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