<tool id="findcluster" name="Find clusters of reads" version="0.3.2">
    <description>in bam files</description>
    <requirements>
        <requirement type="package" version="0.3.2">readtagger</requirement>
    </requirements>
    <version_command>findcluster --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        findcluster
        --input_path '$input'
        --output_bam '$output_bam'
        --output_gff '$output_gff'
        --sample_name '$input.element_identifier'
    ]]></command>
    <inputs>
        <param name="input" argument="--input_path" type="data" format="bam"/>
    </inputs>
    <outputs>
        <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
        <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
            <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
            <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/>
        </test>
    </tests>
    <help><![CDATA[
.. code-block::

    Find clusters of reads that support a TE insertion.

    optional arguments:
      -h, --help            show this help message and exit
      --input_path INPUT_PATH
                            Find cluster in this BAM file. (default: None)
      --output_bam OUTPUT_BAM
                            Write out BAM file with cluster information to this
                            path. Reads will have an additional "CD" tag to
                            indicate the cluster number (default: None)
      --output_gff OUTPUT_GFF
                            Write out GFF file with cluster information to this
                            path. (default: None)
      --version             show program's version number and exit

]]></help>
</tool>