - 5cb6146337d8 - - 480d9e9d156b + - 6f6537780379 - d147d6455873 + - 480d9e9d156b - 4aab5ae907b6 - - 59bb6d34fca6 - - 6f6537780379 + - a62c4a11a67d + - 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 080221143..4a54e5d5a 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -8,31 +8,31 @@ tools: - name: alevin owner: bgruening revisions: + - e32b215b7c04 + - e4c01dcece8b - ecb9ea6269ee - b0fe3e482cb7 - f2000bc73102 - - e4c01dcece8b - - e32b215b7c04 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - e1c3c2f2a834 - - 7a6655aa6eb2 - 707023fa62fe + - e1c3c2f2a834 - c0b037b12765 + - 7a6655aa6eb2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: + - 93dd15e13e6a - 00712416fdaa - - 55e35e9203cf - fb9e030ffae4 - - 93dd15e13e6a - - 6f143dfe902a - 32e547223c9e + - 6f143dfe902a + - 55e35e9203cf - cfc3f5a57dc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -45,13 +45,13 @@ tools: - name: anndata_inspect owner: iuc revisions: - - 39e945f0b2c1 - - 038e32885fec - b9fac48532eb - - 6f0d0c784f09 - 14c576ea6148 + - 39e945f0b2c1 - ee98d611afc6 + - 6f0d0c784f09 - 688357ad5e61 + - 038e32885fec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -63,13 +63,13 @@ tools: - name: anndata_manipulate owner: iuc revisions: + - c4209ea387d4 - d4af736e7b83 - - b85871dd69f9 + - ed4996a16f7f - 3d748954434b - 43cb7b5a6fe7 - - ed4996a16f7f - 9bd945a03d7b - - c4209ea387d4 + - b85871dd69f9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -81,11 +81,11 @@ tools: - name: anndata_ops owner: ebi-gxa revisions: - - a4774b7b2e85 - 7ebc22f77d86 + - a4774b7b2e85 + - fe75d2414dc0 - 2e8022f1923c - 890fb06a2893 - - fe75d2414dc0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d @@ -100,28 +100,28 @@ tools: - name: baredsc_2d owner: iuc revisions: - - 344c2af50552 - - c29e7bb492bf - a90f8efe08b4 - aa4a6f0916b4 + - c29e7bb492bf + - 344c2af50552 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: + - 5b7c81b35b89 - b13d3e4c48e1 - - 050cf43887d3 - c32347702e12 - - 5b7c81b35b89 + - 050cf43887d3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - 02fc39c8610d + - 239193b96d72 - ae969fdb8442 - 1d77986f9ddc - - 239193b96d72 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -157,11 +157,11 @@ tools: - name: dropletutils owner: iuc revisions: - - a9caad671439 - - 8855361fcfc5 - - cfe1e6c28d95 - - 2c1200fba922 - cdf4443d5625 + - 2c1200fba922 + - cfe1e6c28d95 + - 8855361fcfc5 + - a9caad671439 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -197,9 +197,9 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - fb7068d30ec9 - - 952abbc4b1de - c3ffb2c1e314 + - 952abbc4b1de + - fb7068d30ec9 - 01c37e54e86e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -207,45 +207,45 @@ tools: owner: bgruening revisions: - 9d42a6133690 - - 45828071edc3 - - f1c35f3f310d - 57aeaf6b237d + - f1c35f3f310d + - 45828071edc3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 23b8d6b8960c - - cab616fe7e64 - 163fd744e235 - 1a31e75e979e + - cab616fe7e64 + - 23b8d6b8960c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - '920526260066' + - b9ab56aecd18 - 013e53ccc7ac - f47ac4a0b337 - - b9ab56aecd18 + - '920526260066' tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - - 9ea228a9afc8 + - a63e9713c39d - f6a169b5e43b + - 9ea228a9afc8 - b892fa1fcaec - - a63e9713c39d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - ff1af7bac1cb + - 640e0e45518a - f8320df1866b - 45a386d18509 - - 640e0e45518a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel @@ -260,45 +260,45 @@ tools: - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - 37125838e360 - - f881c94fb3b3 - c4ed35f4f77f - 40fee49bc6c3 + - f881c94fb3b3 + - 37125838e360 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - - e06265d204f6 - - 782bdcb775fb - e8760fc0e29b - 2dccb6bb0add + - 782bdcb775fb + - e06265d204f6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - b05f662f9f35 - 30677e95bc89 - - 63c8377c58b3 + - b05f662f9f35 - f0216498a666 + - 63c8377c58b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions owner: bgruening revisions: - - fe3aa71590d5 - - c72fa6cb8817 - 3240e8a7c54f + - c72fa6cb8817 - 8a11d70b6cd8 + - fe3aa71590d5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 3ee5332bf57c - 4f9305d3bb34 - e03780179ee5 + - 3ee5332bf57c - 5dd1aae12f03 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -307,78 +307,78 @@ tools: revisions: - 3a6a5381db36 - 87eb9c58cd19 - - 4401ed529d2c - a315574104c6 + - 4401ed529d2c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - 2ba6cee8e4db - - a83732c79949 - - c0737631eea1 - 574f295b5ba4 + - c0737631eea1 + - a83732c79949 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - ea19190ce5e0 - - 30d7390bc918 - - 62b720dceb56 - 937b7b9832d0 + - 62b720dceb56 + - 30d7390bc918 + - ea19190ce5e0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - 2786a931cad2 + - cd40ca76865a - 2b4d6a8dab36 - 0f5786ffa10d - - cd40ca76865a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops owner: bgruening revisions: - - bf9379529c3e - 4375e25de06a - - 0410b6aada45 - ffc33339cd3e + - bf9379529c3e + - 0410b6aada45 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: - - 5dfba24d7bdd - - 77d8e0fd162a - - 4977f65da0ff - 07dd436ea686 + - 4977f65da0ff + - 77d8e0fd162a + - 5dfba24d7bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - f1b3902f8baf + - f0b1bd38745a - 6c5097f6d41e - 972dcccb5bbc - - f0b1bd38745a + - f1b3902f8baf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - bb8849fca57c - - 7f7c6ead2d0d - 409396ea5cf0 + - 7f7c6ead2d0d + - bb8849fca57c - 3e5c86c2f80d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo owner: bgruening revisions: - - b0f33533181d - e4f8fceab96a + - b0f33533181d - 51e40e9b6c3c - 7fbd6feba1ca tool_panel_section_label: Single-cell @@ -386,91 +386,91 @@ tools: - name: hicexplorer_hicinterintratad owner: bgruening revisions: - - 55b013e59018 - - 32173084d53f - c261b6b05ee3 + - 32173084d53f + - 55b013e59018 - 908fa330b93b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains owner: bgruening revisions: - - b6b8c8672756 - - b376ef118807 - 4b194e675916 + - b6b8c8672756 - febfddb0b3e8 + - b376ef118807 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - - ed900cd4a0a9 - - 910c6a1c3a27 - - 1511a8ebe906 - 1d9799f4b854 + - 1511a8ebe906 + - 910c6a1c3a27 + - ed900cd4a0a9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - - f34ab9882252 - 2aa5b6b65197 - 6d042c96aceb - 5e83c077e31d + - f34ab9882252 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: - - 3f1b286a5c34 - dd9988943f53 - - 9b383d429659 + - 3f1b286a5c34 - ea5d67ec94ab + - 9b383d429659 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - - 6326cd29c1c3 - - 06ced663d24f - - 89cfe7de541b - 11f39d7f6c64 + - 89cfe7de541b + - 06ced663d24f + - 6326cd29c1c3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - b4e780e93c91 + - 1602cc5b673c - beb5b5917d2f + - b4e780e93c91 - 337705015ee8 - - 1602cc5b673c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: + - 8d203e74869b - a10fce08c2dc - - e285920f8585 - 58de3c7c8e89 - - 8d203e74869b + - e285920f8585 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicquickqc owner: bgruening revisions: - b13e7a200525 - - ea8fb5e899e8 - - 21d859ad4502 - 5cbd7a902a8d + - 21d859ad4502 + - ea8fb5e899e8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: + - 36dfa2825a59 + - 1d6af10874d5 - d74cf4a61d65 - f81750434d70 - - 1d6af10874d5 - - 36dfa2825a59 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -489,29 +489,29 @@ tools: owner: bgruening revisions: - f36828ebdc54 - - df64cc4dfb4d - - 27fe5cd1729c - 1de2276f633f + - 27fe5cd1729c + - df64cc4dfb4d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - d890828ab02a - - 11a3385e03b5 - - cef9fb4ece1c - 1d201e8378b3 + - cef9fb4ece1c + - 11a3385e03b5 + - d890828ab02a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: - - db575b4c8b22 - - e98619de2776 - - 59be31ac9dc3 - eeab712b0b99 + - e98619de2776 + - db575b4c8b22 - 4b0adaa31c95 - 7784821452ac + - 59be31ac9dc3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -523,23 +523,23 @@ tools: - name: music_construct_eset owner: bgruening revisions: + - 48f0fb3061b1 - 7ffaa0968da3 - 2cfd0db49bbc - - 48f0fb3061b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 8cd2ecfa2e61 - 56371b5a2da9 + - 8cd2ecfa2e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset owner: bgruening revisions: - - 8c64a2da3869 - fde4c972e7c5 + - 8c64a2da3869 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -557,11 +557,11 @@ tools: - name: raceid_clustering owner: iuc revisions: - - f911a64454fb - - a4b734cd253b - - 49776718ae90 - 7e014059a88d + - 49776718ae90 - c4f39bf4a068 + - f911a64454fb + - a4b734cd253b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -573,10 +573,10 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: - - 8b917923f7d4 - - 7608d5faee41 - 43c146e25a43 - d45f092caf24 + - 8b917923f7d4 + - 7608d5faee41 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf @@ -588,8 +588,8 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: - - 37a47c4fd84d - 2b0d3e2f402a + - 37a47c4fd84d - c7ddb719554d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -602,8 +602,8 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - 69018f285aa3 - df8e4e54d367 + - 69018f285aa3 - 6e90c8adf84f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -644,17 +644,17 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: + - b2df381a6004 + - 4d8f983cd751 + - 77b91b9bdf52 - f9353ee6a0d4 - - cb43c5d3acd3 - 38db3fef7aad - edec35114f72 - - 77b91b9bdf52 - - 4d8f983cd751 - - b2df381a6004 - 8983e7a04ba7 - - aaa5da8e73a9 - 6acb08931836 + - aaa5da8e73a9 - 6f83f8fd381f + - cb43c5d3acd3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -666,16 +666,16 @@ tools: - name: scanpy_filter owner: iuc revisions: - - 72a6bebab2a5 - - 277313130da5 - - 64388be6d510 - - a03ff8633507 - b409c2486353 - - d636ce5cde16 - - fc0321c000a3 - 8cb783c81905 - - 3c86f71498bc - a97abb8cd15b + - 277313130da5 + - 72a6bebab2a5 + - fc0321c000a3 + - a03ff8633507 + - 3c86f71498bc + - 64388be6d510 + - d636ce5cde16 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -687,17 +687,17 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - 6bd82ed14acd - - 18262103fa61 + - 3081ff5c84a3 - 5e9171dc8244 - - c5d3684f7c4c - - c0a80a16560f - f54f0f0598ad - - 6c145a6868cc + - c0a80a16560f + - c5d3684f7c4c - cc0deb593fc8 - - 5c3ebe2adc77 - d86cb2ce311b - - 3081ff5c84a3 + - 6bd82ed14acd + - 6c145a6868cc + - 18262103fa61 + - 5c3ebe2adc77 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -709,17 +709,17 @@ tools: - name: scanpy_normalize owner: iuc revisions: - - c9cb76cf8d6c - - 56c0d4acef02 - - 3bcd5445cd7a + - 94c19fb1281c - 9f354c7c8c92 + - d844935c906c + - 56c0d4acef02 - 4bda4412b8c2 + - c9cb76cf8d6c + - 3bcd5445cd7a - 7b9fafe32c86 - - d844935c906c + - 146ae5d70b47 - a407e7f8bdc1 - - 94c19fb1281c - ab55fe8030b6 - - 146ae5d70b47 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -731,17 +731,17 @@ tools: - name: scanpy_plot owner: iuc revisions: + - 9b0cdb8cf6be + - 40812a65a78b + - aa0c474463c2 + - 62acdd96d4a0 - 7647e5cd1b8b - 6adf98e782f3 - - 40812a65a78b + - 0185bd174ea0 + - 95777145cb92 - dbbe1ea8ecb1 - 6f5349dd5c49 - - aa0c474463c2 - - 0185bd174ea0 - - 9b0cdb8cf6be - f7446fd8d5e7 - - 95777145cb92 - - 62acdd96d4a0 - 1072ce66b426 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -754,17 +754,17 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - 9fb627495ec2 - - 458e8f43a775 - - 215733a383f2 - - bf2017df9837 + - a39040ae0a38 + - 73ab2ac53d06 + - fe8f16c594ec - f2f6c703da06 + - 215733a383f2 - c65fce500915 - d18e7a6e5cd4 - - fe8f16c594ec - - a39040ae0a38 - c5541bfb8feb - - 73ab2ac53d06 + - 458e8f43a775 + - 9fb627495ec2 + - bf2017df9837 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -777,8 +777,8 @@ 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 @@ -790,9 +790,9 @@ tools: - name: scater_filter owner: iuc revisions: + - 7a365ec81b52 - b7ea9f09c02f - 652923ce664f - - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -810,9 +810,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 81e5bdff4853 - - ef4c80837bc5 - 2e41b35b5bdd + - ef4c80837bc5 + - 81e5bdff4853 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter @@ -830,8 +830,8 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 46fc6751d746 - 9e5c0bb18d08 + - 46fc6751d746 - c99ba278dfa9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -1054,15 +1054,15 @@ tools: - name: sinto_barcode owner: iuc revisions: - - d1b34ac42b8f - fb61eb03e313 + - d1b34ac42b8f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: sinto_fragments owner: iuc revisions: - - 6f66f523a9b7 - 29e6bfb2cf49 + - 6f66f523a9b7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: slice_image @@ -1074,15 +1074,15 @@ tools: - name: snapatac2_clustering owner: iuc revisions: - - d3ea0ba3d066 - 8f8bef61fd0b + - d3ea0ba3d066 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 588c811fdd48 - 64fa083411f1 + - 588c811fdd48 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting @@ -1108,8 +1108,8 @@ tools: - name: velocyto_cli owner: iuc revisions: - - 883c33ef3372 - 90e95e9ee190 + - 883c33ef3372 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: vitessce_spatial diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index 48c974bce..ea53e1d0a 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -33,10 +33,10 @@ tools: owner: iuc revisions: - 2f3c6f2dcf39 + - 562f3c677828 - 746e8e4bf929 - 419027d822d6 - 4c07ddedc198 - - 562f3c677828 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass @@ -49,8 +49,8 @@ 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 @@ -63,16 +63,16 @@ tools: - name: dwt_var_perclass owner: devteam revisions: - - 781e68074f84 - cb422b6f49d2 + - 781e68074f84 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - - cb1c59d69557 - - 6c29c7e347e8 - 7a15159140d1 + - 6c29c7e347e8 + - cb1c59d69557 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 - 7442b94d6a1e - - 840f29aad145 + - aef56d0e7a61 + - 9c3e1d3235c8 - b1eda492f063 + - 840f29aad145 - 4c4ec859c31a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 07843f917990 - 30d21a6041f6 - - 9fda0b82f419 - 375bbd555f4a + - 07843f917990 + - 9fda0b82f419 - d0352e8b4c10 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -144,19 +144,19 @@ tools: - 2c58b83c9bad - 8b1b2b91f8d0 - 4cc980df6265 - - cd02bf168d23 - 7ae443e6217d + - cd02bf168d23 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - e10e776f2109 - - ad7e0b4291ee - - 4bbaf77573ef - 7dd3fb35904f - 1dd433d2c92c - bb9fc9d46ea4 + - 4bbaf77573ef + - ad7e0b4291ee + - e10e776f2109 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 06da6b52b..ad33d4d07 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 @@ -27,22 +27,22 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - f18f67056946 - 6c6d26ff01ff + - f18f67056946 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: - - 626658afe4cb - 9cd341095afd - 464b9305180e - aff5135563c6 - - 02026300aa45 - - 6e8d94597139 - 13b6f0007d9e - - 6595517c2dd8 - be25c075ed54 + - 6595517c2dd8 + - 626658afe4cb + - 02026300aa45 + - 6e8d94597139 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -79,11 +79,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 34d29339abab - - 90f657745fea + - 37cde8134c6a - 9cc411a62277 - 557ec8d7087d - - 37cde8134c6a + - 34d29339abab + - 90f657745fea tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -107,22 +107,22 @@ tools: - name: merge_cols owner: devteam revisions: - - dd40b1e9eebe - ae7843d06f8f - f2aac0c5c60d + - dd40b1e9eebe tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 3a6b78c39dca + - 33d61c89fb8d + - cf4397560712 - cf34c344508d + - 3a6b78c39dca - 83069b38aa85 - 623f3eb7aa48 - - 1ea4e668bf73 - 2e8f945f7285 - - 33d61c89fb8d - - cf4397560712 + - 1ea4e668bf73 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace @@ -142,31 +142,31 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - bce29ec10b78 - - b722161a845a - c4d18aa4ec4a - f768f6183386 + - bce29ec10b78 + - b722161a845a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: - - 3bf5661c0280 - 60ff16842fcd + - 3bf5661c0280 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: - - 9ff72e942410 - - 0a8c6b61f0f4 - - 74a8bef53a00 + - ddf54b12c295 - 86755160afbf - fbf99087e067 - d698c222f354 + - 74a8bef53a00 - 12615d397df7 - - ddf54b12c295 - - a6f147a050a2 - f46f0e4f75c4 + - 9ff72e942410 + - a6f147a050a2 + - 0a8c6b61f0f4 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 d25b676de..9e51ea333 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: - - 0d18a3ba2d1c - - 