Mercurial > repos > iuc > bellerophon

comparison bellerophon.xml @ 1:25ca5d73aedf draft

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"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
comparison
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0:eca6296a091a 1:25ca5d73aedf
44 <tests> 44 <tests>
45 <test expect_num_outputs="1"> 45 <test expect_num_outputs="1">
46 <param name="forward" value="forward.bam" ftype="qname_sorted.bam" /> 46 <param name="forward" value="forward.bam" ftype="qname_sorted.bam" />
47 <param name="reverse" value="reverse.bam" ftype="qname_sorted.bam" /> 47 <param name="reverse" value="reverse.bam" ftype="qname_sorted.bam" />
48 <param name="quality" value="20" /> 48 <param name="quality" value="20" />
49 <output name="outfile" file="merged-out.bam" ftype="bam" /> 49 <!-- since the tool expects qname_sorted.bam but the bam files are actually coordinate sorted
50 galaxy sorts them automatically (https://github.com/galaxyproject/galaxy/blob/bfbc537b58e5b00d1e00c37396dbf42a3bd98c5c/lib/galaxy/datatypes/binary.py#L437)
51 this adds a PG line -->
52 <output name="outfile" file="merged-out.bam" ftype="bam" lines_diff="2" />
50 </test> 53 </test>
51 <test expect_num_outputs="1"> 54 <test expect_num_outputs="1">
52 <param name="forward" value="forward.sam" ftype="sam" /> 55 <param name="forward" value="forward.sam" ftype="sam" />
53 <param name="reverse" value="reverse.sam" ftype="sam" /> 56 <param name="reverse" value="reverse.sam" ftype="sam" />
54 <param name="quality" value="12" /> 57 <param name="quality" value="12" />
55 <output name="outfile" file="merged-sam.bam" ftype="bam" /> 58 <output name="outfile" file="merged-sam.bam" ftype="bam"/>
56 </test> 59 </test>
57 </tests> 60 </tests>
58 <help><![CDATA[ 61 <help><![CDATA[
59 Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. This is usually needed when dealing with data from Arima Genomics. 62 Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. This is usually needed when dealing with data from Arima Genomics.
60 ]]></help> 63 ]]></help>