<tool id="dr_disco_detect" name="Dr. Disco (detect)" version="@TOOL_VERSION@">
    <description>Detects break-points in RNA-seq</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    
    <command detect_errors="exit_code"><![CDATA[
        dr-disco
            detect
                --min-e-score '${min_e_score}'
                '${star_discordant_alignment_fixed}'
                '${output_fusion_events}'
    ]]></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" argument="--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_fusion_events" format="tabular" label="${tool.name} on ${star_discordant_alignment_fixed.name}" />
    </outputs>
    
    <tests>
        <test>
            <param name="star_discordant_alignment_fixed" value="detect.bam" />
            <param name="min_e_score" value="8" />

            <output name="output_fusion_events" file="detect.txt" />
        </test>
    </tests>
    
    <help><![CDATA[
**What it does**

* Step 2 in dr-disco pipeline

This tool detects junctions in ('dr-disco fix' prepared) Chimeric alignments and tries to reconstruct fusion genes and genomic breakpoints using a Graph data structure. This software is in particular designed for RNA-Seq data prepared with random hexamer priming because of the presence of intronic reads.

**Attribution**

This work is part of Youri Hoogstrate's PhD thesis.

    ]]></help>
    
     <expand macro="citations"/>
</tool>