85c57cc9b558 - 82fb5e3bb93e + - 85c57cc9b558 + - 0d18a3ba2d1c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -29,66 +29,66 @@ tools: owner: iuc revisions: - c0f8fe52948e - - cb441f258c37 - 23d7e75d850e + - cb441f258c37 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: freebayes owner: devteam revisions: + - 3e954e7125bf - 57def2d7c093 - - 156b60c1530f - a5937157062f - - ef2c525bd8cd - - 3e954e7125bf + - 156b60c1530f - 04fa42777df9 + - ef2c525bd8cd tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 09d6e4693887 - - 435b157bed6d - 791f73caa0c8 + - 435b157bed6d + - 09d6e4693887 - e61c9ac190ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: + - dfadc322b065 - e1461b5c52a0 - - 03627f24605f - - b11e8e9c23bf - 3b4b2121842f - - dfadc322b065 - - 074d44697036 - 65432c3abf6c + - b11e8e9c23bf + - 074d44697036 - 4805fe3d8fda + - 03627f24605f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 7dfca164d2e3 - 701d134358ad - 9cb929f21cfa + - 7dfca164d2e3 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - f4473557ffc7 - - c27549b9aa1f - - 971e07ca4456 - 426d707dfc47 + - 971e07ca4456 + - c27549b9aa1f + - f4473557ffc7 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - aa35ee7f3ab2 - - dbd9f2db9ed8 - cdaab621d454 + - dbd9f2db9ed8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -101,18 +101,18 @@ tools: owner: iuc revisions: - ceff2f6a5368 - - 93c4b04a0769 - 43fffeed243f + - 93c4b04a0769 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: + - c9a8ef2aa380 - 9bccc8404a3c - d220115f882b - - c9a8ef2aa380 - - 5bbf9eada9c2 - fa016f1eea1a + - 5bbf9eada9c2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -154,21 +154,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - e7aff4a85df5 - 40f0591deda0 - - 32f14a2723ec - - 3b1e7c170b10 - ee4a90760848 + - 3b1e7c170b10 + - e7aff4a85df5 + - 32f14a2723ec tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - 42818629ec4c - - 4934c0ac6197 - 02d81b994ef5 - - 9793bc5d741b - adc0645b945c + - 9793bc5d741b + - 42818629ec4c + - 4934c0ac6197 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 9b0f4251b..500697299 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -2,14 +2,14 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - e075b1be5abb - - b7ea370b8f5d + - 6a88248893c4 + - 2c372041ed8c - 8a2e296c07ef - 265fe0f9ea64 - - 2c372041ed8c - - ebe5fc018e72 - 95815a0bb307 - - 6a88248893c4 + - ebe5fc018e72 + - e075b1be5abb + - b7ea370b8f5d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -21,13 +21,13 @@ tools: - name: bcftools_call owner: iuc revisions: - - 0fba2c15b40d - - b03984136ce4 - - 21687e35f066 - 22637b1a55bf - - 544cb432072b - c37b684e7f4e - 1001172b5089 + - b03984136ce4 + - 21687e35f066 + - 544cb432072b + - 0fba2c15b40d 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: - - 8627b2b383b4 - - 3a7084316a6e - - 8408bffd5616 - - ccb83bf54de0 - - 01d6b7d6365e + - 0238f68ad641 - 143796b504eb - 8ca3647c90fd - bf1f4994f104 - - 0238f68ad641 + - 8408bffd5616 + - 3a7084316a6e + - 8627b2b383b4 + - 01d6b7d6365e + - ccb83bf54de0 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: - - f430a1ec7ee4 - abd489215f73 - - 6b6c992d3a14 - - 81426b3cf18b - - 03e0645395d2 - - 9b5abbf50d23 - 62ca6da715bf - d144af39073a + - f430a1ec7ee4 + - 03e0645395d2 + - 6b6c992d3a14 + - 9b5abbf50d23 + - 81426b3cf18b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -79,12 +79,12 @@ tools: owner: iuc revisions: - e522022137f6 - - 2363ef414c9b - - d37e313a41be - 1829900b5dcd - - 8aa352093d73 - 95c6f3f4c77f - 1171446da5db + - 2363ef414c9b + - 8aa352093d73 + - d37e313a41be - d3081540d175 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -97,14 +97,14 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - d58d2e8c7a57 - - b14ff40958cb - 012656fd329f - - 09f37afb3621 - - 348cd212dbad - - 92c0aff8b53e + - d58d2e8c7a57 - 1137ce8efc1e + - 348cd212dbad + - b14ff40958cb - 9b29129fb491 + - 92c0aff8b53e + - 09f37afb3621 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: - - 7291189e98b4 - - ecc9192912b8 + - de68c11034f6 + - cfd81f17580b - 367ba501b6eb + - ecc9192912b8 + - 7291189e98b4 - 1f2183a23823 - - cfd81f17580b - 55c0e906c14c - - de68c11034f6 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: - - ae68ceb4cca3 - - 7cbf3c66d4ad - - 64a8f7dae3ad - - 039ea3f1dea9 - 6c790a091c7c + - 64a8f7dae3ad + - 7cbf3c66d4ad - d237eaef451f - e6f4badbe6f3 + - ae68ceb4cca3 + - 039ea3f1dea9 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: - - 5d6653c989cb - - 277719af4dd7 - - 963a3635b2e1 - - cdb7b4927742 - 46fcafba49ec - 6ea7170a016d + - 277719af4dd7 - e7452697afd9 + - 5d6653c989cb + - cdb7b4927742 - 33bd9301568c + - 963a3635b2e1 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: - - b7f0f59baa7e - - a1213a0b7b66 + - 7b4454382d39 + - 501bfb078342 - 91c1e57d5c7f + - a1213a0b7b66 - 5a321fab1fe4 - - 26d97cdd5410 - a29a2f40b665 - - 501bfb078342 - - 7b4454382d39 + - b7f0f59baa7e + - 26d97cdd5410 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: - - d7d1663559e9 - - 39bca000353d - - c803c34361e0 - - 97d19c008d15 + - 768d04526638 - 5f27e814a119 - - 709dd8291b83 - 81e4014fa809 - - 768d04526638 + - c803c34361e0 + - 97d19c008d15 + - d7d1663559e9 - 15da1ddcfeff + - 709dd8291b83 + - 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: + - 85ee7e6c4204 - 2215287d5cc9 - - 7ba36babba2d + - b931e65638b8 - b84fda8ebef0 - - b1eba148b35b - 86296490704e - - b931e65638b8 + - b1eba148b35b - 5b006286a458 - - 85ee7e6c4204 + - 7ba36babba2d 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: - - f506df85c652 - - ce9396ddcb2b - - 9c711df3258d - - cf06b44624c7 - - 5660b21a0dbd - - 31ea13dfe5e6 - 56556e1267de + - cf06b44624c7 + - 4e1d23e5c691 + - 9c711df3258d - 0a5dcc9a8ec2 + - 31ea13dfe5e6 - 37757ffb4c5f - - 4e1d23e5c691 + - 5660b21a0dbd + - f506df85c652 + - ce9396ddcb2b 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: - - 1ca7418e46ee - - 271965b55437 - - 021693fdadaa - - 6deb4d549bc9 - a404f786a94c - - 48291658fdf6 + - 6deb4d549bc9 - 19905c025d2a + - 48291658fdf6 + - 021693fdadaa + - 1ca7418e46ee + - 271965b55437 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 + - c450406f722b - 97e8145d7e30 - - dadbd61dc4cf - - 71c78e0eea52 - 69d8b7567281 - - c450406f722b - - f7879f1e77f9 + - 71c78e0eea52 + - dadbd61dc4cf + - 3f6fadf8b8ff - 5ad5d4243987 + - f7879f1e77f9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -287,14 +287,14 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: - - 79f7a1acc2cd - - 52f9e4a660e3 - - 6cf13a657cf6 - - 283911fe7e1a - - 0fe007201caf - 2514e684f8a3 + - 52f9e4a660e3 - d31a2e310a52 + - 283911fe7e1a + - 6cf13a657cf6 - cc7f9a4e186b + - 79f7a1acc2cd + - 0fe007201caf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -307,13 +307,13 @@ tools: owner: iuc revisions: - 6963a6841d22 - - 75ddd081f608 - - 1411bef27a75 - 230e424bde67 + - 80e6e399ccd0 + - 1411bef27a75 - 0a62420cb9cd - - 026a989b7cee - a12844ca467a - - 80e6e399ccd0 + - 026a989b7cee + - 75ddd081f608 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -325,14 +325,14 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - 5808f77b2bb6 - - ba20340426fe - 450a265f92e8 + - 5acfca5a76af - 444e6a756c35 - - bca7ce81688f - b10d1510fa84 - - 5acfca5a76af + - 5808f77b2bb6 - e493702b19eb + - bca7ce81688f + - ba20340426fe tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -344,14 +344,14 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - 4d236c696844 - - 12152af85697 - dd72ff87cfd0 + - c43399f161f4 + - 12152af85697 + - 4d236c696844 - d52b8947b269 - 157ffcdd3fa7 - - 68fec03a63b7 - f2482aa4862e - - c43399f161f4 + - 68fec03a63b7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -364,11 +364,11 @@ tools: owner: iuc revisions: - 75becf493cd3 - - 8f2fc0ab30fb - - 6f8e223f78f3 - - 8dbce095986c - cbe39e530cbf - 0e5d11004815 + - 6f8e223f78f3 + - 8f2fc0ab30fb + - 8dbce095986c - 29ba253e2e05 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -381,14 +381,14 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - f544f71adb73 - - a8630d4fbaf8 - - a367a15c6de5 - - e0a856def0b0 - 8f5962c43868 - 88bb477f45f7 + - e0a856def0b0 - 9708e3086f32 - 3ff5654b4e7d + - a8630d4fbaf8 + - a367a15c6de5 + - f544f71adb73 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian @@ -401,13 +401,13 @@ tools: owner: iuc revisions: - 4ed46189d6c6 + - 6ce175385dd9 - 34dc0bbc7e93 - - 31c096c6b156 - - 96d0145c041a - - 5c9729d54721 - 8b260d252ff4 - - 6ce175385dd9 + - 5c9729d54721 + - 96d0145c041a - 03e30f06f15f + - 31c096c6b156 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -419,13 +419,13 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: - - 09f5e45a8212 - - 46eb13bc2c73 - - a1aad8b559c6 - - a730269af659 - - 681bdf1e22ff - 40daf124be88 + - 681bdf1e22ff + - a1aad8b559c6 - 2c4941386820 + - 09f5e45a8212 + - a730269af659 + - 46eb13bc2c73 - 11af7fce71cf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -438,15 +438,15 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - 8cb121b6a1d2 - b74b8cbfc1f1 - - 743cd1472aeb + - 8cb121b6a1d2 + - 882b2e649602 + - 6cbb9c47795c - 0594ea1417c8 - 3897eaadfbff + - 743cd1472aeb - f272b8ba0983 - 12038f59c0f4 - - 6cbb9c47795c - - 882b2e649602 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: - - dba06328556a - eccb508bb678 - - a9826db86d9a + - adee7e8b746f - 238f78e38a8b - cced6715f926 - - adee7e8b746f + - a9826db86d9a - 18cf9de1cf73 + - dba06328556a 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: - - 3ce32adc55b2 + - 9f36041495a3 + - fdec14f69010 - c9935c9e8a24 + - 3ce32adc55b2 + - e0ad88dec40d + - f64e7ca2efd2 - e53501abf992 - 31a1b89eab9b - - fdec14f69010 - - f64e7ca2efd2 - - e0ad88dec40d - - 9f36041495a3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -495,13 +495,13 @@ tools: - name: bcftools_reheader owner: iuc revisions: - - 2331ddcbd5aa - - d68c43202172 - 79489d5685dd - - b7be725976b6 - d43eb39b989e - - fd3539749127 - 3b7b1fe7b937 + - 2331ddcbd5aa + - fd3539749127 + - d68c43202172 + - b7be725976b6 - 4db0695a6fc7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -514,13 +514,13 @@ tools: - name: bcftools_roh owner: iuc revisions: - - 5296d26b0373 - - b0d39ef600a7 - - 58091e1be01b - - 78cd8b69da4c - - 1a989b4110da - 1ccf0e7fb4f6 - 6a636d58dfc2 + - 1a989b4110da + - 58091e1be01b + - 5296d26b0373 + - 78cd8b69da4c + - b0d39ef600a7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -532,13 +532,13 @@ tools: - name: bcftools_stats owner: iuc revisions: - - b641062a2587 - - 4d3ce9dc1525 - - baa8823f8073 - '388983871932' - - b17394940c7a - e8af591435d1 + - b17394940c7a - 591cc8518033 + - 4d3ce9dc1525 + - b641062a2587 + - baa8823f8073 - bf8325a07ce7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -551,14 +551,14 @@ tools: - name: bcftools_view owner: iuc revisions: - - 59fa8742285e - - 3ca3de4e5291 - - e6b5cbbf449b - - 1a2ef636f48e + - 3a233c8eb814 - c2ab91a0d506 - - d1f8f55f564d - 38d75661c235 - - 3a233c8eb814 + - e6b5cbbf449b + - d1f8f55f564d + - 3ca3de4e5291 + - 1a2ef636f48e + - 59fa8742285e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -570,29 +570,29 @@ tools: - name: vcf2tsv owner: devteam revisions: - - e92b3c0f9224 - 285060661b45 + - e92b3c0f9224 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfaddinfo owner: devteam revisions: - - afc0ba768690 - 6ea73d6151ec + - afc0ba768690 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives owner: devteam revisions: - - 57a16b310fe8 - a8a4f94aa321 + - 57a16b310fe8 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 @@ -619,8 +619,8 @@ 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 @@ -647,44 +647,44 @@ tools: - name: vcffilter owner: devteam revisions: - - eae7c08ebb6f - - 6b935ab36d7b - 4bdc111b2470 + - 6b935ab36d7b + - eae7c08ebb6f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - fc5a64fdd5b2 - 11f62f071125 + - fc5a64fdd5b2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten owner: devteam revisions: - - b24e368ae7b1 - f285aa6bdcfb + - b24e368ae7b1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgeno2haplo owner: devteam revisions: - - a3dea556218d - b890055e07bd + - a3dea556218d 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 @@ -711,8 +711,8 @@ tools: - name: vcfselectsamples owner: devteam revisions: - - 2ba3b87f904f - 958b6484a7f1 + - 2ba3b87f904f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfsort diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index ba014588a..f043c888e 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -3,53 +3,53 @@ tools: owner: iuc revisions: - 3f3e247c053d - - c2ef298da409 - 6e9aea89e388 - 78c75f134c16 + - c2ef298da409 - 4efdca267d51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 owner: iuc revisions: - - c45c9dd066e2 - 3f438bf5475d + - c45c9dd066e2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - 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 owner: iuc revisions: - - 1fdc517743e6 - c4ac24510b55 + - 1fdc517743e6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_parseval owner: iuc revisions: - - d6c074a93c51 - 1b52f0c8ad7f + - d6c074a93c51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - fe3ca740a485 - - f29602ae449e + - 1aae04680c4b - 44018dd6b447 - - b5d8e5475247 - 3e1f6f6d557e + - b5d8e5475247 - cd2480f35935 - 4f2967b27e67 - - 133f36c29579 - a79ee60b6926 - - 1aae04680c4b + - fe3ca740a485 + - 133f36c29579 + - f29602ae449e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -62,38 +62,38 @@ tools: - name: augustus_training owner: bgruening revisions: + - aada0deea587 + - dc027fa56d55 + - 6519ebe25019 - f1e653756174 - 7be22100e5e1 - - 6519ebe25019 - - dc027fa56d55 - - aada0deea587 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 28433faa6e42 - - 0fc0f9cf035a - 09855551d713 - - bd0e53f3a891 - ca6d970d931c + - 0fc0f9cf035a + - bd0e53f3a891 + - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - 728dacaf08a9 - - d77802fe76f7 - da5f1924bb2e + - 728dacaf08a9 - 92eee5f31117 + - d77802fe76f7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - fe48aa4ccd5e - - 8fd427007e93 - 7355bbf5e05f + - 8fd427007e93 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -105,8 +105,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 8bd92f2404dd - 1b9a9409831d + - 8bd92f2404dd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -118,17 +118,17 @@ 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: - - 63662ae295d6 - 9d1fbff733cf - d9c3016f7283 + - 63662ae295d6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -158,60 +158,60 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 9f2455341fac - - 14f588312c56 - 9c15ca7e764e - - 582fd74dc2a1 - - 756376aeb1ae + - 14f588312c56 - b6b5cd37f2a2 + - 582fd74dc2a1 - 3bbe70fef6df + - 756376aeb1ae + - 9f2455341fac tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: + - 1691af4a0d17 + - 73428a792541 - 989f7c061f35 - - 8e1ace8f77c6 - 0ffe5be70caf - a230ea445788 - - 73428a792541 - - 1691af4a0d17 - 30fb23d4c31c + - 8e1ace8f77c6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 494f0bb4a993 - - 563a19373357 + - 57c6718cbfcc - 0418d28136de + - 5a5ae61da69c + - 494f0bb4a993 - 30f08d74024f - e94187d661df - - 5a5ae61da69c - - 57c6718cbfcc + - 563a19373357 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 7abc5f6dd595 - - 1bc5a03faf2e - 4b96ced19f75 - - d6c7106b7b2e - f31125bb85ea - - 2bba2ff070d9 - f77d7b685bb3 + - 2bba2ff070d9 + - 7abc5f6dd595 + - d6c7106b7b2e + - 1bc5a03faf2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - d77fdcca400e - - 520e30695ec3 - 52af33194019 - d3af38b9c7e1 - - fed64e676186 - b3cf4684e9c7 + - fed64e676186 + - 520e30695ec3 - 54961e026fe4 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -224,9 +224,9 @@ tools: - name: gff_to_prot owner: iuc revisions: + - 07d7991bf205 - 2aea122fbd25 - 79261884facd - - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -238,10 +238,10 @@ tools: - name: goseq owner: iuc revisions: - - 602de62d995b - - 43798b4caee0 - - ef2ad746b589 - 8b3e3657034e + - ef2ad746b589 + - 43798b4caee0 + - 602de62d995b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -300,18 +300,18 @@ tools: owner: iuc revisions: - d46d803ca6cc - - 370c210d9541 - 3c1a01127868 + - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - c8ac28e8ac44 - 033755194fe9 - - e95d52d295d7 - 624606f7c996 - b815ec682418 + - e95d52d295d7 + - c8ac28e8ac44 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -359,8 +359,8 @@ tools: - name: prokka owner: crs4 revisions: - - d643e3b03500 - 8a22554cdde2 + - d643e3b03500 - bf68eb663bc3 - a17498c603ec tool_panel_section_label: Annotation @@ -374,15 +374,15 @@ tools: - name: repeat_masker owner: bgruening