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comparison samtools_fixmate.xml @ 5:5831b4b77d08 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_fixmate commit 17b880b5009a80a117eb6534bb95cd5795ed0321
author iuc
date Thu, 19 Feb 2026 20:24:42 +0000
parents bb39588ae743
children
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4:bb39588ae743 5:5831b4b77d08
1 <tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
2 <description>fill mate coordinates, ISIZE and mate related flags</description> 2 <description>fill mate coordinates, ISIZE and mate related flags</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
29 -O BAM 29 -O BAM
30 namesorted.bam 30 namesorted.bam
31 '$output' 31 '$output'
32 ]]></command> 32 ]]></command>
33 <inputs> 33 <inputs>
34 <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Select alignment" help="Set of aligned reads." /> 34 <param name="bamfile" type="data" format="sam,unsorted.bam,cram" optional="false" label="Select alignment" help="Set of aligned reads." />
35 <param name="remsec" type="boolean" argument="-r" truevalue="-r" falsevalue="" checked="false" label="Remove secondary and unmapped reads" /> 35 <param name="remsec" type="boolean" argument="-r" truevalue="-r" falsevalue="" checked="false" label="Remove secondary and unmapped reads" />
36 <param name="noprop" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Disable FR proper pair check" /> 36 <param name="noprop" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Disable FR proper pair check" />
37 <param name="tempcigar" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Add template cigar ct tag" /> 37 <param name="tempcigar" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Add template cigar ct tag" />
38 <param name="addms" type="boolean" argument="-m" truevalue="-m" falsevalue="" checked="false" label="Add ms (mate score) tags" help="These are used by markdup to select the best reads to keep." /> 38 <param name="addms" type="boolean" argument="-m" truevalue="-m" falsevalue="" checked="false" label="Add ms (mate score) tags" help="These are used by markdup to select the best reads to keep." />
39 </inputs> 39 </inputs>
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" />