Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add IGB display support for CRAM files #19428

Merged
merged 1 commit into from
Feb 11, 2025
+14 −0
Merged

Add IGB display support for CRAM files #19428

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions lib/galaxy/config/sample/datatypes_conf.xml.sample
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@
<datatype extension="probam" type="galaxy.datatypes.binary:ProBam" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="cram" type="galaxy.datatypes.binary:CRAM" mimetype="application/octet-stream" display_in_upload="true" description="CRAM is a file format for highly efficient and tunable reference-based compression of alignment data." description_url="http://www.ebi.ac.uk/ena/software/cram-usage">
<converter file="cram_to_bam_converter.xml" target_datatype="bam"/>
<display file="igb/cram.xml"/>
</datatype>
<datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" description="BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Bed">
<converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
Expand Down
13 changes: 13 additions & 0 deletions lib/galaxy/datatypes/display_applications/configs/igb/cram.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
<display id="igb_cram" version="0.0.0" name="display in IGB">
<link id="View" name="View">
<url>http://bioviz.org/galaxy.html?version=${cram_file.dbkey}&amp;feature_url_0=${cram_file.url}&amp;sym_name_0=${niceName}&amp;sym_method_0=${cram_file.url}&amp;query_url=${cram_file.url}&amp;server_url=galaxy</url>
<param type="data" name="cram_file_for_name" viewable="False"/>
<param type="template" name="niceName" viewable="False" strip="True">
#import re
#set nm=$cram_file_for_name.name
${re.sub('\W',"_",nm)}
</param>
<param type="data" name="crai_file" url="${niceName}.cram.crai" metadata="cram_index" />
<param type="data" name="cram_file" url="${niceName}.cram" />
</link>
</display>
Loading