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<tool id="reheader" name="Reheader BAM file">
  <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>
  <requirements>
    <requirement type="package" version="3.4.1">python3</requirement>
    <requirement type="package" version="0.1.3_9af04e0e9125">MiModD</requirement>
  </requirements>
  <command>
	mimodd reheader $template $input -o $output --verbose
  </command>
  
  <inputs>
    <param name="input" type="data" format="bam" label="Input file in BAM format" help="The file to reheader." />
    <param name="template" type="data" format="sam" label="Header template file in SAM format" help="Use the header information of this file" />
  </inputs>
  
  <outputs>
    <data name="output" format="bam" label="(Re)headered bam file from MiModd ${tool.name} on ${on_string}">
    </data>
  </outputs>

<help>
.. class:: infomark

   **What it does**

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.

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.

</help>

</tool>