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1 <tool id="samtools_reheader" name="Replace header" version="1.0.0">
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2 <description>on a BAM or SAM file</description>
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3 <requirements>
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4 <requirement type="package" version="1.1">samtools</requirement>
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5 </requirements>
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6 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
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7 <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Error" />
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10 </stdio>
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11 <inputs>
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12 <param name="input_header" type="data" format="sam" label="SAM file or header" />
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13 <param name="input_file" type="data" format="sam,bam" label="File to reheader" />
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14 </inputs>
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15 <outputs>
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16 <data format="bam" name="output" label="${tool.name} on ${on_string}" />
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17 </outputs>
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18 <tests>
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19 </tests>
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20 <help>
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21 **What it does**
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22
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23 This tool runs the ``samtools reheader`` command in the SAMtools toolkit.
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24
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25 Replace the header for a SAM or BAM file with a different header.
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26
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27 **Citation**
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28
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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>`_
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30
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31
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32 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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33 </help>
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34 </tool>
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35
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