Mercurial > repos > devteam > samtools_reheader
comparison samtools_reheader.xml @ 0:c50efc142ad0 draft
Uploaded initial tool definition.
| author | devteam |
|---|---|
| date | Fri, 17 Oct 2014 14:03:47 -0400 |
| parents | |
| children | 77a6694ebf7a |
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| -1:000000000000 | 0:c50efc142ad0 |
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| 1 <tool id="samtools_reheader" name="Replace header" version="1.0.0"> | |
| 2 <description>on a BAM or SAM file</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.1">samtools</requirement> | |
| 5 </requirements> | |
| 6 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> | |
| 7 <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command> | |
| 8 <stdio> | |
| 9 <exit_code range="1:" level="fatal" description="Error" /> | |
| 10 </stdio> | |
| 11 <inputs> | |
| 12 <param name="input_header" type="data" format="sam" label="SAM file or header" /> | |
| 13 <param name="input_file" type="data" format="sam,bam" label="File to reheader" /> | |
| 14 </inputs> | |
| 15 <outputs> | |
| 16 <data format="bam" name="output" label="${tool.name} on ${on_string}" /> | |
| 17 </outputs> | |
| 18 <tests> | |
| 19 </tests> | |
| 20 <help> | |
| 21 **What it does** | |
| 22 | |
| 23 This tool runs the ``samtools reheader`` command in the SAMtools toolkit. | |
| 24 | |
| 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. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ | |
| 30 | |
| 31 | |
| 32 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* | |
| 33 </help> | |
| 34 </tool> | |
| 35 |