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view snpEff_download.xml @ 17:13d81e5226cd

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Put gene info in Summary Report extra_files_path
author Jim Johnson <jj@umn.edu>
date Mon, 10 Nov 2014 09:33:36 -0600
parents 3790e16a0be0
children 36f3c82323e6
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<tool id="snpEff_download" name="SnpEff Download" version="4.0.1">
    <description>Download a new database</description>
    <expand macro="requirements" />
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <command>
    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genome_version > $logfile 
    </command>
    <inputs>
        <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)">
            <help>http://sourceforge.net/projects/snpeff/files/databases/</help>
            <validator type="regex" message="A genome version name is required">\S+</validator>
        </param>
    </inputs>
    <outputs>
        <data format="txt" name="logfile" />
        <data format="snpeffdbv4" name="snpeff_db" label="${tool.name} ${genome_version}" />
    </outputs>
    <expand macro="stdio" />
    <help>

@EXTERNAL_DOCUMENTATION@

@CITATION_SECTION@

    </help>
</tool>