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comparison samtools_reheader.xml @ 0:020e144b5f78 draft

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author devteam
date Tue, 21 Apr 2015 16:57:10 -0400
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1 <tool id="samtools_reheader" name="Reheader" version="2.0">
2 <description>copy SAM/BAM header between datasets</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
8 <expand macro="version_command"></expand>
9 <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command>
10 <inputs>
11 <param name="input_header" type="data" format="sam,bam" label="Select source dataset" help="Header from this dataset will be used to replace header in the target dataset. May be either SAM or BAM dataset."/>
12 <param name="input_file" type="data" format="bam" label="Select target dataset" help="Header from the source dataset will be inserted here. Should be a BAM dataset."/>
13 </inputs>
14 <outputs>
15 <data format="bam" name="output" label="${tool.name} on ${on_string}" />
16 </outputs>
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>
23 </tests>
24 <help>
25 **What it does**
26
27 Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command.
28
29 </help>
30 <expand macro="citations"></expand>
31 </tool>
32