annotate samtools_reheader.xml @ 0:020e144b5f78 draft

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<tool id="samtools_reheader" name="Reheader" version="2.0">
    <description>copy SAM/BAM header between datasets</description>
    <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio"></expand>
  <expand macro="version_command"></expand>
    <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command>
    <inputs>
        <param name="input_header" type="data" format="sam,bam" label="Select source dataset" help="Header from this dataset will be used to replace header in the target dataset. May be either SAM or BAM dataset."/>
        <param name="input_file" type="data" format="bam" label="Select target dataset" help="Header from the source dataset will be inserted here. Should be a BAM dataset."/>
    </inputs>
    <outputs>
        <data format="bam" name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_header" ftype="bam" value="reheader_input_header.bam"/>
            <param name="input_file" ftype="bam" value="reheader_input_file.bam"/>
            <output name="output" ftype="bam" file="reheader_out.bam"/>
        </test>
    </tests>
    <help>
**What it does**

Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command.

    </help>
    <expand macro="citations"></expand>
</tool>