<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.0">
    <description>modifies proper_pair flag in bam files</description>
    <requirements>
        <requirement type="package" version="0.3.0">readtagger</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        allow_dovetailing -i '$input' -o '$output'
    ]]></command>
    <inputs>
        <param name="input" argument="--input_path" type="data" format="bam"/>
    </inputs>
    <outputs>
        <data name="output" format="bam"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="not_a_proper_pair.bam" ftype="bam"/>
            <output name="output" file="proper_pair.bam" ftype="bam" lines_diff="2"/>
        </test>
    </tests>
    <help><![CDATA[
.. code-block::

    usage: allow_dovetailing [-h] -i INPUT_PATH -o OUTPUT_PATH

    Allow dovetailing.

    optional arguments:
      -h, --help            show this help message and exit
      -i INPUT_PATH, --input_path INPUT_PATH
                            Input alignment file to manipulate
      -o OUTPUT_PATH, --output_path OUTPUT_PATH
                            Output alignment file
    ]]></help>
</tool>