view snpeff33/snpEff_download.xml @ 2:e3fb8f296482 draft

Uploaded

<tool id="snpEff_download" name="SnpEff Download" version="3.3">
    <description>Download a new database</description>
    <requirements>
        <requirement type="package" version="3.3">snpEff</requirement>
    </requirements>
    <command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
    <inputs>
        <param name="genomeVersion" type="select" label="Genome">
            <options from_file="snpeffect_genomedb.loc">
                <column name="name" index="1"/>
                <column name="value" index="0"/>
            </options>
        </param>
    </inputs>

    <outputs>
        <data format="txt" name="logfile" />
    </outputs>
        <stdio>
          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
          <exit_code range="1:"  level="fatal"   description="Error" />
        </stdio>

    <help>

This tool downloads a SnpEff database.


For details about this tool, please see the snpEff_ web site.

.. _snpEff: http://snpEff.sourceforge.net
.. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
    </help>


</tool>