<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" help="" />
         <param name="mapping_quality" type="integer" value="30" label="mapping quality must be greater than X " help="(optional. default: 30)" />
    </inputs>

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

</tool>