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comparison samtools_reheader.xml @ 2:77a6694ebf7a draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:55:18 -0400
parents c50efc142ad0
children 0b97d4e945ab
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1:8546afbbd7f1 2:77a6694ebf7a
1 <tool id="samtools_reheader" name="Replace header" version="1.0.0"> 1 <tool id="samtools_reheader" name="Reheader" version="2.0">
2 <description>on a BAM or SAM file</description> 2 <description>copy SAM/BAM header between datasets</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 $2 }'</version_command> 6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
8 <expand macro="version_command"></expand>
7 <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command> 9 <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command>
8 <stdio>
9 <exit_code range="1:" level="fatal" description="Error" />
10 </stdio>
11 <inputs> 10 <inputs>
12 <param name="input_header" type="data" format="sam" label="SAM file or header" /> 11 <param name="input_header" type="data" format="sam,bam" label="Select source dataset" help="Header from this dataset will be used to replace header in the target dataset. May be either SAM or BAM dataset."/>
13 <param name="input_file" type="data" format="sam,bam" label="File to reheader" /> 12 <param name="input_file" type="data" format="bam" label="Select target dataset" help="Header from the source dataset will be inserted here. Should be a BAM dataset."/>
14 </inputs> 13 </inputs>
15 <outputs> 14 <outputs>
16 <data format="bam" name="output" label="${tool.name} on ${on_string}" /> 15 <data format="bam" name="output" label="${tool.name} on ${on_string}" />
17 </outputs> 16 </outputs>
18 <tests> 17 <tests>
18 <test>
19 <param name="input_header" ftype="bam" value="reheader_input_header.bam"/>
20 <param name="input_file" ftype="bam" value="reheader_input_file.bam"/>
21 <output name="output" ftype="bam" file="reheader_out.bam"/>
22 </test>
19 </tests> 23 </tests>
20 <help> 24 <help>
21 **What it does** 25 **What it does**
22 26
23 This tool runs the ``samtools reheader`` command in the SAMtools toolkit. 27 Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command.
24 28
25 Replace the header for a SAM or BAM file with a different header.
26
27 **Citation**
28
29 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;`_
30
31
32 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
33 </help> 29 </help>
30 <expand macro="citations"></expand>
34 </tool> 31 </tool>
35 32