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comparison samtools_fixmate.xml @ 7:84819580b8a5 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 20:24:52 +0000
parents c05afbeaf42d
children
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6:68a116f469db 7:84819580b8a5
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>