<tool id="add_tradis_tags" name="add tradis tags" version="@VERSION@">
    <description>Create insertion site plot for Artemis</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
    
    tradis_plot -b $input_bam -m $mapping_quality

    ]]>    </command>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="BAM file" />
        <param name="mapping_quality" type="integer" min="0" value="30" label="mapping quality must be greater than X " />
    </inputs>

    <outputs>
        <data name="output_bam" format="bam" label="${tool.name} on ${on_string} Plot" from_work_dir="tradis.plot" />
    </outputs>

    <tests>
    </tests>
    <help><![CDATA[
        Adds transposon sequence and quality tags to the read strings and
        outputs a BAM.

        Usage: add_tags -b file.bam [options]

        Options:
        -b  : bam file with tradis tags
        -v  : verbose debugging output
    ]]>    </help>
    <expand macro="citations" />

</tool>