revisions: - - ba6d2c32f797 - 3f987772e283 + - ba6d2c32f797 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 @@ -406,23 +406,23 @@ tools: - name: snpeff owner: iuc revisions: + - c7275bd8b4d6 + - 68693743661e + - 8f92c2b26e6d - 6322be79bd8e - - cfcf33df7fc0 - - 5c7b70713fb5 - 5b80f544c67f - - 68693743661e - - 268d162b9c49 - - c7275bd8b4d6 - 5a29ab10dba6 - - 8f92c2b26e6d + - 5c7b70713fb5 + - 268d162b9c49 + - cfcf33df7fc0 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 @@ -441,25 +441,25 @@ tools: - name: tbprofiler owner: iuc revisions: - - ac8250086ac3 - - 37213cf56392 - - 809dfc93d593 - 4839e590cb26 - - 8cb134b8c1a5 - - d03af1c7002c - - e1a9d6fd258d + - 809dfc93d593 - 200c378d85f3 - - 45083d070fb8 + - ac8250086ac3 - ba6f87115e13 - 037a11682176 - 51dd22484644 + - 37213cf56392 + - e1a9d6fd258d + - d03af1c7002c + - 45083d070fb8 + - 8cb134b8c1a5 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 88f1a6f1c..ad66a2a00 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,45 +2,45 @@ tools: - name: abyss owner: iuc revisions: + - 8f1b150a2487 - 7547fcab5d19 - - 553bfe8bd0b5 + - 890b794c997d - a929ce596a34 - - d6d5ccc2c581 - - fa5259cc561b - 841084c5fc46 - - 890b794c997d - - 8f1b150a2487 - - 0124fce4654a - db9b10824c61 + - d6d5ccc2c581 + - 0124fce4654a + - 553bfe8bd0b5 + - fa5259cc561b - 0e93176640ac tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 94fe43e75ddc - - b9e31c5c01c7 - 067592b6b312 - - 21e491ad532a - b2860df42e16 - ddddce450736 + - b9e31c5c01c7 + - 94fe43e75ddc + - 21e491ad532a 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: - - a7f16f24e9a1 - 3371c5bdc17a - - faee8629b460 - - 22286dab5aa1 + - a7f16f24e9a1 - 5258e18bbe23 + - 22286dab5aa1 + - faee8629b460 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -53,31 +53,31 @@ tools: - name: busco owner: iuc revisions: + - 2dd755c1c6ff + - 94170eee0ad8 - 46ae58b1d792 - - 41030a6c03b7 + - 5ecdeca79a0d + - e824f5d958d0 + - 4048d82f0c88 + - 2babe6d5c561 - 1e62c28ba91d - - cf13a1e03e5b - - bb935709506a - - 602fb8e63aa7 - - 94170eee0ad8 - - 2dd755c1c6ff - e5c372c91e46 - - 2babe6d5c561 - - 4048d82f0c88 - - 5ecdeca79a0d - - 0d243f458b53 - - 1440ae06552f - ea8146ee148f - - e824f5d958d0 + - bb935709506a - e4bd1e99bacf + - 0d243f458b53 + - 41030a6c03b7 + - 1440ae06552f + - 602fb8e63aa7 + - cf13a1e03e5b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - 5732f959936a - 86f150c8019d - c5b7390290b1 - - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -90,45 +90,45 @@ tools: owner: bgruening revisions: - 1f0769f0b56b + - cd11366d92cf + - e27815e82dd4 + - 1ce9b1d72ec3 + - 3e4f8642c77e - 276f5d8712d5 - 8d4f03b5fe9d - - 3e4f8642c77e - - 1ce9b1d72ec3 - 3ee0ef312022 - - e27815e82dd4 - cb8dfd28c16f - - cd11366d92cf - 291923e6f276 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 3169a38c2656 - - 01210c4e9144 - - b2f674562a18 - 460fad600dce + - b2f674562a18 + - 01210c4e9144 + - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: + - 06bcf65179fb - ba88bc5a6446 - 8b330a577046 - 7348b69e5109 - - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 6ec1b853c8fd + - 764f2516d837 - 690c2caa367e - - 3fba9c77550a - - 5127a713de83 + - 6ec1b853c8fd - f4a3eff8ab85 + - 5127a713de83 + - 3fba9c77550a - 3ef480892a9f - - 764f2516d837 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -140,24 +140,24 @@ tools: - name: hifiasm owner: bgruening revisions: - - 60024a528cbd - - 366a11d316a7 - - 5161f204ba63 - - 5f625c63b8bc - - 5bec28269d95 - - 0ee0c3089254 - - df25d4fb79b7 - - 9ef6920c3089 - - 6505bd37670d - - 2061fb3b81b4 - - f3c89da3af16 - - 3f7be05a1597 - - 045c7c3d8e59 + - 284a1cb82b61 - ec9e21e9c71b - 71740308d412 - - da9d8bf98802 + - 045c7c3d8e59 + - 9ef6920c3089 + - 0ee0c3089254 - 41cea2aa2dce - - 284a1cb82b61 + - 5161f204ba63 + - da9d8bf98802 + - 2061fb3b81b4 + - 3f7be05a1597 + - df25d4fb79b7 + - 5bec28269d95 + - 5f625c63b8bc + - f3c89da3af16 + - 6505bd37670d + - 60024a528cbd + - 366a11d316a7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -181,43 +181,43 @@ tools: - name: megahit owner: iuc revisions: - - 14ddfc8ffb93 + - 7518ee87b53d - de387b2b2803 + - 14ddfc8ffb93 - a96f3ad4e0d8 - - 7518ee87b53d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - f8113c25bc6b + - 09c589057ee8 - d7edbc9c3a07 + - f8113c25bc6b - eb7b00ec347d - - 9d79beb19ac3 - 39edec572bae - - 09c589057ee8 + - 9d79beb19ac3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 29dabd8db6f2 - - 51c2360aa807 - eadfd71dde37 + - 51c2360aa807 + - 29dabd8db6f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 2ecf5a570907 - - 3ca2d2a9068c - - f369ef5f210b - 99ecfdafc64f + - f369ef5f210b + - 3ca2d2a9068c - f338e9942b27 - - 606b09cc9860 + - 2ecf5a570907 + - eb7a370f6588 - e731ea24e48d + - 606b09cc9860 - fd128c111ab0 - - eb7a370f6588 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -229,11 +229,11 @@ tools: - name: miniasm owner: iuc revisions: - - a7b889b90140 - - 73a3846701e1 - b799a615995d - 8b6d0d85252b + - 73a3846701e1 - 8dee0218ac7d + - a7b889b90140 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -251,8 +251,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 7c2f5268d01c - 64a1c751d99b + - 7c2f5268d01c - 15200570e926 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -265,45 +265,45 @@ tools: - name: pretext_map owner: iuc revisions: + - bbe19ef04a74 - 8fef980d48b5 + - 02831bf9e95f + - d256a51a656b - c6cec5ab35c1 - - 2b16ba799da9 - - bbe19ef04a74 - dfb8a4497339 - - d256a51a656b - - 02831bf9e95f + - 2b16ba799da9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - e9bd16ba5ebd - a315c25dc813 + - e9bd16ba5ebd - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 59db8ea8c845 - 3061c8b029e5 + - 875d0f36d66f - ebb0dcdb621a - - 342a1d1fed7b + - 6fcbee531de6 - 7594365c546b - - 72472698a2df + - 59db8ea8c845 + - 342a1d1fed7b - 675488238c96 - - 875d0f36d66f - - 6fcbee531de6 + - 72472698a2df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - aa39b19ca11e - - cd06929b224b + - a199cd7ac344 - 39bed8de8017 + - cd06929b224b - d865b62f501c - - a199cd7ac344 + - aa39b19ca11e - 78c533842eeb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -317,11 +317,11 @@ tools: owner: iuc revisions: - f11b994b7eb2 - - 3edba9afc9bc - - 5c55448d0f33 - 33b7d8481a76 + - 3edba9afc9bc - f8564b2d7f63 - 2b2a352488fa + - 5c55448d0f33 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast @@ -334,13 +334,13 @@ tools: - name: rnaspades owner: iuc revisions: - - 28189050e437 - - 378e55aeeb25 - - 1d06c8b38e77 - 5fc94b3a4704 + - 378e55aeeb25 - ef69617ecb42 - - 53c2bc8c2ae3 - e122f9101584 + - 1d06c8b38e77 + - 53c2bc8c2ae3 + - 28189050e437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -352,127 +352,127 @@ tools: - name: shovill owner: iuc revisions: + - ee17a294d3a3 + - d9f6a00b6db7 - f698c7604b3b + - 83ead2be47b2 + - ad80238462c1 - 196a599ec43d - 865119fcb694 - - d9f6a00b6db7 - - ee17a294d3a3 - - ad80238462c1 - - 83ead2be47b2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 5e0825476fb7 - - 015283de3004 - 24e471d13fe9 + - 015283de3004 + - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: + - 904bf932cf78 + - 051fd2db8a27 - 604782a8a53a - 7490b213baa9 - - 1bb12736175c - - 051fd2db8a27 - c33a476f4001 - - 904bf932cf78 + - 1bb12736175c - 1fc82fe7ebef tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 9678993ca5bd - - 34305b013402 + - ad8b536d1caa + - fee85957cebe - 655fa188c3cc - 808b3a0a6716 - - ad8b536d1caa + - 34305b013402 + - 9678993ca5bd - d6e617c4e338 - - fee85957cebe tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 8d4b90bf9caf - - e5a3b75a271f - 6b5a5842531e - 7e27faaad80e - 21da31ed41a1 - - 037f9927c4ff + - 8d4b90bf9caf + - e5a3b75a271f - b8002c3f7141 + - 037f9927c4ff tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 9de69775f512 - - 328aa71f0f3c - - 2a10645aeadd - 7922870efcca + - 2a10645aeadd - 86f66ab58e14 - - f1532cb33c75 + - 328aa71f0f3c - 5b26685e5d3b + - f1532cb33c75 + - 9de69775f512 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 340bc17f49cf - - 1708851f8804 + - 85fb02c43042 - 8cc856b935ee - e41dcb0e913b - 6aad515a5270 - - 85fb02c43042 + - 340bc17f49cf + - 1708851f8804 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - 249f6a28c751 - - 6357b127161e - - b65a43f70b99 - d159735a6a9f - - de1260f8a300 - d5fb354f745d - b3490b036c5a + - 6357b127161e + - b65a43f70b99 + - 249f6a28c751 + - de1260f8a300 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - dd7ad84f3943 + - 9006e5836729 - d5887ace0dd4 - - a90db5dbaaf3 - d2d1df21dfb9 - - 9006e5836729 - - 33368fec3b70 + - a90db5dbaaf3 - b7829778729f + - 33368fec3b70 - 7897763d14ec + - dd7ad84f3943 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 6f4c8ad6ea01 - 0368ac680e70 - 505a9833ab5d - - 189e837009c9 - ced385aa976d + - 6f4c8ad6ea01 - 8f631679571f + - 189e837009c9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e - - 9ded6109434a - 356afed970b4 - - 19bdfd1e6fe3 + - 9ded6109434a - e59bee4565b3 + - d40ed4eb0c0e - a7ed21de23fe + - 19bdfd1e6fe3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition @@ -480,61 +480,61 @@ tools: revisions: - 80a17897564d - 7673a6c920b2 - - 4688ae3b49b5 - - b23249f81bc4 - ebd801e712bc - 6dd935e4984b + - b23249f81bc4 + - 4688ae3b49b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - 937ea677d437 - - ed312479d9eb - b64696992ee9 - - 59bd28f6265d - b5e35a2ca4f3 + - 59bd28f6265d - cb1e3db43020 + - ed312479d9eb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 05bd7504fdb2 + - 383bb5ad32e2 - cb4768eeca3b - - 6015aa0303f2 + - 05bd7504fdb2 - 2628f6790eda + - 6015aa0303f2 - b9b0246a2be3 - - 383bb5ad32e2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 0a3a602cd1e3 - - 6e26c9afd301 - - 8f9f06995f98 - 3e44ef016b45 - - e022dff952df - - 9e3e80cc4ad4 + - 6e26c9afd301 - e92675014ac9 + - 9e3e80cc4ad4 + - e022dff952df + - 0a3a602cd1e3 + - 8f9f06995f98 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - 8d09f8be269e - - 5da9a0e2fb2d - - 920677cd220f - 08256557922f + - 920677cd220f + - 5da9a0e2fb2d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: + - 4a53b89fa703 - 37d88f41c810 - 82398ba86ba7 - - 4a53b89fa703 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko @@ -546,8 +546,8 @@ 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 9e5375443..903fe7c82 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,10 +2,10 @@ tools: - name: integron_finder owner: iuc revisions: - - 392f100eebcd - bfd290fe1588 - - 1ae00120dd24 - 4768f7f8e93f + - 392f100eebcd + - 1ae00120dd24 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst @@ -23,5 +23,6 @@ tools: - 5c8ff92e38a9 - 17fcac7ddf54 - 24a7a95867b0 + - cf767360ede1 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index 0a595555c..4a31abf01 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,21 +2,21 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 204a131e47db - - d1f62024a08b - - d58c27d2c5a7 - 1c427e24fb79 - 0840ba83860c - - 7beb76ffbc0f - - 159b04e36791 - a9c9d768b751 + - 159b04e36791 + - 204a131e47db + - 7beb76ffbc0f + - d58c27d2c5a7 + - d1f62024a08b tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge owner: iuc revisions: - - 1bb2b5b52030 - cab19c0452c4 + - 1bb2b5b52030 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_tadpole diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index 52cc9eb18..e1efc5897 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - 07e8b80f278c - - 87ee588b3d45 - - 0a5c785ac6db - - 64e2edfe7a2c - dde39ba9c031 - - a68aa6c1204a + - 87ee588b3d45 - 589e7e57fd6d - - b28e0cfa7ba1 - - ce3c7f062223 + - a68aa6c1204a + - e19bebe96cd2 - a8eabd2838f6 - a1a923cd89e8 - - e19bebe96cd2 + - 07e8b80f278c + - ce3c7f062223 + - 0a5c785ac6db + - 64e2edfe7a2c + - b28e0cfa7ba1 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 cb4c72229..bb7b8e94f 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,24 +8,24 @@ tools: - name: diamond owner: bgruening revisions: - - f921014aba5a - - 62c9df8382c2 - 54f751e413f4 + - 62c9df8382c2 - e8ac2b53f262 + - f921014aba5a tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - d999e774072a - - acf4e47b734c - 0e3cf9594bb7 - 5edc472ec434 - a52d2d93e595 - e25d3acf6e68 - - 6f386c5dc4fb - - 2889433c7ae1 - cbf3f518b668 + - 2889433c7ae1 + - acf4e47b734c + - 6f386c5dc4fb + - d999e774072a 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 97b2c0741..eb67fe46f 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: + - f4230f116196 + - c8cdde00b105 + - 27ee142314a9 + - 6ca543ec1bf8 - 095ad4d096d1 - da6bd1975a71 - - 6ca543ec1bf8 - - c8cdde00b105 - 710301bc46fa - - 27ee142314a9 - - f4230f116196 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -111,8 +111,8 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - 2a868592ebcb - 67ee76f0e497 + - 2a868592ebcb tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -131,73 +131,73 @@ tools: owner: chemteam revisions: - 0fac8e2afc13 - - 79cfd9ead848 - bfb65cb551d8 - 88076940fa94 + - 79cfd9ead848 - 3b8a9d5ced85 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - 55918daa5651 - - f5d979cb4b54 - - d532b7e5f64b - b46d4b4d995c + - d532b7e5f64b + - 55918daa5651 - 715cd0e87781 - eb6564a60136 + - f5d979cb4b54 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: + - dae135dfd519 - d2f955aea23a - 5579659312e6 - fdf2cc80adb5 - - dae135dfd519 - f26afd1b7104 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - d1d0efda35c0 - bc31d02be922 + - d1d0efda35c0 - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 2c349b027a01 - ed736e6eee39 - cac1886249a2 - 070e3ecc3fda + - 2c349b027a01 - 4da9ee404eab tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: + - c0c9a5024177 + - 73008ef1f487 + - 807aa4c9293d - da8753545526 - 525ca7c8065f - d1f803b5943c - - f197e34c33a9 - 2e219a2d9327 - - 73008ef1f487 - - 807aa4c9293d - - c0c9a5024177 + - f197e34c33a9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 27ea4e1a3f95 - - 2c8ed1b52bf7 - - 61094e01eff9 - 7568ae18908a - c4fbab8e03c5 + - 2c8ed1b52bf7 + - 61094e01eff9 - 1809414a9454 + - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -209,11 +209,11 @@ tools: - name: md_converter owner: chemteam revisions: + - ba83f0923369 + - ccfbd956a2d3 - 79e8ab8f1e81 - - 730ef07b90ae - d7ec25187599 - - ccfbd956a2d3 - - ba83f0923369 + - 730ef07b90ae 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 - 4242b4d68e9c - b59c91adeac1 - e6011617c748 + - e2c36f62e22f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -283,8 +283,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 75ee9c410951 - 7672039a0bb0 + - 75ee9c410951 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -351,10 +351,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 85fad59f8168 - - d4c67ced6abc - bf99565cec1f - 9b48456a96fe + - 85fad59f8168 + - d4c67ced6abc tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 50212377b..5e2bed99b 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,10 +2,10 @@ tools: - name: diffbind owner: bgruening revisions: - - 2605cbdaa7d8 + - fa56d93f7980 - f907216064f6 + - 2605cbdaa7d8 - c97a786e8fb5 - - fa56d93f7980 - 163688bb8f73 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -26,23 +26,23 @@ tools: owner: iuc revisions: - 424aefbd7777 - - 86e2413cf3f8 - - 640d3af5d833 - 495a4173006f - f5d67c722d67 + - 86e2413cf3f8 + - 640d3af5d833 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator owner: pjbriggs revisions: - - b695071de766 - 087d9872fb0d + - b695071de766 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer owner: devteam revisions: - - 5c2cc3b58c7d - 74c9214cc8e6 + - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index 2307509d2..cfc121dcf 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.