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comparison samtools_sort.xml @ 12:0149126ce6af draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:33:28 -0400
parents 797e773f1c3f
children cf4d627c5cc0
comparison
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11:797e773f1c3f 12:0149126ce6af
1 <tool id="samtools_sort" name="Samtools sort" version="2.0.2"> 1 <tool id="samtools_sort" name="Samtools sort" profile="18.01" version="2.0.3">
2 <description>order of storing aligned sequences</description> 2 <description>order of storing aligned sequences</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"/>
19 #if $prim_key_cond.prim_key_select == '-t': 19 #if $prim_key_cond.prim_key_select == '-t':
20 $prim_key_cond.tag 20 $prim_key_cond.tag
21 $prim_key_cond.sec_key_select 21 $prim_key_cond.sec_key_select
22 #end if 22 #end if
23 -O bam 23 -O bam
24 -T sorttmp 24 -T "\${TMPDIR:-.}"
25 '${input1}' 25 '${input1}'
26 > '${output1}' 26 > '${output1}'
27 ]]></command> 27 ]]></command>
28 <inputs> 28 <inputs>
29 <param name="input1" type="data" format="sam,bam,cram" label="BAM File" /> 29 <param name="input1" type="data" format="sam,unsorted.bam,cram" label="BAM File" />
30 <conditional name="prim_key_cond"> 30 <conditional name="prim_key_cond">
31 <param name="prim_key_select" type="select" label="Primary sort key"> 31 <param name="prim_key_select" type="select" label="Primary sort key">
32 <option value="">coordinate</option> 32 <option value="">coordinate</option>
33 <option value="-n">name (-n)</option> 33 <option value="-n">name (-n)</option>
34 <option value="-t">tag (-t)</option> 34 <option value="-t">tag (-t)</option>