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comparison samtools_split.xml @ 3:ac469d103b51 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:16:29 -0400
parents 76449db9ee44
children 229681b8c662
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2:51390195d350 3:ac469d103b51
1 <tool id="samtools_split" name="Split" version="1.1"> 1 <tool id="samtools_split" name="Split" version="@TOOL_VERSION@">
2 <description>BAM dataset on readgroups</description> 2 <description>BAM dataset on readgroups</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"/>
7 <expand macro="stdio"></expand> 7 <expand macro="stdio"/>
8 <expand macro="version_command"></expand> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 samtools split -f 'Read_Group_%!.bam' 10 samtools split -f 'Read_Group_%!.bam'
11 #if $header: 11 #if $header:
12 -u "${output}":"${header}" 12 -u '${output}:${header}'
13 #else: 13 #else:
14 -u "${output}" 14 -u '${output}'
15 #end if 15 #end if
16 "${input_bam}" 16 "${input_bam}"
17 ]]></command> 17 ]]></command>
18 <inputs> 18 <inputs>
19 <param name="input_bam" type="data" format="bam" label="BAM file" /> 19 <param name="input_bam" type="data" format="bam" label="BAM file" />
20 <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" /> 20 <param name="header" type="data" format="bam,sam" optional="True" label="Replace header in output file" />
21 </inputs> 21 </inputs>
22 <outputs> 22 <outputs>
23 <data format="bam" name="output" label="${tool.name} on ${on_string}"> 23 <data name="output" format="bam" label="${tool.name} on ${on_string}">
24 <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" /> 24 <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" />
25 </data> 25 </data>
26 </outputs> 26 </outputs>
27 <tests> 27 <tests>
28 <test> 28 <test>
32 <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" /> 32 <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" />
33 <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" /> 33 <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" />
34 </output> 34 </output>
35 </test> 35 </test>
36 </tests> 36 </tests>
37 <help> 37 <help><![CDATA[
38 **What it does** 38 **What it does**
39 39
40 Splits BAM files on readgroups. 40 Splits BAM files on readgroups.
41 41
42 This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset. 42 This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset.
43 43 ]]></help>
44 </help> 44 <expand macro="citations"/>
45 <expand macro="citations"></expand>
46 </tool> 45 </tool>
47