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 + - 25136a2b0cfe + - 33151a38533a tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - dfde09461b1e - 3ddd99c7efee + - dfde09461b1e tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -33,8 +33,8 @@ tools: revisions: - 2dae863c8f42 - baabc30154cd - - 0046692724f9 - 6cbe2f30c2d7 + - 0046692724f9 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index 1177ac0bf..a5a1393aa 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -2,9 +2,9 @@ tools: - name: agat owner: bgruening revisions: - - d6ede73082da - e7449b2c14bf - abba05ead5d7 + - d6ede73082da tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -16,32 +16,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 4a6ee918c13a - - a3b86937ead6 - e3cbd2287f63 - - 3b6f97e7094c - - 0b3c3ad92827 - - 6ef0b5664c69 + - 367b1ed91207 + - a3b86937ead6 + - f3a19509108a - 5e1240a87bcb + - 4a6ee918c13a + - 6ef0b5664c69 + - 3b6f97e7094c - ab9350a8ab4d - - f3a19509108a - - 367b1ed91207 + - 0b3c3ad92827 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: + - bd46669113b9 - 584008e574b2 - - 1b5fc03380d4 + - 33c99804a32f + - 091bb5922a82 - 54ccb7e1f49a - - 501c21cce614 + - d4d4e9febf5c - e525f9ffb9ac - - 33c99804a32f - 72ed72122deb + - 1b5fc03380d4 - e177a8ea0bf1 - - bd46669113b9 - - 091bb5922a82 - - d4d4e9febf5c + - 501c21cce614 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -59,24 +59,24 @@ 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: - 8979c288aefb - - 186b8d913e6c - 77b41c89d856 + - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: + - 614a63f14adf - 43807a65369f - 4b347702c4aa - - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa @@ -95,9 +95,9 @@ tools: - name: gffread owner: devteam revisions: + - 3e436657dcd0 - 154d00cbbf2d - 4dea02886337 - - 3e436657dcd0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -122,8 +122,8 @@ tools: - name: samtools_bam_to_cram owner: iuc revisions: - - 18dbde5680c0 - b9ea85dfaf45 + - 18dbde5680c0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta @@ -143,11 +143,11 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: - - b9b385097f13 - 63769c4217a7 - - 26c6706bfb07 - - 92ac8e086317 - 19e45916daf9 + - b9b385097f13 + - 92ac8e086317 + - 26c6706bfb07 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf @@ -160,17 +160,17 @@ tools: - name: ucsc_twobittofa owner: iuc revisions: - - 3c6f9e8a4c17 - - 8067dfa00ed2 - e9bbe2f71784 + - 8067dfa00ed2 + - 3c6f9e8a4c17 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig owner: iuc revisions: + - a2f83a375bf2 - fa49730d1d4b - 98704d357ede - - a2f83a375bf2 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 620b159c8..6066dceaf 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,70 +2,70 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - c929a006727f - - a1ca9bccc7f2 - - e821645ef8fc - 29451af70c52 - - 5f6d123679f4 - 268e91e540ee + - e821645ef8fc + - a1ca9bccc7f2 - de72ba3ed6f2 + - c929a006727f + - 5f6d123679f4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 12af64f93288 - - 2d2cf5c1ea8a - 7a7fd0f5f15d + - 0e143b4c3987 + - 12af64f93288 - 0e49b109abc2 + - 2d2cf5c1ea8a - bb1e4f63e0e6 - - 0e143b4c3987 - 5d11599b8a7d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 7c1beb6d6eca - 81b1e3e1fc6c + - 195e98217334 + - 7c1beb6d6eca + - c06951d10364 - 1d848bc4585f - dc059492a995 - - c06951d10364 - - 195e98217334 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - a67ac707496a + - bfff7454b59a + - 93eb012d9eed - 07418a30ed01 - 26e7304d6737 - 71aa86af6762 - 3d211717a775 - - bfff7454b59a - - 93eb012d9eed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 56d5b797ce84 - - b8858746dc1f - - dd0b7398bb96 - - 5be24eba848d + - 2bc10a9ca58b - 29fcfd36e90a + - b8858746dc1f - 26983857c91a - - 2bc10a9ca58b + - 56d5b797ce84 + - 5be24eba848d + - dd0b7398bb96 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - c3e012dfe21f - - 7e6bcd2e5128 - - 72bfafe3330b - - ee3a1b0f45f1 - 7ef978dc1b8a + - ee3a1b0f45f1 + - 72bfafe3330b + - 7e6bcd2e5128 - 9384cd033f30 - e6d0bff01239 tool_panel_section_label: DeepTools @@ -73,134 +73,134 @@ tools: - name: deeptools_compute_matrix owner: bgruening revisions: + - 514fa53b5efb + - 167788df3b46 - fd1275e01605 - a60c359ec43c - - 514fa53b5efb - - fb9cf9c97ec4 - d9a637e83828 + - fb9cf9c97ec4 - b73e213add0c - 9470f29702f8 - - 167788df3b46 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - a02cfa31e9cb + - ca0616bb2cdf - e479c7ca5570 - - c34d11ea4ba6 - - 5bffaa8354a1 - - 86febdcc4283 - 2c37ce318bc3 - - ca0616bb2cdf + - 86febdcc4283 + - 5bffaa8354a1 + - a02cfa31e9cb + - c34d11ea4ba6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: + - 192ef85c0b0b - 1fcb7adc39b8 - 78f405266706 - - 004aea905d4d - - 192ef85c0b0b + - 2d466b530754 - 01fb6a7654e6 + - 004aea905d4d - 69a8621ca2f0 - - 2d466b530754 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 3c9f0c486cca - - 459cfa861f0b - - db940c262830 - 137c4beed34b - - d580d6acd1df + - db940c262830 - 9ecba5e225a6 + - 3c9f0c486cca + - 459cfa861f0b - 2f9e4843f480 + - d580d6acd1df - d9ce4897dbb2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: + - fbe773640707 - bd7db9e2f2cb - 2c66e43f1c86 + - bad3ca889618 - f264afa9fa6f - - fd408d755394 - - fbe773640707 - 32e451def88c - - bad3ca889618 + - fd408d755394 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: + - 56bce3c82278 - 9368fbc49c8b - 7fda5607e777 - - 56bce3c82278 - - 4e12ea27f788 - - 231994413f89 - - 7e361d147872 - 3b9d990a0a0e + - 7e361d147872 + - 231994413f89 + - 4e12ea27f788 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - c03c3384cd81 - - d9114ef1c8a5 - e65d16fb2724 - - 4431f39ede55 - - ce4ce3316f74 - - b1779366c8e9 - 94ca68515826 + - b1779366c8e9 + - ce4ce3316f74 + - d9114ef1c8a5 + - c03c3384cd81 + - 4431f39ede55 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - f8fc4e5aff9d - 23f7c5f1fdaf - - 4ed32329e0ed - - d57251071381 - - 793665fff0f8 - 2da482e408b8 - - f8fc4e5aff9d + - 793665fff0f8 - b88ebb3672a1 + - 4ed32329e0ed + - d57251071381 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: + - ba6efa77fb79 - 010e58e9d822 - - a7849312d328 - a4dfb122e52b - - 512155688d98 + - c60570fa602f - e4c7985d4585 - - ba6efa77fb79 + - a7849312d328 + - 512155688d98 - 25d830337d31 - - c60570fa602f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 38e3f226248b + - aa200e4f3939 - 69264da0ce77 - - 4d678170d29b - - c899e0ccff8c - 00d869ea03a1 - - aa200e4f3939 + - c899e0ccff8c - 443d9a9d6d11 + - 4d678170d29b + - 38e3f226248b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - c361b12d207a - d806504e96d9 + - 10301d137111 + - c361b12d207a - 6662b1a8d326 - - aac8444d6681 - a2d70c4fd406 - - 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 d6bf8ce14..9e8b7e689 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -23,8 +23,8 @@ tools: - 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 diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index 9e65a9209..b265e8fe5 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - ce385837c160 - - 832c20329690 - dba489bfcd62 + - 832c20329690 - 63dd26468588 + - ce385837c160 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 1a3ca1996..f82942c0c 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -9,10 +9,10 @@ tools: owner: iuc revisions: - 62f5fab76dfb - - 6da3972210ee - - d82648ad25a3 - - 29bdbc353f20 - cf1322aeb137 + - 29bdbc353f20 + - d82648ad25a3 + - 6da3972210ee tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index 9bf967aed..fce70e04a 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: - - 8c0175e03cee - - fe74900d6dc7 - - 4e5056fefd88 - 093678460093 - - c4b82dce8335 - de6cebe3c043 + - c4b82dce8335 + - 5eb7e84243f2 + - fe74900d6dc7 - 8665bcc8b847 - - 5915ea1ec9b1 - - c053d4cad713 - - 288f97432497 - - e4691e1589d3 - 49370cb85f0f - - b1c926deaa2d - - 5eb7e84243f2 + - 8c0175e03cee + - e4691e1589d3 - 64172f1c1202 + - 5915ea1ec9b1 + - 288f97432497 - 48f587c13075 - c5e2e5902201 - - 135b80fb1ac2 - 660cffd8d92a + - c053d4cad713 + - 135b80fb1ac2 - 44e2cc14f75b + - b1c926deaa2d + - 4e5056fefd88 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: falco @@ -68,8 +68,8 @@ tools: owner: devteam revisions: - 516b97a23d7e - - 9457a20156db - 859422bcb689 + - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences @@ -90,127 +90,127 @@ tools: - name: fasta_stats owner: iuc revisions: + - 0dbb995c7d35 - 9c620a950d3a - cd0874854f51 - - 0dbb995c7d35 - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - dbfc505896e9 + - a626e8c0e1ba + - 65b93b623c77 + - c59d48774d03 - dbf9c561ef29 + - d60c3f704da0 - 1d8fe9bc4cb0 - - c59d48774d03 - ecb9f4854617 - - d60c3f704da0 - - 65b93b623c77 - - a626e8c0e1ba + - dbfc505896e9 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: + - b05e39b9c170 - f1dc2a761c30 - 9115b978ce10 - - b05e39b9c170 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: - - 8611b80a14d6 - - 47e5dbc3e790 - e9f8633db0a2 + - 47e5dbc3e790 + - 8611b80a14d6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation owner: devteam revisions: - - e30352e889fe - - 5b87038565bb - 7861f3b10c68 + - 5b87038565bb + - e30352e889fe tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality owner: devteam revisions: - - 4e1d64e6385f - - 9282652e7234 - 9dfda4e310ed + - 9282652e7234 + - 4e1d64e6385f 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 + - 03d57fea6482 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer owner: devteam revisions: - - b41c2c1bcfbf - 3e396e702cea + - b41c2c1bcfbf - 2ccb8dcabddc tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner owner: devteam revisions: - - 8d958759cf2a - - c885369b207b - 09a2199cd356 + - c885369b207b + - 8d958759cf2a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - - 35e38452bb3f - - 397dc333436b - e39cc71d3ed6 + - 397dc333436b - 249c8393f2d4 + - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: - - 74db4cffab1f - 045f0e1043f7 - 54053ea6c77e + - 74db4cffab1f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats owner: devteam revisions: - - f86c27295151 - f0e7deab6518 + - f86c27295151 - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer owner: devteam revisions: + - b63b2bfb3ea3 - 33794bdb7fe0 - f0b18efb97f1 - - b63b2bfb3ea3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -218,24 +218,24 @@ tools: revisions: - 567d5b3c52b1 - d5e9e83cd3d8 - - 09070cacefd8 - 529bccd5e4a1 + - 09070cacefd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - 0b7ec11b3c7c - - 4bedca26c133 - 8abdedf55101 + - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - - 736b8f6ee456 - - bdf1ce174e39 - 90858c306551 + - bdf1ce174e39 + - 736b8f6ee456 - cb1e251cac37 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -243,34 +243,34 @@ tools: owner: devteam revisions: - 7ce1891db6f5 - - 07497255281e - 421f0af4ee95 + - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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_reverse_complement owner: devteam revisions: - - e246088b6e34 + - 177f0621c266 - 0c2907307ba4 + - e246088b6e34 - 6027ef51ef91 - - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - 73194cdd4f57 - - 377ac2829eac - 61b4cedc8934 + - 377ac2829eac - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -280,13 +280,19 @@ tools: - 03acc0e3772e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu +- name: ncbi_fcs_gx + owner: iuc + revisions: + - 32d058f3462a + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu - name: pear owner: iuc revisions: - - f69501361cec - 2f804526f5fd - - 037f0acc7830 + - f69501361cec - b4c6f054210a + - 037f0acc7830 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id @@ -307,17 +313,17 @@ tools: - name: seqkit_stats owner: iuc revisions: - - fe1ae2ebf63d - 795cd16de38f - 812705bcf39c + - fe1ae2ebf63d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - 4b494533146a - - a019807f4e67 - 3da72230c066 + - a019807f4e67 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic @@ -330,40 +336,40 @@ tools: - name: ucsc_fasplit owner: iuc revisions: + - bf04bd405d5b - 71f649c23021 - d3f58a0dc09d - - bf04bd405d5b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - a535cf1e5da4 - - 8250ea3a1501 - - 24013bf85a6f - - e654095ab143 - 71ad4a56c40c + - e654095ab143 - b557acca0b56 + - 8250ea3a1501 + - a535cf1e5da4 + - 24013bf85a6f 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: - - 7a7e33d28f62 - - 7accf7407811 + - f3759eec3018 - 015cf18f4a15 + - 7accf7407811 + - 27ac32a22ad2 - 828dba98cdb4 + - 7a7e33d28f62 - 9fa7803d1c51 - 6a675c3aa610 - - f3759eec3018 - - 27ac32a22ad2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group @@ -377,7 +383,7 @@ tools: owner: iuc revisions: - 953b4821b183 - - 4c8a1c7d3608 - e4e12f0b3af1 + - 4c8a1c7d3608 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastq_quality_control.yml b/usegalaxy.org.au/fastq_quality_control.yml index 24702c60e..4941a9886 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,30 +2,30 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 7b4468117008 + - 64e9a6afdd0c - e41385662e5e + - 7b4468117008 - ce9cd02d5b88 - - 64e9a6afdd0c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - c64d534a763c - 8050e091e99b + - c64d534a763c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - 9da02be9c6cc - - ff9530579d1f - f2e8552cf1d0 + - ff9530579d1f - 5ec9f6bceaee - 2b0c9d9fc6ca - 2c64fded1286 - - e7b2202befea - 3d0c7bdf12f5 + - e7b2202befea tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -39,17 +39,17 @@ tools: - name: fastx_nucleotides_distribution owner: devteam revisions: + - ad116ae3f4d9 - 18a51655db17 - b6b54ba71bd8 - - ad116ae3f4d9 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - 7306ec78632a - - cc0fd298cc17 - 59003d0543cd + - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong @@ -63,23 +63,23 @@ tools: - name: multiqc owner: iuc revisions: - - abfd8a6544d7 - - c1a4b5f3b432 - - 1c2db0054039 - - 9a913cdee30e + - 3d93dd18d9f8 + - 75c93c70d094 - f7e2f1eb3a16 - bf675f34b056 - - 3d93dd18d9f8 - - 5e33b465d8d5 - b2f1f75d49c4 - - 75c93c70d094 + - c1a4b5f3b432 + - 5e33b465d8d5 + - 1c2db0054039 + - abfd8a6544d7 + - 9a913cdee30e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: + - 949f01671246 - 084bbd8ba7b8 - cd7e644cae1d - - 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/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index b5ac011a6..2a6aade30 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -9,8 +9,8 @@ tools: - name: sample_seqs owner: peterjc revisions: - - 7c40a1fbc82e - bdaefd241921 + - 7c40a1fbc82e tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_filter_by_id diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index 104443280..f844fe5fb 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -9,30 +9,30 @@ tools: - 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 + - f2f3bc622a16 - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden owner: iuc revisions: - - df57188562f0 - 1a4c5adcd587 + - df57188562f0 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets owner: iuc revisions: - - 7cf9bc210044 - 62647e2637f6 + - 7cf9bc210044 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info @@ -59,8 +59,8 @@ 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 @@ -87,8 +87,8 @@ tools: owner: iuc revisions: - b2c25142267e - - cf61daf064fe - 45296e47d565 + - cf61daf064fe tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -108,23 +108,23 @@ tools: - name: gemini_pathways owner: iuc revisions: - - 6b09debcfc49 - 9199331c3421 + - 6b09debcfc49 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - da74170c55c7 - 840fb4850be3 - 666f60a9331a + - da74170c55c7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -144,15 +144,15 @@ tools: - name: gemini_roh owner: iuc revisions: - - 93967598e18e - 345d41f3f574 + - 93967598e18e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -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 2e186f768..18d33de94 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -9,22 +9,22 @@ 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: - - 9744e1124d0f - 39a996d44e16 + - 9744e1124d0f 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 c6211d3ad..b85253502 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -3,8 +3,8 @@ tools: owner: galaxyp revisions: - 983bf725dfc2 - - b39347891609 - c1b437242fee + - b39347891609 - e9df53a75f3c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -17,43 +17,43 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - 28587613264f - e063168e0a81 - 1c58de56d587 + - 28587613264f tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 734abc7ac21d - - 516a54ddf218 + - 6591f049cf7e - 4df8de2d0e48 - - ba931a59dd59 - - f8054ea1c365 - - 69ebb7f46e45 - - e407b9da183a + - 6ea73833cf67 + - 8848455c0270 - 7068f48d0ef9 - - e08a7ad4378b + - e407b9da183a - 9a776b080193 - - 83c7d564b128 - - 1790dcf3c32d - - c441583adae5 - - f5ea3ce9b9b0 - aad3885b3216 - - 5e6237d58b0c - - 8848455c0270 - - 6ea73833cf67 + - 4317d3cb6cba + - 516a54ddf218 - 653e89d73fc4 + - 5e6237d58b0c + - c441583adae5 + - 734abc7ac21d + - 83c7d564b128 + - 69ebb7f46e45 + - f5ea3ce9b9b0 + - e08a7ad4378b + - 1790dcf3c32d + - ba931a59dd59 + - f8054ea1c365 - 1ec814014652 - - 4317d3cb6cba - - 6591f049cf7e tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 9aaa46d45472 - 75b3b3d0adbf + - 9aaa46d45472 - 34758ab8aaa4 - 21a560af5913 tool_panel_section_label: Get Data @@ -61,10 +61,10 @@ tools: - name: uniprot_rest_interface owner: bgruening revisions: - - 054483e27a35 - - 468c71dac78a - bfdc6a7ffd3a - - af5eccf83605 - 95fb5712344f + - af5eccf83605 + - 