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comparison samtools_split.xml @ 1:76449db9ee44 draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:56:13 -0400
parents 5c2a97bb018b
children ac469d103b51
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0:5c2a97bb018b 1:76449db9ee44
1 <tool id="samtools_split" name="Split" version="1.0.0"> 1 <tool id="samtools_split" name="Split" version="1.1">
2 <description>a BAM file by read group</description> 2 <description>BAM dataset on readgroups</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="1.1">samtools</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> 6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
8 <expand macro="version_command"></expand>
7 <command><![CDATA[ 9 <command><![CDATA[
8 samtools split -f 'Read_Group_%!.bam' 10 samtools split -f 'Read_Group_%!.bam'
9 #if $header: 11 #if $header:
10 -u "${output}":"${header}" 12 -u "${output}":"${header}"
11 #else: 13 #else:
12 -u "${output}" 14 -u "${output}"
13 #end if 15 #end if
14 "${input_bam}" 16 "${input_bam}"
15 ]]></command> 17 ]]></command>
16 <stdio>
17 <exit_code range="1:" level="fatal" description="Error" />
18 </stdio>
19 <inputs> 18 <inputs>
20 <param name="input_bam" type="data" format="bam" label="BAM file" multiple="true" /> 19 <param name="input_bam" type="data" format="bam" label="BAM file" />
21 <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" /> 20 <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" />
22 </inputs> 21 </inputs>
23 <outputs> 22 <outputs>
24 <data format="bam" name="output" label="${tool.name} on ${on_string}"> 23 <data format="bam" name="output" label="${tool.name} on ${on_string}">
25 <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="" />
36 </test> 35 </test>
37 </tests> 36 </tests>
38 <help> 37 <help>
39 **What it does** 38 **What it does**
40 39
41 This tool runs the ``samtools split`` command in the SAMtools toolkit. 40 Splits BAM files on readgroups.
42 41
43 Split BAM files by read group. 42 This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset.
44 43
45 **Citation**
46
47 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
48
49
50 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
51 </help> 44 </help>
45 <expand macro="citations"></expand>
52 </tool> 46 </tool>
53 47