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comparison samtools_split.xml @ 0:5c2a97bb018b draft

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Uploaded initial tool definition.
author devteam
date Fri, 24 Oct 2014 16:22:16 -0400
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children 76449db9ee44
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1 <tool id="samtools_split" name="Split" version="1.0.0">
2 <description>a BAM file by read group</description>
3 <requirements>
4 <requirement type="package" version="1.1">samtools</requirement>
5 </requirements>
6 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
7 <command><![CDATA[
8 samtools split -f 'Read_Group_%!.bam'
9 #if $header:
10 -u "${output}":"${header}"
11 #else:
12 -u "${output}"
13 #end if
14 "${input_bam}"
15 ]]></command>
16 <stdio>
17 <exit_code range="1:" level="fatal" description="Error" />
18 </stdio>
19 <inputs>
20 <param name="input_bam" type="data" format="bam" label="BAM file" multiple="true" />
21 <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" />
22 </inputs>
23 <outputs>
24 <data format="bam" name="output" label="${tool.name} on ${on_string}">
25 <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" />
26 </data>
27 </outputs>
28 <tests>
29 <test>
30 <param name="input_bam" value="phiX.bam" ftype="bam" />
31 <output name="output" file="samtools_split_out.bam">
32 <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" />
33 <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" />
34 <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" />
35 </output>
36 </test>
37 </tests>
38 <help>
39 **What it does**
40
41 This tool runs the ``samtools split`` command in the SAMtools toolkit.
42
43 Split BAM files by read group.
44
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>
52 </tool>
53