<tool id="update_mapq" name="Update MAPQ score" version="0.4.9">
    <description>of supplementary alignments</description>
    <requirements>
        <requirement type="package" version="0.4.9">readtagger</requirement>
    </requirements>
    <version_command>update_mapq --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        update_mapq --source_path '$source_path' --remapped_path '$remapped_path' --output_path '$output_path'
    ]]></command>
    <inputs>
        <param argument="--source_path" label="Update supplementary MAPQ scores in this BAM file" type="data" format="bam"/>
        <param argument="--remapped_path" label="Extract MAPQ scores for secondary alignments from this BAM file." type="data" format="bam"/>
    </inputs>
    <outputs>
        <data name="output_path" format="bam"/>
    </outputs>
    <tests>
        <test>
            <param name="source_path" value="supplementary.bam" ftype="bam"/>
            <param name="remapped_path" value="remapped_supplementary.bam" ftype="bam"/>
            <output name="output_path" file="supplementary_new_mapq.bam" ftype="bam"/>
        </test>
    </tests>
    <help><![CDATA[
.. code-block::

    Usage: update_mapq [OPTIONS]

      Update supplementary read MAPQ score after remapping.

    Options:
      --source_path PATH    Alignment file where supplementary reads should be
                            updated with new MAPQ scores  [required]
      --remapped_path PATH  Alignment file that contains reads that have been
                            remapped and contain an updated MAPQ score  [required]
      --output_path PATH    Write all alignments in original_path to this
                            location. Supplementary reads will take the MAPQ score
                            as determined by remapping to the alignment file at
                            `remapped_path`  [required]
      --version             Show the version and exit.
      --help                Show this message and exit.


    ]]></help>
</tool>