Mercurial > repos > iuc > bellerophon

changeset 1:25ca5d73aedf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/davebx/bellerophon commit bf1c72ac01d7b761a32d0304b7b5054228f33274"
author iuc
date Fri, 27 Aug 2021 10:46:26 +0000
parents eca6296a091a
children 321347bd0494
files bellerophon.xml test-data/merged-out.bam test-data/merged-sam.bam
diffstat 3 files changed, 5 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/bellerophon.xml	Fri May 28 20:54:47 2021 +0000
+++ b/bellerophon.xml	Fri Aug 27 10:46:26 2021 +0000
@@ -46,13 +46,16 @@
             <param name="forward" value="forward.bam" ftype="qname_sorted.bam" />
             <param name="reverse" value="reverse.bam" ftype="qname_sorted.bam" />
             <param name="quality" value="20" />
-            <output name="outfile" file="merged-out.bam" ftype="bam" />
+            <!-- since the tool expects qname_sorted.bam but the bam files are actually coordinate sorted
+                 galaxy sorts them automatically (https://github.com/galaxyproject/galaxy/blob/bfbc537b58e5b00d1e00c37396dbf42a3bd98c5c/lib/galaxy/datatypes/binary.py#L437) 
+                 this adds a PG line -->
+            <output name="outfile" file="merged-out.bam" ftype="bam" lines_diff="2" />
         </test>
         <test expect_num_outputs="1">
             <param name="forward" value="forward.sam" ftype="sam" />
             <param name="reverse" value="reverse.sam" ftype="sam" />
             <param name="quality" value="12" />
-            <output name="outfile" file="merged-sam.bam" ftype="bam" />
+            <output name="outfile" file="merged-sam.bam" ftype="bam"/>
         </test>
     </tests>
     <help><![CDATA[
Binary file test-data/merged-out.bam has changed
Binary file test-data/merged-sam.bam has changed