| Previous changeset 0:eca6296a091a (2021-05-28) Next changeset 2:321347bd0494 (2023-09-04) |
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Commit message:
"planemo upload for repository https://github.com/davebx/bellerophon commit bf1c72ac01d7b761a32d0304b7b5054228f33274" |
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modified:
bellerophon.xml test-data/merged-out.bam test-data/merged-sam.bam |
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| diff -r eca6296a091a -r 25ca5d73aedf bellerophon.xml --- a/bellerophon.xml Fri May 28 20:54:47 2021 +0000 +++ b/bellerophon.xml Fri Aug 27 10:46:26 2021 +0000 |
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| @@ -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[ |
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| diff -r eca6296a091a -r 25ca5d73aedf test-data/merged-out.bam |
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| Binary file test-data/merged-out.bam has changed |
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| diff -r eca6296a091a -r 25ca5d73aedf test-data/merged-sam.bam |
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| Binary file test-data/merged-sam.bam has changed |