<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.5">
    <description>from SAM/BAM alignment files as FASTQ</description>
    <requirements>
        <requirement type="package" version="0.4.5">readtagger</requirement>
    </requirements>
    <version_command>write_supplementary_fastq --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        write_supplementary_fastq --input_path '$input' --output_path '$output'
    ]]></command>
    <inputs>
        <param name="input" argument="--input_path" type="data" format="bam"/>
    </inputs>
    <outputs>
        <data name="output" format="fastqsanger"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="supplementary.bam" ftype="bam"/>
            <output name="output" file="supplementary.fastq" ftype="fastqsanger"/>
        </test>
    </tests>
    <help><![CDATA[
.. code-block::

    Usage: write_supplementary_fastq [OPTIONS]

      Write all supplementary alignments in `input_path` to an output fastq file
      at `output_path`.

    Options:
      --input_path PATH   Collect supplementary reads in this alignment file.
      --output_path PATH  Write supplementary reads to this FASTQ file.
      --help              Show this message and exit.


    ]]></help>
</tool>