<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.11">
    <description>based on softclips in control files</description>
    <requirements>
        <requirement type="package" version="0.4.11">readtagger</requirement>
    </requirements>
    <version_command>confirm_insertions --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        ln -fs $putative_insertions putative_insertions.gff &&
        ln -fs $all_insertions all_insertions.gff &&
        #for i, p in enumerate($all_controls)
            ln -fs '$p' all_controls_${i}.gff &&
        #end for
        confirm_insertions
        --putative_insertions_path putative_insertions.gff
        --all_treatments_path all_insertions.gff
        #for i, p in enumerate($all_controls)
            --all_controls_paths all_controls_${i}.gff
        #end for
        --output_path '$output'
        $output_discard
    ]]></command>
    <inputs>
        <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/>
        <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/>
        <param name="all_controls" label="Path to all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/>
        <param name="output_discard" label="Output discarded records? Discarded records will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/>
    </inputs>
    <outputs>
        <data name="output" format="gff3"/>
    </outputs>
    <tests>
        <test>
            <param name="putative_insertions" value="putative_insertions.gff" ftype="gff3"/>
            <param name="all_insertions" value="all_treatment_insertions.gff" ftype="gff3"/>
            <param name="all_controls" value="all_control_insertions.gff" ftype="gff3"/>
            <output name="output" file="confirmed_insertions.gff" ftype="gff3"/>
        </test>
    </tests>
    <help><![CDATA[
.. code-block::


    Usage: confirm_insertions [OPTIONS]

      Confirm insertions by checking that control file does not contain the same
      clipping pattern.

    Options:
      -p, --putative_insertions_path PATH
                                      Path to file containing putative somatic
                                      insertions  [required]
      -t, --all_treatments_path PATH  Path to file containing all treatment
                                      insertions  [required]
      -c, --all_controls_path PATH    Path to file containing all control
                                      insertions  [required]
      -o, --output_path TEXT          Write annotated output to this Path.
      --output_discarded_records / --no_output_discarded_records
                                      Discard an alternative flag if the current
                                      read is in a proper pair.
      --version                       Show the version and exit.
      --help                          Show this message and exit.
    ]]></help>
</tool>