468c71dac78a + - 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 cc2610713..55b25a297 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: - - fd59d783248a - - c4bde687c846 - - 7f13dc906cb9 - - a64dc31ab7f2 - 290a11559985 - df7356989ac1 + - a64dc31ab7f2 - 740057a5126d - ae9994cf526f - 4b519282a05b + - fd59d783248a + - 7f13dc906cb9 + - c4bde687c846 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,8 +28,8 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 7cf5b1d072b5 - f95284aa2946 + - 7cf5b1d072b5 - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -42,31 +42,31 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: + - '566197475670' + - 51c6ccaace7e - 3b37b1b1c3a7 - 48b42ee61bc5 + - ca7cb0eaad62 - 53460afd5115 - 374e9062d874 - - 51c6ccaace7e - - ca7cb0eaad62 - - '566197475670' tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: + - 1a72f938213e - 391a4cc45fea - - da4c086cff5b + - 3d059e9c2fba - d3a9e32672ec - 10515715c940 - - 3d059e9c2fba - - 1a72f938213e + - da4c086cff5b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram owner: iuc revisions: - - 6fc8bab811da - b0d96516e6a5 + - 6fc8bab811da tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_pca @@ -79,19 +79,19 @@ tools: - name: ggplot2_point owner: iuc revisions: - - 1acf88921176 - - d0fc8b746d57 + - 5298e06f14f9 + - e3a675da7fd0 - 5fe1dc76176e - 299307abd804 - - e3a675da7fd0 - - 5298e06f14f9 + - d0fc8b746d57 + - 1acf88921176 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - - 17b666467c32 - 0e7290688b50 + - 17b666467c32 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -110,8 +110,8 @@ tools: - name: graphlan owner: iuc revisions: - - 6e8eb0c0d91f - 8f62f666dcb6 + - 6e8eb0c0d91f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -129,17 +129,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 6cd09d7b5f37 + - 112eb40ba6cf - fd5dbf0f732e - - 667e17248bfe - 4542035c1075 - - a6e57ff585c0 - - 112eb40ba6cf - - 2bb2e07a7a21 - - 17359b808b01 - ca2def38369c - - 1cfc579079a6 + - 6cd09d7b5f37 + - 667e17248bfe - 836d1aa3e89a + - 17359b808b01 + - a6e57ff585c0 + - 1cfc579079a6 + - 2bb2e07a7a21 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -157,9 +157,9 @@ tools: - name: pathview owner: iuc revisions: - - f1691de443a7 - - fe154a7af404 - 03c13085aecc + - fe154a7af404 + - f1691de443a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -179,17 +179,17 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 62e3a4e8c54c + - f234e2e59d76 - 85da91bbdbfb + - 62e3a4e8c54c - 1c5dcef5ce0f - - f234e2e59d76 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 7b21a9b5922f - 9958188c6195 + - 7b21a9b5922f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -202,9 +202,9 @@ tools: owner: iuc revisions: - 6c571966cfb9 - - 44c66e8d21e6 - - 7c9417381ad5 - 26f2fe7e53a1 + - 7c9417381ad5 + - 44c66e8d21e6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -216,23 +216,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 14e7c35f3d00 + - 4ac4e7083b7e - 326a3db8d9d1 - 36b848d5f3ec - - a1abfa420d9d - - 4ac4e7083b7e - 7dd841a32245 - 360df4999907 - 2824d77cd8f8 + - 14e7c35f3d00 + - a1abfa420d9d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - 73b8cb5bddcd - 83c573f2e73c - - 44608d0193ed - 99ace6c1ff57 - - 73b8cb5bddcd + - 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 6298709e3..dbbc29785 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -21,17 +21,17 @@ 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 owner: ebi-gxa revisions: - - 6417cccad133 - - 7779b9dcf040 - bc9e8de21efb + - 6417cccad133 - 22bd5861706d + - 7779b9dcf040 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells @@ -39,43 +39,43 @@ tools: revisions: - 361608369dda - 55ccc0a121bc - - e9283529cba1 - bf1e0bdec1db + - e9283529cba1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes owner: ebi-gxa revisions: - da611a744112 + - 474a69c47184 - 23d838d1569d - cc64914b0cf4 - - 474a69c47184 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster owner: ebi-gxa revisions: - - 36735850e461 - - ad6995afd2e6 - 2ccd9f9e2cd0 + - ad6995afd2e6 - fc4b3b46dc9d + - 36735850e461 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers owner: ebi-gxa revisions: - - 0a8e527d1517 - - 49653e680ea4 - 81c34e67f262 + - 49653e680ea4 - d8f5224005bb + - 0a8e527d1517 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 64dd8bb151e1 - 79da59a0b180 - 4667fe07bd68 + - 64dd8bb151e1 - 2861ca3bfe4d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -103,9 +103,9 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: + - 94697510d55f - ff6decc0f432 - 9a2f72d7dbd2 - - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -118,10 +118,10 @@ tools: - name: scanpy_normalise_data owner: ebi-gxa revisions: + - 6b97ffba31da + - 28b1546857b0 - 3027cb62adbd - 8d9c22419c56 - - 28b1546857b0 - - 6b97ffba31da tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator @@ -135,23 +135,23 @@ tools: owner: ebi-gxa revisions: - 35f6611fb8c3 - - 7d5c97823f8b - - 1be0fc4d8654 - 56d22aa6cb3b + - 1be0fc4d8654 + - 7d5c97823f8b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - cb1992d1804b - d3df472a21dc + - cb1992d1804b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x @@ -164,9 +164,9 @@ tools: - name: scanpy_regress_variable owner: ebi-gxa revisions: + - 0bab2ae44e7a - d18ed15697bb - 36daab33aecf - - 0bab2ae44e7a tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap @@ -201,36 +201,36 @@ tools: owner: ebi-gxa revisions: - 4428dba93375 - - 3ee74b58c72d - 59028945c857 + - 3ee74b58c72d - 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 - - 181d61d2f3cd - 8b0d6f6f44c8 + - 3fb53f5e46ea - abdb61e4afa3 + - 181d61d2f3cd tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: - - ea91cfd0444e - 767a675b5254 - fe562424a0a6 - - 0f98603d0116 - bd4a244faeb8 + - 0f98603d0116 + - 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 + - f86b2c3bc459 - 4cc9362782b4 - 5605f8452eb3 - - f86b2c3bc459 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 10fd5b8c1..e6b7d8f9a 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -4,58 +4,58 @@ tools: revisions: - 29f66c353bcb - 9edf8894a22d - - 921a2da49a0c - ed2cca6b5de4 - - 0f611e7d7858 - - a4c13ddcc8ee + - 921a2da49a0c - d9967770de96 + - a4c13ddcc8ee + - 0f611e7d7858 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - d404277cc87a - - 11de0d28ab30 - - 478aacfbaa37 - 78fb5e286609 + - 755df866ad0c + - 478aacfbaa37 + - d404277cc87a - ec4b948dc6f0 - 5746d61f0a91 - - 755df866ad0c + - 11de0d28ab30 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 9d93c8fbe0a6 - - 11fa44ee0603 + - 4d511437b1e5 - 977dc15add20 - - 03dd3c16ae4e - 9e357a8b2ec3 + - 9d93c8fbe0a6 - f72063d9426b - - 4d511437b1e5 + - 11fa44ee0603 + - 03dd3c16ae4e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - c3e5e2cf12b7 - - 1da5f169b491 - f86ca478c6af - - 77919cc3618e + - 41dbf4d162a2 - 0ba4f56a3613 + - 77919cc3618e - 3b5b54ed6392 - - 41dbf4d162a2 + - c3e5e2cf12b7 + - 1da5f169b491 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - 025a128652dc - - 7babd8a46fe0 - - 12d51d7be66f - 9939786dd9c9 - - b63363075c2e + - 7babd8a46fe0 - f741330d4a71 + - b63363075c2e + - 12d51d7be66f - 5308ca68ef3d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index e6469fdb1..f09cfd3b8 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: + - 81f0cbca04a7 + - 3df9f0a4bf34 + - 7db4fc31dbee - 8bccb36e055a - 0c777d708acc - 699a5e9146b3 - - 81f0cbca04a7 - - 7db4fc31dbee - - 3df9f0a4bf34 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5bc8cdc17fd0 - - 5791a7f65275 - 2436a8807ad1 + - 5791a7f65275 - 0a53256b48c6 + - 5bc8cdc17fd0 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features @@ -30,8 +30,8 @@ tools: - name: 2d_histogram_equalization owner: imgteam revisions: - - b1c2c210813c - 77f7159d775a + - b1c2c210813c - 70316d792fc9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -54,32 +54,32 @@ tools: revisions: - fcadded98e61 - f3360fbeda64 - - 85edbb7a436b - - b07f4839ca77 - 10eed33aa9b2 + - b07f4839ca77 + - 85edbb7a436b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 6e65fd971e13 - 984358e43242 + - 6e65fd971e13 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - - 5bf8eb50b280 - 664232d2a3f7 - b58447a2eed2 + - 5bf8eb50b280 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - 0e4dccaafef5 - - e917a2424690 - eb6c08714244 + - e917a2424690 + - 0e4dccaafef5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -92,49 +92,49 @@ tools: - name: cp_common owner: bgruening revisions: - - 670975e92458 - e7273daa5ae2 - 6070780813d9 + - 670975e92458 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - ef4aed1d34c4 - df3ad3ba5c6f - cdf8e3c57dae + - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - 2484086dee41 - - 5d28ac336861 - 6a7da2e5f696 + - 5d28ac336861 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: + - f2ed92b011a9 - bace5a93a97c - 11f177b1a59e - - f2ed92b011a9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: + - d0178bdcd00e - f8fa0f6718a3 - f24c370e5ea4 - - 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 @@ -149,16 +149,16 @@ tools: owner: bgruening revisions: - ff1a86a87364 - - 6100a22bf4f2 - c09dcda1143f + - 6100a22bf4f2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: + - b178453ea8d1 - 667a513e67e4 - 3a05117669cf - - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity @@ -180,41 +180,41 @@ tools: - name: cp_measure_image_intensity owner: bgruening revisions: + - 5499dc6f8ac1 - 8536b1ae0254 - b64af54c5c09 - - 5499dc6f8ac1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - e972e07c7845 - - 6f4715b8540a - d3890df07463 + - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - 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 - 79e10d12d90a - acf3aa487283 + - d85f11570109 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: + - 80b200ae516b - 035a58c7f54a - b76841ee5560 - - 80b200ae516b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -235,9 +235,9 @@ tools: - 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 diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index cc12b95e8..be6f3d4e0 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -3,92 +3,92 @@ tools: owner: iuc revisions: - a38934e303b9 - - 78bbd17d0703 - - 1069f6db0a0e - 3a72fede57ce + - e4ee04da1c19 + - 3e4f434a69c6 + - f362150bef41 - 40737febe339 - e319b5b65879 - - 3e4f434a69c6 + - 1069f6db0a0e - d6e72da3ec35 - - f362150bef41 - - e4ee04da1c19 + - 78bbd17d0703 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - c88553ec696e + - 72ddd32392cd - fcbeda41d0ac - - 618297d23022 - - 7fe36019c073 - - 9537184d421f + - c88553ec696e - 8f8df367470d - - f91cfb73d369 - - 72ddd32392cd - 0135f1d487a0 - 2b95d5c04908 + - 618297d23022 + - 9537184d421f + - f91cfb73d369 + - 7fe36019c073 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - fafb3d685fa9 - - d7e79eb3bcb3 - - 2cf4a1cafc16 - ad0dc9f4c9e2 + - 2cf4a1cafc16 + - d7e79eb3bcb3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - 5dc33613c288 - - a1c2aecd7a0d - - 8d36959b000d - - 7f1cfa4c0e32 - - 6a1515bb0687 + - ee2beb764a7b + - 94df24c6bc00 + - ee29337f905c + - 28a6f1908fcc - 9eaadf03e0df + - 8d36959b000d - 43aac8d29685 + - 3d18f8c3c0f6 - 8c05afb547fa - - ee29337f905c - bd2a7d1316b9 - - 3d18f8c3c0f6 - - 28a6f1908fcc - - 94df24c6bc00 - - ee2beb764a7b + - 7f1cfa4c0e32 + - a1c2aecd7a0d + - 6a1515bb0687 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 5d6ed46cc101 - - 5671e1d3d5ee + - 364f4ffec275 - c092052ed673 - - 86a20ae274fc - - e3bb03cf207a + - 5d6ed46cc101 - bcaa0d571ce2 - - a250929be21b - - 364f4ffec275 - d37ede8589b2 - cb903c9dc33d - 9f978da6528a - - 8858fa037a15 + - e3bb03cf207a - db536ad45f28 + - 8858fa037a15 + - 86a20ae274fc + - a250929be21b + - 5671e1d3d5ee tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - c5c9f02b6167 - - 230b05597996 - - ed28dd32141c - - 49236b03e4fd + - 194e3ceee923 - abbc8041e8ec + - 230b05597996 + - 38b91a3190cd + - e1a015876aa9 + - c5c9f02b6167 - 3b6a16d82c1b - f95f403841ad - - e1a015876aa9 - - 194e3ceee923 - - 38b91a3190cd + - 49236b03e4fd - 12d66d0d05ac + - ed28dd32141c - 584beffa972b 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 6a544bee0..a1a9ae56b 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: + - 17e3b698dd52 - f198773344e4 - b8a457820315 - - 17e3b698dd52 - 0f1724dd59d2 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - a513e3fbb4c5 - - ba0c40780ecf - 22c2a1ac7ae3 - ac092723240d + - ba0c40780ecf + - a513e3fbb4c5 - 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 620d6b2b9..d7bbfd851 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -3,98 +3,98 @@ tools: owner: bgruening revisions: - 772e0e89fc68 - - 66d7efc06000 - 522137aaa9c4 + - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - f22a9297440f - - 8a794e6d3388 - 4d81e3e2fb63 + - 8a794e6d3388 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - 2af1346e68c9 - b6ef6d0cb6b7 - - e1317b5502fa - - f1b9a42d6809 - 818f9b69d8a0 + - f1b9a42d6809 + - e1317b5502fa + - 2af1346e68c9 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: + - c80db5d6fd8c - 947c2eacccb8 - 05143043ca13 - 1588f9076e32 - 8334dc98c48e - - c80db5d6fd8c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 1552b8cb4a94 - 83228baae3c5 - 29e4122c90de - 9991c4ddde14 + - 1552b8cb4a94 - 25b46af53232 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: + - 1a53edc4b438 + - f3dfa4bdf87e - 841a6cc5fc58 - - 53616c8b0865 - a07ab242b0b5 - 060ca94ac049 - - f3dfa4bdf87e - - 1a53edc4b438 + - 53616c8b0865 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 2fc89dcd41c8 - - 40f4447733b2 - dc4b5fd604a6 - d4808d5b83da - - 91c4e3331208 - 927586a18553 + - 40f4447733b2 + - 2fc89dcd41c8 + - 91c4e3331208 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - c6ae57f774c6 - 36e8d6d5d01b + - c6ae57f774c6 - 25ab6b4e376e - - e5a5ad882f1f - 301e07345c93 - 7626ea9c2e1b + - e5a5ad882f1f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 4ed102b922cb + - 02d2be90dedb - f9639b488779 - 0630258dcf35 - - 80852884053f - - 02d2be90dedb - b7c3e9a3b954 + - 4ed102b922cb + - 80852884053f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 14180f9c831e - - 61634a87efc7 - ec69cbe34b73 + - 61634a87efc7 + - 14180f9c831e - 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 bed3714d4..94eb01005 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - 749c918495f7 + - cd659e8cc5fa + - a6d65b0c67af - 17062a0decb7 + - 3ba8d4563129 - 0d4acadabb04 - - a6d65b0c67af - - 017aba02828d - - cd659e8cc5fa - d5ceb9f3c25b + - 937aa69e715f - 03e9b2fbc005 - f6877ad76b00 - - 3ba8d4563129 - - 937aa69e715f + - 749c918495f7 + - 017aba02828d tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -31,12 +31,12 @@ tools: - name: bwa owner: devteam revisions: - - 53646aaaafef - 64f11cf59c6e - - 2477830927ec - dfd8b7f78c37 - - e188dc7a68e6 + - 53646aaaafef + - 2477830927ec - 3fe632431b68 + - e188dc7a68e6 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: - - 60afcc2c1d05 - - 3e1ea2facca6 - 2ff111fac1d7 - - e7f19d6a9af8 + - 3e1ea2facca6 - 37b497aa133f + - e7f19d6a9af8 + - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: + - 09b53c1d4ab1 + - 3f4d6399997b + - 53c0b7a1a0c3 - 5cc34c3f440d - c0c2d0941de8 - - 77b2770508f6 - - 8c6cd2650d1f - - 3f4d6399997b + - 6b1e195506a3 - 037c6e54df11 - - 11a0d50a54e6 + - be1d967337e4 - f54f5baedfdd - - 53c0b7a1a0c3 + - 77b2770508f6 + - 11a0d50a54e6 + - 8c6cd2650d1f - b3eab4b67562 - - 09b53c1d4ab1 - - 6b1e195506a3 - - be1d967337e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 79b885ce78d7 + - 381a32c51141 + - ec9cbd6b9a49 - b8f5f6e87f5c - - 00fbfac99d39 - - 13022c3d3076 - - 9ee34ba73ebf + - e403d27e8f24 + - 79b885ce78d7 + - 42ce70172b72 - 5ef7ec16b04f + - 00fbfac99d39 - 1cd2511a396e - - ec9cbd6b9a49 + - 13022c3d3076 - 178bdbdb6d24 - - 42ce70172b72 - - e403d27e8f24 - - 381a32c51141 + - 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 9129c521d..35b512f5d 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -14,8 +14,8 @@ tools: - name: biotransformer owner: recetox revisions: - - 6cd2a9e6ac49 - 90dc951da294 + - 6cd2a9e6ac49 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_annotate @@ -57,8 +57,8 @@ tools: - name: isolib owner: recetox revisions: - - 2b1118bce0b1 - 6b0fef8a77c0 + - 2b1118bce0b1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: lcmsmatching @@ -83,8 +83,8 @@ tools: - name: matchms_filtering owner: recetox revisions: - - a177ac3c752c - 83c4b4359ac4 + - a177ac3c752c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity @@ -104,15 +104,15 @@ tools: - name: matchms_metadata_export owner: recetox revisions: - - f04610d25411 - 8832425b1ff6 + - f04610d25411 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match owner: recetox revisions: - - 03bc9b7f40f6 - 330b0dfae8da + - 03bc9b7f40f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge @@ -124,8 +124,8 @@ tools: - name: matchms_networking owner: recetox revisions: - - 8147d93d372d - f04b378325e5 + - 8147d93d372d tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key @@ -149,15 +149,15 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: - - 9ff95a1a2705 - 7ba589b01dbc + - 9ff95a1a2705 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split owner: recetox revisions: - - ea6c5636c0cf - 0cf68b536cd1 + - ea6c5636c0cf tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting @@ -169,8 +169,8 @@ 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 @@ -225,17 +225,17 @@ tools: - name: ramclustr owner: recetox revisions: - - 9b716db0a786 - da7722f665f4 + - 9b716db0a786 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features owner: recetox revisions: - - c53a97599181 - - 7b42ee54d757 - ec196e27a61a - 79ad928a0dae + - c53a97599181 + - 7b42ee54d757 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters @@ -243,63 +243,63 @@ tools: revisions: - 18ec7635bac6 - 149b9cc7499b - - f3a18e020cdd - 59c393d35e0e + - f3a18e020cdd tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - 134be5abb208 - - 481d769e2f7a - - dfebc82ba1f0 - 50b9918aeff2 + - dfebc82ba1f0 + - 481d769e2f7a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - a82db010c53e - - 30bf4e35da3e - - 501a232f3cd5 + - 02c772a49998 - 51332c2520c7 + - 501a232f3cd5 + - 30bf4e35da3e - 9064aecc78a7 - - 02c772a49998 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: + - e7305ba0dd38 - b341cfd4baf8 - 89178a72388a - - e7305ba0dd38 - b3413f335327 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - b7c8a44b9cc1 - - cf061712a184 - - 17a48d0a80f4 - dd7bbc2b99d1 + - 17a48d0a80f4 + - cf061712a184 + - b7c8a44b9cc1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - 24278c6b6d1c - 99d118321d5f - f92b1b64da93 - d7f5878a98c3 + - 24278c6b6d1c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - ea0758b41473 - - 7acd11ddc061 - d90187b0f247 + - 7acd11ddc061 + - ea0758b41473 - ffbabefbd2e2 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -312,8 +312,8 @@ 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 diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index f642a888b..32f539279 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -2,15 +2,15 @@ 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: - - 0e63d03c8790 - 0094893f5001 + - 0e63d03c8790 - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -90,21 +90,21 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 3a89c3f99f3d + - 7c2100246a2f + - 76d3d2b10738 - 63f86089423e + - 3a89c3f99f3d - 5b5a7af9fbb4 - - 76d3d2b10738 - - 7c2100246a2f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - 00f5005840fa - - 84fd33a60b35 - - 1c35dadbe76f - 96336c6a2bb7 + - 84fd33a60b35 - 18a502a9d287 + - 1c35dadbe76f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim @@ -113,113 +113,113 @@ tools: - f732237754fc - 34e55239e68b - addaf9d22850 - - a9f4a217dcd6 - e8fba04706d3 + - a9f4a217dcd6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 5fe3edf19b9c + - 0776d824d896 - 04c15826a0b8 - - 8c202e741d68 - 75403243703a - - 0776d824d896 + - 5fe3edf19b9c + - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 1c9b3bcd4261 - - 75c8945b0da2 - - 43c99742158b - e96bbb9e24ea + - 43c99742158b + - 1c9b3bcd4261 - 8470de786d47 + - 75c8945b0da2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 35176674168c - 306a40d4bb8f - - 1d75bd0595e2 + - 35176674168c - 84743da21318 - 5c865a382933 + - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - ac72310b038a + - 8daf4564ccda - 78faebd0879c - 32c9ea835770 - - 8daf4564ccda - 555ccac8a4c5 + - ac72310b038a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - f947b4bb5107 - - d60df8727f59 - - 7b8cb2b02978 - a58e4a43f49c + - d60df8727f59 + - f947b4bb5107 - cae017b76acb + - 7b8cb2b02978 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 7136e9ab70db - 1770d188f72d - - 7f3b59dee073 - - 04144473e59e + - 7136e9ab70db - 1bc3657cd694 + - 04144473e59e + - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 19299bb1c6af - - a7817705348e - 9058d8943303 - - d943081510da + - 19299bb1c6af - 0a1224c4b781 + - d943081510da + - a7817705348e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - c7e73acfa3eb - bc939965ce41 + - c7e73acfa3eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: - - 65d52c693b8e - c4db8c4de66f - - f8f56dd6449f + - 65d52c693b8e - 4d9445dff47b - - b907a3c0434f - - 5c7ba3d85a01 - dbf1798c0dcc + - 5c7ba3d85a01 + - b907a3c0434f - a68b985913ab + - f8f56dd6449f 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: + - 654548ae1357 - 6c84982ee6f7 - 6d364c65c946 - - 654548ae1357 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -231,25 +231,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - e66ab198ec15 - - 6aad8ca3918b - bd7a9c6efb10 + - 6aad8ca3918b + - e66ab198ec15 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: + - b084117133af - d77397f09da1 - c6676a890f50 - - b084117133af 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 @@ -274,15 +274,15 @@ tools: - name: humann_join_tables owner: iuc revisions: - - 6bf703133209 - f01ca38fb6c5 + - 6bf703133209 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_reduce_table owner: iuc revisions: - - 6552df6efe6b - 60749924ad62 + - 6552df6efe6b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_regroup_table @@ -290,31 +290,31 @@ tools: revisions: - e88b731dad59 - c409a495841f + - 8237a0f225db - 31c6d107e7a5 - 79706f10d680 - - 8237a0f225db tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 714d5a28cc5c + - 172920f67a84 + - aabf8cfb8fef - 71ea608ddfa3 + - 714d5a28cc5c - 094ad9c068af - d24841f5c3d2 - - 172920f67a84 - - aabf8cfb8fef tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - a293a742194f - 4137b492233e + - a293a742194f + - 12fb63b5f63f - 2bdd84912a2b - d7e9a3c41657 - a4d7148ccee4 - - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -326,13 +326,13 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - e2c71b852aba + - a92c06a3afa7 - 6fcb8ac37a3e - - 75bedfb2078b - 97f7bb0851e7 - - a92c06a3afa7 - - cf87759761eb + - e2c71b852aba - 64bc7acc22a9 + - cf87759761eb + - 75bedfb2078b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -351,21 +351,21 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: + - 4e5e73d03f0d + - c82508e76ad1 - 080ea153677c - 2d35528d2141 - - c82508e76ad1 - 5e5a999ffaa9 - - 4e5e73d03f0d - 4033827c76b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - fc6c328c292f - - 2cd76b089570 - c2803012bbb3 + - 2cd76b089570 - 6b7622dda516 + - fc6c328c292f - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -399,15 +399,15 @@ tools: - 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 owner: iuc revisions: - - adb3dd5a899f - 1061711538c6 + - adb3dd5a899f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance @@ -420,8 +420,8 @@ 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 @@ -448,9 +448,9 @@ tools: owner: iuc revisions: - 4a9da2b6c2e3 - - 20e2f64aa1fe - - cdee7158adf3 - 328c607150ff + - cdee7158adf3 + - 20e2f64aa1fe tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -476,8 +476,8 @@ tools: - name: kraken_report owner: devteam revisions: - - 6c09bed3444f - 1c677354ab18 + - 6c09bed3444f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_taxonomy_report @@ -496,8 +496,8 @@ 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_beta_diversity owner: iuc revisions: - - 4505d7643673 - c254d75b8b67 + - 4505d7643673 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_combine_kreports @@ -530,16 +530,16 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: + - 88d274322340 - 02bbace216f2 - 2deaada69b14 - - 88d274322340 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa owner: iuc revisions: - - d33cf727ed94 - bb96a1e6583d + - d33cf727ed94 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: lotus2 @@ -569,14 +569,14 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 7f5d7b0e9884 - 327d9f4cc95f - - 3cc4a60615c0 - 27250f92a01a - - 2cff76cf35c6 - - 4fd3b5d8706b - - 0270541aaf46 - e073891b2afc + - 0270541aaf46 + - 4fd3b5d8706b + - 2cff76cf35c6 + - 3cc4a60615c0 + - 7f5d7b0e9884 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 @@ -650,26 +650,26 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - fdbd63e92b01 - ebb74774457e + - fdbd63e92b01 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - fd69c607b43f - - a92a632c4d9b - - 1a6cdf55390f - - ef65b083bd0c - ff8f55893e7d - - 1a037928504c - - b89b0765695d - - 740fd2d16a28 + - ec368db926f4 - a16313517e55 - - 289b3807e80c + - b89b0765695d + - 1a037928504c - 6dee4abadccb + - 289b3807e80c + - ef65b083bd0c + - 1a6cdf55390f + - 740fd2d16a28 + - a92a632c4d9b - 2131d7dca455 - - ec368db926f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -707,36 +707,36 @@ 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: - - 709adbfcf308 - 415cb5d91168 + - 709adbfcf308 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline owner: iuc revisions: - - f53beb324696 - 6077821e8ae7 + - f53beb324696 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline owner: iuc revisions: - - d6bb2e3febda - 540aedfc81c7 + - d6bb2e3febda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -755,8 +755,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 0ba7dfaa941d - 8e2ac1b8f70a + - 0ba7dfaa941d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -774,8 +774,8 @@ 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 @@ -800,27 +800,28 @@ 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: - - 4b9a8031ab74 - - 4d83eccf5f81 + - 141afacabcfa + - aeaa20b96ef2 - 3b22de20bd4b - be818ae858e4 - - 141afacabcfa + - 4b9a8031ab74 - 2fd4d4c9c5c2 - - aeaa20b96ef2 + - 4d83eccf5f81 + - 3548a93b39c1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - 576963db5f1b - - 9495df9dd6ef - b3c7199d8786 + - 9495df9dd6ef tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index 2f857a822..d28bbc559 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - 63b74bfc8052 - f4d7d5755f01 + - 63b74bfc8052 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 72be09dfd803 - 2344ed181ae6 + - 72be09dfd803 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 6345e5bdf..404fa1989 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: - - a74dbfee5a86 - - cd07731e4434 + - 098506c54016 + - 9baa871cb1d1 + - 94b8c6013083 + - 80f03df2e2ce + - 9422c5a87ee2 - 8b67dd48fec1 + - cd07731e4434 - 9eeb13a92d79 + - a74dbfee5a86 - 6ae5a7b5a0a2 - - 94b8c6013083 + - 48c13389050d - bdfbaf0c10aa - - 098506c54016 - - 80f03df2e2ce - - 9baa871cb1d1 - - 9422c5a87ee2 - 2263989660f5 - - 48c13389050d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - c44f824c051a - - '764845535798' - f14193ec1f50 - - fc2e49f91e52 - - be78f13134e2 - - c18157c68134 - - 4a60927aaca5 + - '764845535798' - bc3831dd65c1 - - f0af8936ed41 + - 4a60927aaca5 + - be78f13134e2 - 3ff17bad4006 - - d7ce0ec78e51 + - 5abf2c2249aa + - fc2e49f91e52 - d390fe1567dc + - f0af8936ed41 + - c18157c68134 + - d7ce0ec78e51 - 2e093badc689 - - 5abf2c2249aa - aaa0d6a8b808 + - c44f824c051a tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,82 +46,82 @@ 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: - - 5b097fde95dd - d6694932c5e0 + - 5b097fde95dd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko owner: iuc revisions: - - 1de657a3198d - 5efbd15675ca + - 1de657a3198d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mafft owner: rnateam revisions: + - f0d493f8f84f + - a65296ffb4a0 - c5908940967d + - 15974dd17515 - 6f28e90db932 - - f1a5908ea2cb - bf28a8cff401 - - f0d493f8f84f + - f1a5908ea2cb - 8e649f27aa0d - - 15974dd17515 - - a65296ffb4a0 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 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - 5561a1193611 - - 60698466facd - c9685bc0407c + - 60698466facd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - 57f042937ba7 - - 48823c9635a4 - bcd65de9725b + - 48823c9635a4 + - 57f042937ba7 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 636b049e6141 - 7cd7a55a678d - e18267f90096 + - 636b049e6141 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - b4124df98b26 - - cf3c9489c088 - 959c1f8dae95 + - cf3c9489c088 + - b4124df98b26 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 87a7757ed..7466c41e4 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -24,28 +24,28 @@ tools: owner: galaxy-australia revisions: - 6942f170cc43 + - fc5b6491cf78 - 63d8ecfcfab1 - 99c9427219d3 - - fc5b6491cf78 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus_pipeline owner: iuc revisions: - - 0e9e7fcdd543 - fc8804320156 - - 79e9a869f40e - - 72b5e9dda577 - a7228a7ea146 + - 79e9a869f40e - cb34f00cc10f + - 72b5e9dda577 + - 0e9e7fcdd543 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: + - db25ec99c3ea - d6cddc06aeae - fa11aa8103b2 - - db25ec99c3ea - 18505fe2bdb1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -58,22 +58,22 @@ tools: - name: medaka_variant owner: iuc revisions: - - edf6d4003fad - - 0f5f4a208660 - - 222669c4afb6 - - 19f3b583a9b3 - ec699520444c - - cc36773a3681 + - 0f5f4a208660 - 2bf63b38ee9b - 43815fa60f3a + - cc36773a3681 - eb746fa6f514 + - edf6d4003fad + - 19f3b583a9b3 + - 222669c4afb6 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - b833eff63b10 - c0fb573c1e8d + - b833eff63b10 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -86,44 +86,44 @@ tools: owner: iuc revisions: - a38bdcec9e4c - - a3c4fe6f49ab - - 0f1c34698076 - - edbb6c5028f5 - - 7b379e98b9a9 - a02b8b3f5a0c + - 7b379e98b9a9 + - edbb6c5028f5 + - a3c4fe6f49ab - 645159bcee2d + - 0f1c34698076 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - d219b6d8158a - 3b6f94fc7e1d - 85a394edc247 + - d219b6d8158a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - 90a922f32523 - a8d4be409446 + - 90a922f32523 - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 4857d5bcce52 - d376944466bf - 449e9aeded2d + - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - a3afc5f0a96c - - bec636361cfd - de5b3d8f5b90 + - bec636361cfd tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop @@ -214,8 +214,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - c5c5a3e84989 - 64a83664b814 + - c5c5a3e84989 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index f9e388178..f12f61a1d 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -28,18 +28,18 @@ tools: owner: iuc revisions: - adfd6bf710bd - - 97b1b5ad1cda - d74850cf4e42 - - baceff842902 - 3e73c97f025d + - baceff842902 + - 97b1b5ad1cda tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: + - 83da94c0e4a6 - 1586b111d2a3 - 9dd107db92c2 - - 83da94c0e4a6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -51,21 +51,21 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 2f27f3b86827 - - 13851aefa67a - ed1518ce2237 - 8c533e19b697 - - e9ee4d074d5d - - e4b4837f06f5 - - 19b6a2f0dbe2 - 1e34d2e3d285 + - 13851aefa67a + - 2f27f3b86827 + - 19b6a2f0dbe2 + - e4b4837f06f5 + - e9ee4d074d5d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 9e993022c762 - 46066df8813d + - 9e993022c762 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -84,16 +84,16 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 5711fc06a63e - - 38ccd4589990 - 48a42ca61006 + - 38ccd4589990 + - 5711fc06a63e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -106,8 +106,8 @@ tools: - name: data_manager_fetch_busco owner: iuc revisions: - - 2b4526fdf7fb - 15b97817550a + - 2b4526fdf7fb tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta @@ -126,17 +126,17 @@ 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: - 52b6a4d98009 + - 172815da3d41 - b4b2b284230a - 27a6a256cd23 - - 172815da3d41 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -148,8 +148,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d210e1f185bd - d74c740bdb25 + - d210e1f185bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -161,9 +161,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 87febc68b45b - - fea85c467896 - 19bbd19b74b3 + - fea85c467896 + - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -176,8 +176,8 @@ tools: - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 4c7ebbad42cf - 15c2fc266540 + - 4c7ebbad42cf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -195,19 +195,19 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 2c61c30a57e7 - d8dc037e3c13 - - 0cb27ea69dc1 - 5fe20c915fa6 - - 4ba60cb14cb0 - 9c43baa60906 + - 