<tool id="dr_disco_intronic" name="Dr. Disco (intronic)" version="@TOOL_VERSION@-g0">
    <description>Detects break-points in RNA-seq</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    
    <command><![CDATA[
        ## old thing that evolved as such - depending on what the future will bring leave it out or include it...
        touch empty.txt &&
        
        dr-disco
            intronic
                -m '${min_e_score}'
                '${output}'
                empty.txt
                '${star_discordant_alignment_fixed}'
    ]]></command>
    <inputs>
        <param name="star_discordant_alignment_fixed" type="data" format="bam" label="Discordant alignment file of STAR (processed with dr-disco fix)" />
        <param name="min_e_score" type="integer" value="8" min="0"
            label="Minimal score to initiate pulling sub-graphs"
            help="Larger numbers boost performance but result in suboptimal results. Values of 8 and below are considered to be very safe (this corresponds to initiate merging already from clusters that consist of 2 or 3 reads)." />
    </inputs>
    
    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${$star_discordant_alignment_fixed.name}" />
    </outputs>
    
    <tests>
    </tests>
    
    <help>
    </help>
    
     <expand macro="citations"/>
</tool>