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comparison samtools_split.xml @ 2:135c85f4cfaf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
author iuc
date Mon, 29 Jul 2019 08:49:33 -0400
parents b7f7826ef1cd
children 5d9ae78f34d3
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1:b7f7826ef1cd 2:135c85f4cfaf
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 samtools split -f 'Read_Group_%!.bam' 10 @ADDTHREADS@
11 #if $header: 11 samtools split -f 'Read_Group_%!.bam'
12 -u '${output}:${header}' 12 #if $header:
13 #else: 13 -u '${output}:${header}'
14 -u '${output}' 14 #else:
15 #end if 15 -u '${output}'
16 "${input_bam}" 16 #end if
17 -@ \$addthreads
18 '$input_bam'
17 ]]></command> 19 ]]></command>
18 <inputs> 20 <inputs>
19 <param name="input_bam" type="data" format="bam" label="BAM file" /> 21 <param name="input_bam" type="data" format="bam" label="BAM file" />
20 <param name="header" type="data" format="bam,sam" optional="True" label="Replace header in output file" /> 22 <param name="header" type="data" format="bam,sam" optional="True" label="Replace header in output file" />
21 </inputs> 23 </inputs>
22 <outputs> 24 <outputs>
23 <data name="output" format="bam" label="${tool.name} on ${on_string}"> 25 <data name="output" format="bam" label="${tool.name} on ${on_string}">
24 <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" /> 26 <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" assign_primary_output="false"/>
25 </data> 27 </data>
26 </outputs> 28 </outputs>
27 <tests> 29 <tests>
28 <test> 30 <test>
29 <param name="input_bam" value="phiX.bam" ftype="bam" /> 31 <param name="input_bam" value="phiX.bam" ftype="bam" />
30 <output name="output" file="samtools_split_out.bam"> 32 <output name="output">
31 <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" /> 33 <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" />
32 <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" /> 34 <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" />
33 <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" /> 35 <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" />
34 </output> 36 </output>
35 </test> 37 </test>