<tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@">
    <description>Fixes chimeric alignments from STAR</description>
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />
    <expand macro="version_command" />

    <command detect_errors="exit_code"><![CDATA[
        dr-disco fix
            '${star_discordant_alignment}'
            '${alignment_fixed}'
    ]]></command>

    <inputs>
        <param name="star_discordant_alignment" type="data" format="bam" label="Discordant alignment file of STAR" />
    </inputs>

    <outputs>
        <data name="alignment_fixed" format="bam" label="${tool.name} on ${star_discordant_alignment}" />
    </outputs>

    <tests>
        <test>
            <param name="star_discordant_alignment" value="fix_test-01.bam"/>

            <output name="alignment_fixed" file="fix_test-01.fixed.bam" />
        </test>
    </tests>
    
    <help><![CDATA[

**What it does**

Dr. Disco fix prepares chimeric alignment files produced by STAR for analysis with Dr. Disco (detect) and for visualization in genome browsers.

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