<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**

* Step 1 in dr-disco pipeline

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

**Attribution**

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

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