Merge pull request #19428 from paige-kulzer/cram-support

Add IGB display support for CRAM files

lib/galaxy/config/sample/datatypes_conf.xml.sample

@@ -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"/>

lib/galaxy/datatypes/display_applications/configs/igb/cram.xml

@@ -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>