annotate dr-disco_fix.xml @ 11:3743fd602fa9 draft default tip

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d

<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>