0cb27ea69dc1 + - 2c61c30a57e7 + - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - d9339bb8127e - 14785f8a3725 + - d9339bb8127e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite @@ -221,10 +221,10 @@ tools: - name: data_manager_pangolearn owner: iuc revisions: - - 29c738066906 - 6e24e79d3d69 - - ed7a967cb11b + - 29c738066906 - df30a2f1db55 + - ed7a967cb11b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -242,17 +242,17 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - defd3e9ddd2d - - 3e4d45aca422 - - 1865e693d8b2 - ad90c2da4f38 + - 1865e693d8b2 + - 3e4d45aca422 + - defd3e9ddd2d 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 @@ -264,18 +264,18 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - d63c1442407f - - 71c994a11f71 - - 64deddb6a8ec - c520a52b5174 + - 64deddb6a8ec + - 71c994a11f71 + - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - 94a50db37d1a - - 9946bc39c834 - 625fd9476402 + - 9946bc39c834 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -320,12 +320,6 @@ tools: - 70227007b991 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu -- name: ncbi_fcs_gx - owner: iuc - revisions: - - 32d058f3462a - tool_panel_section_label: None - tool_shed_url: toolshed.g2.bx.psu.edu - name: no_unzip_datatype owner: lecorguille revisions: @@ -792,8 +786,8 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - 544f6d2329ac - d64562a4ebb3 + - 544f6d2329ac tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes @@ -805,11 +799,11 @@ tools: - name: salsa owner: iuc revisions: - - ab5b7f6b7198 - - f77f7a7f3b83 - - 58a870ef434c - ba7b0f11e470 + - 58a870ef434c - 9a22227bb6d0 + - f77f7a7f3b83 + - ab5b7f6b7198 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index 97e568efe..2d2ddb35e 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 @@ -33,66 +33,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 107d3ba7024a - - 3f59ebfbfe3d - - d7c7ef3353fe - - f04a1264e2a2 - - 6a457678efcb - - cce7b18495e4 - - f73435dc282b - - d033ffc1c161 - 5a7c56a5cc08 - 8834daeb9892 - - c78f3d7dd1db - - 26de3a7b1cb9 - - b89cac5156ec + - 3b8b5bde0bd9 + - d7c7ef3353fe - a6619171428e + - b89cac5156ec + - f73435dc282b + - 6a457678efcb + - c78f3d7dd1db + - d033ffc1c161 + - f04a1264e2a2 + - cce7b18495e4 + - 107d3ba7024a - '841557158611' + - 3f59ebfbfe3d - 81e66674859e - - 3b8b5bde0bd9 + - 26de3a7b1cb9 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - aa8cc71438cf - - 3b96e92e8ec3 - - 4755f52427c4 - - 6283babe736e - - 6a726db04d4b + - df47d4845b62 + - 5b777002c2de - 02b8758214b0 - a185b079b095 + - 4755f52427c4 + - aa8cc71438cf + - 7a2092844346 - b0af57c1a968 - 88c4aa435ded - - 5fcd1ece3a6e - - df47d4845b62 - - 7a2092844346 - - 5b777002c2de - - 659517798cc4 - 6223845127ea + - 6a726db04d4b + - 5fcd1ece3a6e + - 6283babe736e + - 3b96e92e8ec3 - e75442c7f4da + - 659517798cc4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - f87ac61981f0 - - d1c340a5664b - - f97743d52b87 - c1d53e95327f - 24d024316465 + - f97743d52b87 - b8476e82ac20 - 111bd54f6bc4 - 70acec670c30 + - d1c340a5664b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - 4f6349228462 - - feb40665d7cd - - daddf188c13f - 9e10ba792be2 + - daddf188c13f + - feb40665d7cd tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -104,26 +104,26 @@ tools: - name: pangolin owner: iuc revisions: - - 03ed9524dcd1 - - 3a43c3982401 - - 83a69484cb87 - - a2099fb98cdb - 2fa9d4f1b48f + - abf6dbe8c9d7 + - 3a43c3982401 + - 7bb8726be37c + - 9d61d3fa046c + - 14ae456b8cc5 - b7e297c2ede6 - - 8ad84c5753ea - 81804a978fc0 - - 5f8727ff21e7 - b6abccb1f25b - - abf6dbe8c9d7 - - 36912871ccdc + - 8ad84c5753ea + - a2099fb98cdb + - 83a69484cb87 + - 437e28791761 - 42a174224817 + - 03ed9524dcd1 + - 36912871ccdc - ca337cce3888 - ca0d8cf80567 - - 7bb8726be37c - - 14ae456b8cc5 - - 9d61d3fa046c - 2f1019071464 - - 437e28791761 + - 5f8727ff21e7 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -142,23 +142,23 @@ tools: - name: raxml owner: iuc revisions: - - ea30d3089354 - - 29ff6a849eac - - b1e68bbe4cef + - a4b71be30c3c - ba29b5e2a4be + - 29ff6a849eac - 73a469f7dc96 - - a4b71be30c3c + - b1e68bbe4cef + - ea30d3089354 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 91887494eb97 - dbe2b2204555 - e88a7de55d6e - - f1ccc8a6eb05 - 9b2b122d0415 - - 809e42326fc2 + - f1ccc8a6eb05 - 15ac71df11a0 + - 91887494eb97 + - 809e42326fc2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/picard.yml b/usegalaxy.org.au/picard.yml index 4255d381c..c990c890a 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - fc288950c3b7 - a1f0b3f4b781 - - b502c227b5e6 - - 3f254c5ced1d + - 1aac2a13842a - 881d7645d1bf - f6ced08779c4 - f9242e01365a - - 1aac2a13842a + - b502c227b5e6 + - fc288950c3b7 - 7d34178f2812 + - 3f254c5ced1d 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 d2d66817e..bd3102297 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,18 +2,18 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - 5b85006245f3 - - 6ab1a261520a - - a58f7eb0df2c - - 3f188450ca4f + - e7f1b552a695 - c0e71cb2bd1b + - 6ab1a261520a + - 7fbec959cf2b - 2f7702fd0a4c - - e7f1b552a695 + - e4a053d67e24 + - 3f188450ca4f + - eb085b3dbaf8 - 3bd420ec162d - ca90d17ff51b - - eb085b3dbaf8 - d00e15139065 - - 7fbec959cf2b - - e4a053d67e24 + - 5b85006245f3 + - a58f7eb0df2c 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 1ceb4d7d9..4bae70b66 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,72 +2,72 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - b18329a8ac14 - - 277dc652246e - - 0a18ac48ac53 - - b574b84afc4d - 4c177985028a - f28ad96b76dc + - 277dc652246e - ece627528a78 + - b574b84afc4d + - b18329a8ac14 + - 0a18ac48ac53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - a9a28e46d54a + - e988563cc6e5 + - b41107d8fe89 - bf06d196e23d - e215f71d7983 - 525f201b86c1 - - b41107d8fe89 - - e988563cc6e5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - bb6397b94018 - - 56da27be956a - 4fbffddde8cd + - 56da27be956a - 8da3511c9467 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - f23d67e28cc8 - 528fb09022be - - 890845926d4b - - a8157342d9a3 - b8c79e70516d + - f23d67e28cc8 + - a8157342d9a3 + - 890845926d4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: + - a69865da6f80 + - a95a82eb4d50 - 80600735685d - - 25b83cbd596a - ae304a72db7b + - 25b83cbd596a - 59e85306eae5 - - a69865da6f80 - - a95a82eb4d50 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - ed9ed1e6cca2 - 83aac7741200 - - 798da6bdff3d - 611d80c0e29d - e0669b1854b1 + - 798da6bdff3d + - ed9ed1e6cca2 - f1897eb07081 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - d426a9107a6c - a7fb9b395ddf + - d426a9107a6c - 5a35e3a8d013 - 74b61bf5bc4b tool_panel_section_label: Proteomics @@ -75,21 +75,21 @@ tools: - name: cardinal_segmentations owner: galaxyp revisions: + - 91f0f5922011 - cc430977c8ff - df2187f9013b - - 91f0f5922011 - 82f6c2f4332d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 043f9c91f686 - - c5aa9fca18c6 - ba92b59cd529 - - d2483487e077 - 1693b2126f30 + - 043f9c91f686 - 10566783d718 + - d2483487e077 + - c5aa9fca18c6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -107,10 +107,10 @@ tools: - name: diann owner: galaxyp revisions: - - ae4dc0c041f9 - - ff8c9e0e8a7b - - bf0728e000cd - 9fa3dbf06f17 + - bf0728e000cd + - ff8c9e0e8a7b + - ae4dc0c041f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -130,16 +130,16 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: + - 1c5cbf8f79ce - 0fa397f4f40b - 4081e4faa4ab - - 1c5cbf8f79ce 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 @@ -159,9 +159,9 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - e66f552a3c47 - - 160538a890a6 - d286ff4600dd + - 160538a890a6 + - e66f552a3c47 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: - - 7f432d87c82c - 97a7f34fcb6a + - f522c08e900c + - 4d17fcdeb8ff + - 2133b0be850a - 837224ad1694 - - 9c52362ae7bb - 1f39c833f65f - - 2133b0be850a - - 4d17fcdeb8ff - - f522c08e900c - - 37d669de2828 + - 9c52362ae7bb - e42225f8a659 + - 7f432d87c82c + - 37d669de2828 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -202,28 +202,28 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - a72ac2c7cc5b + - e63db1aa82ee - 85b8866f06d7 + - a72ac2c7cc5b - 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 + - 1974224d63c2 + - 990b4560ead7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: + - 99450519d727 - 35cc7ca0bdc7 - - deaf035bbe9f - 4f359549383c - - 99450519d727 + - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample @@ -231,33 +231,33 @@ tools: revisions: - 06f6826d380c - c7745841de24 - - e79958768a2c - c1343e3389ca + - e79958768a2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - da986f83631b - d46d64e7964d - b9d453dca8d3 + - da986f83631b - d2eac53666f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 8bd7734309f6 - 1199751329b0 - - 944b43462104 + - 8bd7734309f6 - 9bf325045235 + - 944b43462104 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus owner: galaxyp revisions: - - e0104a9f20f0 - 8295d959ca28 + - e0104a9f20f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert @@ -270,10 +270,10 @@ tools: - name: msstats owner: galaxyp revisions: - - 593839e1f2c3 - - de7593c29499 - - 28434abe6c5c - 8212e342e482 + - 28434abe6c5c + - de7593c29499 + - 593839e1f2c3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -286,18 +286,18 @@ 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 owner: galaxyp revisions: - - 370141bc0da3 - 25529df60a81 - 06cca574e337 + - 370141bc0da3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate @@ -305,52 +305,52 @@ tools: revisions: - f7fef900f5b2 - 6ccbf9a2072c - - 518b1730cf2a - c9eff69a7c62 + - 518b1730cf2a - 9cdf15d3cfc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - dff6c756eee5 + - 9876bda3ec53 - ca88bd28f116 + - dff6c756eee5 - 5e948629bc73 - - 9876bda3ec53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 41859bbdc16e - 1595601708ec - - 890025d6e426 + - 41859bbdc16e - 658494a2cb00 + - 890025d6e426 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 6634cad7d797 - 9b7977080f6d - - 2a93a25f0599 + - 6634cad7d797 - 5ad0b5bf1deb + - 2a93a25f0599 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: + - d6878d27f051 - 05d5e1ddc985 - - fe4e4587d265 - 0bb5056cb775 - - d6878d27f051 + - fe4e4587d265 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 52ba9695e752 - 5ad830edc021 + - 52ba9695e752 - febd569ad26f - 4af67edd5aef tool_panel_section_label: Proteomics @@ -358,84 +358,84 @@ tools: - name: openms_filemerger owner: galaxyp revisions: - - b2fc8da99bcc - 39e8fde08881 - 27cba4c5fc42 - 92352a475eed + - b2fc8da99bcc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - d3546bb9fd8e - 9e26f5c770f8 - - d413dc49d650 - 0efbc235f314 + - d3546bb9fd8e + - d413dc49d650 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - ca1740533b59 - - 8a04ed1c1d1b - 3720e349ba2a - c28f13cab67a + - 8a04ed1c1d1b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - ca799a7246e7 - - 382cde407f81 + - c55dddc5844a - c427a8628cbe - a5d785af0ad8 - - c55dddc5844a + - ca799a7246e7 + - 382cde407f81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - b5d0905419da + - adca857b4884 - 8ddb7bab1138 + - b5d0905419da - 39caaa778d2e - - adca857b4884 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 1c5f31b8d632 - - 34e7afee141d - 18f93351f8b6 - - f817513840a9 - 8d4db262964c + - f817513840a9 + - 34e7afee141d + - 1c5f31b8d632 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: + - 986e03d3201e - c69f69d7867a - - 111c3a00136d - 5d9f175dff81 - - 986e03d3201e + - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - be74a8cd7d66 - - 0e52c85f3b15 - 4204882495f2 - 476b5e296979 + - 0e52c85f3b15 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - f5ec766d80cf - - c18d8efa4474 - - a407b6790342 - 2b2a7551a857 + - a407b6790342 + - c18d8efa4474 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver @@ -449,42 +449,42 @@ tools: - name: openms_mztabexporter owner: galaxyp revisions: - - bf32e0bcf554 - - ee860980edc6 - 8098330f6d91 - 2735db4dd8d9 + - bf32e0bcf554 + - 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: + - de7a553552a6 - 8c01da82292c - 2a9ff56cb279 - - de7a553552a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: + - e8f64a7dc470 - c1809c05ae8c - 1bf940c18d93 - - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -506,25 +506,25 @@ tools: - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - f82b320ceb90 - 05ec9fb05ed1 + - f82b320ceb90 - f9ed7e074900 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - d31426ef20f6 - 6e8cc5ed2a9b - 18826fb8e5db + - d31426ef20f6 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 @@ -532,59 +532,59 @@ tools: revisions: - 5ae104d0da6e - 3d8d4ada5405 - - decc397c3b7e - 6b01678ec2fc + - decc397c3b7e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - d6aca689dd48 + - 539a3a4dcc9e - e039cc5c7aed - dd173849c3d8 - - 539a3a4dcc9e + - d6aca689dd48 - 5182338d5e7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 16026cdb1330 - - 8a45fd5a608a - 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 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: - 9020199dba0a - - 1b03536aa3c9 - d063e2fe4ba4 + - 1b03536aa3c9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - ad2ba3a95a02 - f036e8cf1a55 + - ad2ba3a95a02 - 78c080d36945 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: + - fb52e95a370c - c8b225c69a7f - - 7f6a1f27553e - 5c2a97a234d6 - - fb52e95a370c + - 7f6a1f27553e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -610,14 +610,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - a72c48001f7c - - 3634c90301af - 1beff3ddce58 - - 7fdd9119cc4f - - 3ec27b4cee7c - 943a34df6047 - da885ca16cb2 - 07ff622ec007 + - a72c48001f7c + - 3ec27b4cee7c + - 3634c90301af + - 7fdd9119cc4f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -677,11 +677,11 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 1a5690a5eedc - - 265c35540faa - 4ddc8da62671 - a371252a2cf6 - 12692567c7f9 + - 265c35540faa + - 1a5690a5eedc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/usegalaxy.org.au/qiime_2.yml b/usegalaxy.org.au/qiime_2.yml index 52697721b..bf015d3f9 100644 --- a/usegalaxy.org.au/qiime_2.yml +++ b/usegalaxy.