Mercurial > repos > iuc > samtools_fixmate

comparison samtools_fixmate.xml @ 5:c05afbeaf42d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit c508c3af0f4121dcc38e0be63db00a604e997b8a
author iuc
date Thu, 19 Jun 2025 12:59:44 +0000
parents e5ece8fa99de
children
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4:d2df79922531 5:c05afbeaf42d
59 <output name="output" file="4_reverse_read_pp_equal.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> 59 <output name="output" file="4_reverse_read_pp_equal.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
60 </test> 60 </test>
61 <!-- test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");--> 61 <!-- test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");-->
62 <test> 62 <test>
63 <param name="bamfile" value="5_ct.sam" ftype="sam" /> 63 <param name="bamfile" value="5_ct.sam" ftype="sam" />
64 <param name="tempcigar" value="-c" /> 64 <param name="tempcigar" value="true" />
65 <output name="output" file="5_ct.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> 65 <output name="output" file="5_ct.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
66 </test> 66 </test>
67 <!-- test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");--> 67 <!-- test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");-->
68 <test> 68 <test>
69 <param name="bamfile" value="6_ct_replace.sam" ftype="sam" /> 69 <param name="bamfile" value="6_ct_replace.sam" ftype="sam" />
70 <param name="tempcigar" value="-c" /> 70 <param name="tempcigar" value="true" />
71 <output name="output" file="6_ct_replace.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> 71 <output name="output" file="6_ct_replace.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
72 </test> 72 </test>
73 <!-- test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");--> 73 <!-- test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");-->
74 <test> 74 <test>
75 <param name="bamfile" value="7_two_read_mapped.sam" ftype="sam" /> 75 <param name="bamfile" value="7_two_read_mapped.sam" ftype="sam" />