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1 <tool id="reheader" name="Reheader BAM file">
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2 <description>From a BAM file generate a new file with the original header (if any) replaced by that found in a second SAM file</description>
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3 <requirements>
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4 <requirement type="package" version="3.4.1">python3</requirement>
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5 <requirement type="package" version="0.1.3_9af04e0e9125">MiModD</requirement>
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6 </requirements>
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7 <command>
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8 mimodd reheader $template $input -o $output --verbose
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9 </command>
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10
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11 <inputs>
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12 <param name="input" type="data" format="bam" label="Input file in BAM format" help="The file to reheader." />
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13 <param name="template" type="data" format="sam" label="Header template file in SAM format" help="Use the header information of this file" />
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14 </inputs>
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15
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16 <outputs>
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17 <data name="output" format="bam" label="(Re)headered bam file from MiModd ${tool.name} on ${on_string}">
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18 </data>
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19 </outputs>
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20
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21 <help>
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22 .. class:: infomark
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23
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24 **What it does**
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25
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26 The tool replaces the header of the input BAM file (i.e., its metadata) with that found in the template SAM file and writes the result to a new BAM file.
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27
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28 Typically, you will generate the header template file with the *NGS Run Annotation* tool, but any SAM file with header information can be used instead.
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29
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30 </help>
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31
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32 </tool>
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