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 18c6b2b6740f - 10447a4b0cc3 + - 18c6b2b6740f tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index c962cc92d..82a9d91c0 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,109 +2,109 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 42201b90e3f4 + - 289b7d6b69a4 + - e345aadf914f - 2f1d464ebfd2 + - 42201b90e3f4 - 110a346daf36 - cd5f98911089 - - 289b7d6b69a4 - - e345aadf914f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - c207119ba5f6 - - 8501601a118d + - fcce77c09289 + - 0cd2df8af811 - 42d9087b4789 + - 8501601a118d - 0345dbaaa79b - - 0cd2df8af811 - - fcce77c09289 + - c207119ba5f6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - 405a212b32ab - - 89eb29319bf4 - ad5ab22ffe24 - 04db7fd6b238 - 421c33b8bf17 + - 405a212b32ab + - 89eb29319bf4 - 33486216eec0 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - 7370bb65bad4 - - fa51dc5e8386 + - 7b72fde3d27e - f6e91108b7b1 - - 1d839ead7ad3 - eb784fa07f80 - - 7b72fde3d27e + - 1d839ead7ad3 + - fa51dc5e8386 + - 7370bb65bad4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: + - 8a55d29c8fcf - 3d70c2996730 - d30e36c48c93 - c9b77ced9a78 - - a3e86cd9cac7 - 1544278c272e - - 8a55d29c8fcf + - a3e86cd9cac7 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - a5969aa9347e + - b242deb58952 - 887cf585cafc + - 564c33e5c3e3 + - a5969aa9347e - e2db212d64ad - 7b881f5f5ad5 - - 564c33e5c3e3 - - b242deb58952 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - e897c74a48bb - bd5ff77e2036 - - 9a171f9a450b + - e897c74a48bb - b4bab607eb05 - 8cff84759bf6 + - 9a171f9a450b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - adc7a7610d4f + - 33f0793edf93 - 5e10f396979e + - 887e0991eb24 - 4f65e343ecdf - 6dafad990086 - - 33f0793edf93 - - 887e0991eb24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - c287418eb288 - - c5d7050e4ad7 - - 17d39bf0a63a - - 43e3eeb2e0ec - 97575d01f06b + - 17d39bf0a63a - 4e280b27a831 + - 43e3eeb2e0ec + - c5d7050e4ad7 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - d9bf483266a1 + - 9586f08634c0 - 09b8edb56d80 - - cd034465d4a4 - a819ec3b362d - - 9586f08634c0 + - cd034465d4a4 - 0b8c84a7fdb5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -113,21 +113,21 @@ tools: revisions: - a4b4bd84f69e - 95351dd0fd3f - - 2645575d1bf2 + - bf0e43ab0416 - 69842dd5aa48 - a9c34a289493 - - bf0e43ab0416 + - 2645575d1bf2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - cfb504394ae1 - 912f904a6e1e - - d1fda11e602f - - 8a35a3bc6752 - bb0475c884ff + - d1fda11e602f - d033e1ccb386 + - 8a35a3bc6752 + - cfb504394ae1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -163,9 +163,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - 95286af4139b - d1fad35bdb4a - d504d945a655 + - 95286af4139b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index f2e3e7b49..e4a953d7f 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,19 +2,19 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 7acb00fc980a - 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: - 7a5a2d28c539 - - 125d20cb23d7 - 703a2cb3fb38 - 32e542c2a773 + - 125d20cb23d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -34,8 +34,8 @@ tools: - name: blockclust owner: rnateam revisions: - - dbb6ee3179bc - aab6cf87b40a + - dbb6ee3179bc tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cemitool @@ -105,19 +105,19 @@ tools: - name: cuffmerge owner: devteam revisions: - - cf747d1bd79a - - 22cf48ad7b16 - - 6a6717a5f421 - - 04adc9db1581 - 86285ddd4512 + - 04adc9db1581 + - 6a6717a5f421 + - 22cf48ad7b16 + - cf747d1bd79a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: - - 28b94cfbfdb9 - - 6cbfede05833 - 9a854107dbb2 + - 6cbfede05833 + - 28b94cfbfdb9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -151,47 +151,47 @@ tools: - name: deseq2 owner: iuc revisions: - - d027d1f4984e - - 9a882d108833 - 24a09ca67621 + - 9a882d108833 + - d027d1f4984e - 6a3a025714d3 - - 8fe98f7094de - - 0696db066a5b - cd9874cb9019 + - 0696db066a5b + - 8fe98f7094de tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - df929f257179 - - b47c006d90c5 - 2872c633f07e - 62adf13b86ea + - b47c006d90c5 - 9a7c5b6d8f1e + - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - ae2aad0a6d50 - - 5bf899c13979 - - f2843df56434 - - 0cb907a2a810 - - 334ce9b1bac5 - - 9bdff28ae1b1 - - 6e53e565fc6a - 070900306913 - - 3d89af8a44f0 + - 334ce9b1bac5 + - 555659de7321 - a8305cf0c951 + - 9bdff28ae1b1 + - 5bf899c13979 - df0c8d0a5992 - - 555659de7321 + - 3d89af8a44f0 + - 0cb907a2a810 + - f2843df56434 + - 6e53e565fc6a + - ae2aad0a6d50 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea owner: iuc revisions: - - 31ea4992b948 - fba1660fb717 + - 31ea4992b948 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: express @@ -203,18 +203,18 @@ tools: - name: featurecounts owner: iuc revisions: - - e6a2a912677a + - f3a5f075498f - a37612abf7f9 - - f9d49f5cb597 + - 1b851f87fbe0 - a56fbe2d6ba7 - - 90d16db017d7 - - ea04b737afa0 - - f3a5f075498f - 7db9d3ea71c9 - 38b6d12edc68 - - 1b851f87fbe0 + - 90d16db017d7 - af814359d244 - 6f66ae7c5f7a + - f9d49f5cb597 + - e6a2a912677a + - ea04b737afa0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -238,8 +238,8 @@ tools: - name: gffcompare owner: iuc revisions: - - 3c5e024a18cf - 3c97c841a443 + - 3c5e024a18cf - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -254,19 +254,19 @@ tools: revisions: - 3fb01a8c902d - 26371a1df031 + - d4b55e2beb12 + - a86e80d3c09c - 6ab42baa56e9 - 6c19daec423d - - a86e80d3c09c - - d4b55e2beb12 - f4af63aaf57a 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 @@ -278,33 +278,33 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 01247aaf0a10 - - ce5d418183c5 - - 1c75aa5de15e - 87c11c05d238 + - ce5d418183c5 + - 01247aaf0a10 - 5ae5c312d718 + - 1c75aa5de15e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: + - 10c98fab6c5a - c971db6f0fe5 - 40985510cd98 - - 10c98fab6c5a - 4f9c4e6566e5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 97e06a4c7c75 - - 58c35179ebf0 - - 32511f586472 + - 708348a17fa1 - 119b069fc845 + - 58c35179ebf0 - d6f5fa4ee473 - - e827f9aae031 - - 708348a17fa1 + - 32511f586472 - 0921444c832d + - 97e06a4c7c75 + - e827f9aae031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -360,21 +360,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 0a563fd2f22e + - c772497b2c32 + - 980d2a2e1180 + - 5ec75f5dae3c + - b0f2be869d6d + - 7ed2edc1337f + - 4df95e2d7f61 - e132e7d02a3e + - b9e04854e2bb + - c7c55b694974 + - 79de45b5069b + - 0a563fd2f22e - 53255f6eecfc - 99b17b74a8cd - - 7ed2edc1337f - - 79de45b5069b - - 980d2a2e1180 - - c772497b2c32 - 4074fc1940e2 - 3ea5a2a63fa2 - - c7c55b694974 - - 4df95e2d7f61 - - 5ec75f5dae3c - - b0f2be869d6d - - b9e04854e2bb tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -386,36 +386,36 @@ tools: - name: salmon owner: bgruening revisions: + - f4d5237a84f6 - e3d32471da11 - - 49121db48873 + - 15cd64d7c58b - ebab418107f5 + - 53e9709776a0 + - 49121db48873 - cc05793bb896 - - 15cd64d7c58b - 2c0ca397d302 - - f4d5237a84f6 - - 53e9709776a0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - 8c28affc7c48 - - c0fd285eb553 - fab6ff46e019 + - c0fd285eb553 - 56242ff81c84 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 1ebd14235b92 - 76d290331481 - - cef79931dda5 + - ae618321f34a + - cbf488da3b2c - 914cfcba0ec8 + - cef79931dda5 - 258d696dbd7e - - cbf488da3b2c - - ae618321f34a - dd4df992d93d + - 1ebd14235b92 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -445,28 +445,28 @@ tools: - name: transdecoder owner: iuc revisions: - - c6334cb383ff - 0db979fead3a - - ffd1300599a1 + - c6334cb383ff - d0d4cef4f967 + - ffd1300599a1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - d6a479fd4281 - - 74217fbfba4d - bcc5f03f1900 + - 74217fbfba4d - ba3720d7e68b + - d6a479fd4281 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - c2b82a94493e - 2fb4ee002432 - - 478f36effca1 - 56162e446004 + - 478f36effca1 + - c2b82a94493e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -480,56 +480,56 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 870ac06dff8e + - 34a018cbee9c - be3f26533209 - 4687ecf0eb2d - - 34a018cbee9c + - 870ac06dff8e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: + - c5fbddcac63a - 05ab8d5e04a2 - - 33406f5a445c - 5192f657f305 - 65e7dea767ea - - c5fbddcac63a + - 33406f5a445c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - e406ac71165d - 1fdb25a8384d - - 6f0fb35b799c - a35cba31d904 + - 6f0fb35b799c + - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - - 37a1129c89d2 - - 964b7efe2639 - c2c039e421af + - 37a1129c89d2 - 7c7fbf13aadd + - 964b7efe2639 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - 24e94d84adc9 - - 047c22569787 - eafea3083352 + - 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 - 1812dbc5bb7b + - 3a4ac03d1266 - 04bb8bb7c198 + - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_stats @@ -548,14 +548,14 @@ tools: owner: iuc revisions: - 48636f857c4b + - d84caa5a98ad + - db1f362cca3e - d2bc35f3d1c5 - - 32b86cd8eb50 - 8f1c3df4dd49 - - c9cfec002f71 - - d84caa5a98ad - - 9fa24d5aac68 - cee61b3fcf78 - - db1f362cca3e + - 9fa24d5aac68 + - c9cfec002f71 + - 32b86cd8eb50 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 700ffb5e7..6715dd810 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -3,8 +3,8 @@ tools: owner: nilesh revisions: - 27e16a30667a - - 473382134e56 - 1a052c827e88 - 080fd5739bb4 + - 473382134e56 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 4ba8d551c..d17a214b4 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,18 +2,18 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 10184eaa85fc - 3c661e57a88f + - 10184eaa85fc - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - - 1dfd95ee241e - 993b19f20c76 - - 108db6635177 + - 1dfd95ee241e - cb20f99fd45b + - 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: - - 30a201c9c310 + - 19ece8afbaab - e7fd6754d093 - 5f8e69cc4c6e - - 19ece8afbaab + - 30a201c9c310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -123,26 +123,26 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - 649a225999a5 - 56c31114ad4a + - 649a225999a5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - - 9149ad20699a - - 46c6639921f1 - 6856f8a01905 + - 46c6639921f1 - 12749212f61b + - 9149ad20699a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: + - 33208952b99d + - 06dc50b7b711 - 92ec40abcdcf - 26b4f9f98aca - - 06dc50b7b711 - - 33208952b99d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_coverage @@ -160,63 +160,63 @@ tools: - name: samtools_fastx owner: iuc revisions: - - a8d69aee190e - - b3d99709fe1a - 720217c23995 - - 66e23b11feae + - b3d99709fe1a + - a8d69aee190e - b906586a6596 + - 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: - - cc61ade70eb8 - - fefd89ab563c - db17d5321bad - - 22970df7a40e - fe34990e5ce7 + - fefd89ab563c + - 22970df7a40e + - cc61ade70eb8 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - 7def34e6cf4d + - fa5d3e61e429 - 7a6034296ae9 - 88b8c2916784 - - fa5d3e61e429 - 811fc2d75ad4 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: - 65a38e8c8e2a + - cae2794d2deb - 36677f429310 - b40e2d865d52 - - cae2794d2deb - 740ce0a18f0d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 583abf29fc8e - - b61f5d6a7f25 - 9da0311ab1dd + - b61f5d6a7f25 + - 583abf29fc8e - 329deb17a9f7 - 8da515fbc1bf tool_panel_section_label: SAM/BAM @@ -233,8 +233,8 @@ tools: revisions: - db000c6007a0 - 30388d878f81 - - 85e38b31e8b3 - bb8cfc6f6e0c + - 85e38b31e8b3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -246,9 +246,9 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - 344fc91e1bfd - - b8beef827165 - a4a10c7924d1 + - b8beef827165 + - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -256,44 +256,44 @@ tools: revisions: - cab3f8d35989 - d54a4df48867 - - e613c1ad4c4c - 6c2c1836728b + - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: + - bd850490c7f1 + - b7f7826ef1cd - 818030fa6bbf - 5d9ae78f34d3 - - bd850490c7f1 - 135c85f4cfaf - bcedabb53ddf - - b7f7826ef1cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 145f6d74ff5e + - 24c5d43cb545 - 1cc79f49b8d5 - - 3a0efe14891f - 541082d03bef - - 24c5d43cb545 + - 3a0efe14891f + - 145f6d74ff5e - 5a08c09b9311 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - b72793637686 - 32dc5f781059 - - c370440f901e - - 2dce91e11ca7 - - 6be888be75f9 - 0dbf49c414ae - 350bbc5c2ffd + - b72793637686 - b01db2684fa5 - - bf328cec6a42 + - 6be888be75f9 + - c370440f901e - 5826298f6a73 + - 2dce91e11ca7 + - bf328cec6a42 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 073253e2c..ef2f05264 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: - - 59bb6d34fca6 - a62c4a11a67d + - 6f6537780379 - d147d6455873 - - 480d9e9d156b - - 5cb6146337d8 - 4aab5ae907b6 + - 59bb6d34fca6 - ea5e944f447d - - 6f6537780379 + - 5cb6146337d8 + - 480d9e9d156b 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 17b6a2d09..3a5389252 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -8,32 +8,32 @@ tools: - name: alevin owner: bgruening revisions: - - e4c01dcece8b - - b0fe3e482cb7 - e32b215b7c04 - - f2000bc73102 - ecb9ea6269ee + - f2000bc73102 + - e4c01dcece8b + - b0fe3e482cb7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - 707023fa62fe - - e1c3c2f2a834 - c0b037b12765 + - e1c3c2f2a834 - 7a6655aa6eb2 + - 707023fa62fe tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 6f143dfe902a + - 00712416fdaa + - fb9e030ffae4 - 93dd15e13e6a - 55e35e9203cf - - fb9e030ffae4 - - 32e547223c9e + - 6f143dfe902a - cfc3f5a57dc6 - - 00712416fdaa + - 32e547223c9e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -42,49 +42,49 @@ tools: - b9fac48532eb - 14c576ea6148 - 688357ad5e61 - - 39e945f0b2c1 - 038e32885fec - - 6f0d0c784f09 - ee98d611afc6 + - 6f0d0c784f09 + - 39e945f0b2c1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - c4209ea387d4 - - 3d748954434b + - 9bd945a03d7b - d4af736e7b83 - 43cb7b5a6fe7 + - c4209ea387d4 - b85871dd69f9 - ed4996a16f7f - - 9bd945a03d7b + - 3d748954434b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - - a4774b7b2e85 + - fe75d2414dc0 - 2e8022f1923c + - a4774b7b2e85 - 890fb06a2893 - 7ebc22f77d86 - - fe75d2414dc0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 02b1fe7aed76 - - 769d815e4b0d - - 4fff5a293013 - 0e70b2dfe4be + - 4fff5a293013 + - 769d815e4b0d + - 02b1fe7aed76 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: + - a90f8efe08b4 - 344c2af50552 - aa4a6f0916b4 - - a90f8efe08b4 - c29e7bb492bf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -92,16 +92,16 @@ tools: owner: iuc revisions: - c32347702e12 - - 5b7c81b35b89 - 050cf43887d3 + - 5b7c81b35b89 - b13d3e4c48e1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 239193b96d72 - 1d77986f9ddc + - 239193b96d72 - 02fc39c8610d - ae969fdb8442 tool_panel_section_label: Single-cell @@ -139,11 +139,11 @@ tools: - name: dropletutils owner: iuc revisions: - - 2c1200fba922 - - a9caad671439 - cfe1e6c28d95 + - a9caad671439 - 8855361fcfc5 - cdf4443d5625 + - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: episcanpy_build_matrix @@ -173,9 +173,9 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - c3ffb2c1e314 - fb7068d30ec9 - 01c37e54e86e + - c3ffb2c1e314 - 952abbc4b1de tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -184,44 +184,44 @@ tools: revisions: - 9d42a6133690 - 57aeaf6b237d - - 45828071edc3 - f1c35f3f310d + - 45828071edc3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: + - 1a31e75e979e - 163fd744e235 - cab616fe7e64 - - 1a31e75e979e - 23b8d6b8960c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - f47ac4a0b337 - - 013e53ccc7ac - b9ab56aecd18 + - 013e53ccc7ac - '920526260066' + - f47ac4a0b337 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - a63e9713c39d - - f6a169b5e43b - 9ea228a9afc8 - b892fa1fcaec + - f6a169b5e43b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - f8320df1866b - 640e0e45518a - - ff1af7bac1cb - 45a386d18509 + - f8320df1866b + - ff1af7bac1cb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel @@ -229,52 +229,52 @@ tools: revisions: - 6f8debcf2ac9 - c354255ff705 - - f963c251ac77 - 9d02f1819e81 + - f963c251ac77 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - c4ed35f4f77f - - f881c94fb3b3 - 37125838e360 + - f881c94fb3b3 - 40fee49bc6c3 + - c4ed35f4f77f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - e8760fc0e29b + - 2dccb6bb0add - 782bdcb775fb - e06265d204f6 - - 2dccb6bb0add tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - f0216498a666 - 30677e95bc89 - - 63c8377c58b3 - b05f662f9f35 + - f0216498a666 + - 63c8377c58b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions owner: bgruening revisions: - c72fa6cb8817 - - 3240e8a7c54f - - fe3aa71590d5 - 8a11d70b6cd8 + - fe3aa71590d5 + - 3240e8a7c54f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - 5dd1aae12f03 - - e03780179ee5 - 4f9305d3bb34 + - e03780179ee5 - 3ee5332bf57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -282,18 +282,18 @@ tools: owner: bgruening revisions: - a315574104c6 + - 3a6a5381db36 - 4401ed529d2c - 87eb9c58cd19 - - 3a6a5381db36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - 2ba6cee8e4db - - a83732c79949 - 574f295b5ba4 + - a83732c79949 - c0737631eea1 + - 2ba6cee8e4db tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix @@ -301,15 +301,15 @@ tools: revisions: - 937b7b9832d0 - ea19190ce5e0 - - 30d7390bc918 - 62b720dceb56 + - 30d7390bc918 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - cd40ca76865a - 2786a931cad2 + - cd40ca76865a - 2b4d6a8dab36 - 0f5786ffa10d tool_panel_section_label: Single-cell @@ -317,62 +317,62 @@ tools: - name: hicexplorer_hicdetectloops owner: bgruening revisions: + - bf9379529c3e + - ffc33339cd3e - 4375e25de06a - 0410b6aada45 - - ffc33339cd3e - - bf9379529c3e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: - 5dfba24d7bdd - - 07dd436ea686 - 77d8e0fd162a - 4977f65da0ff + - 07dd436ea686 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - 6c5097f6d41e - - f0b1bd38745a - 972dcccb5bbc + - f0b1bd38745a - f1b3902f8baf + - 6c5097f6d41e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 3e5c86c2f80d - - 7f7c6ead2d0d - bb8849fca57c - 409396ea5cf0 + - 7f7c6ead2d0d + - 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eeab712b0b99 - e98619de2776 - - 59be31ac9dc3 - 4b0adaa31c95 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -499,23 +499,23 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 2cfd0db49bbc - - 7ffaa0968da3 - 48f0fb3061b1 + - 7ffaa0968da3 + - 2cfd0db49bbc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 56371b5a2da9 - 8cd2ecfa2e61 + - 56371b5a2da9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset owner: bgruening revisions: - - 8c64a2da3869 - fde4c972e7c5 + - 8c64a2da3869 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -534,35 +534,35 @@ tools: owner: iuc revisions: - 7e014059a88d - - c4f39bf4a068 - 49776718ae90 - f911a64454fb + - c4f39bf4a068 - a4b734cd253b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: + - 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