comparison dr-disco_fix.xml @ 1:9495360713d4 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b

0:fca9c1ace23c

<tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@-g0">
    <description>Fixes and annotates chimeric alignments</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    
    <expand macro="requirements" />
    <expand macro="version_command" />
    
    <command><![CDATA[
        dr-disco fix '${output}' '${star_discordant_alignment}'
    ]]></command>
    <inputs>
        <param name="star_discordant_alignment" type="data" format="bam" label="Discordant alignment file of STAR" />
    </inputs>
    <outputs>
        <data name="output" format="bam" label="${tool.name} on ${star_discordant_alignment}" />
    </outputs>
    <tests>
    </tests>
    
    <help>
    </help>
    
     <expand macro="citations"/>
</tool>

1:9495360713d4

<tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@-g0">
    <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 '${alignment_fixed}' '${star_discordant_alignment}'
    ]]></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 (extract) and for visualization in genome browsers.

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