Mercurial > repos > devteam > samtools_reheader
view samtools_reheader.xml @ 1:8546afbbd7f1 draft
Uploaded correct tool dependency definition.
author | devteam |
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date | Fri, 17 Oct 2014 14:04:50 -0400 |
parents | c50efc142ad0 |
children | 77a6694ebf7a |
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<tool id="samtools_reheader" name="Replace header" version="1.0.0"> <description>on a BAM or SAM file</description> <requirements> <requirement type="package" version="1.1">samtools</requirement> </requirements> <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command> <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> <inputs> <param name="input_header" type="data" format="sam" label="SAM file or header" /> <param name="input_file" type="data" format="sam,bam" label="File to reheader" /> </inputs> <outputs> <data format="bam" name="output" label="${tool.name} on ${on_string}" /> </outputs> <tests> </tests> <help> **What it does** This tool runs the ``samtools reheader`` command in the SAMtools toolkit. Replace the header for a SAM or BAM file with a different header. **Citation** 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. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help> </tool>