<tool id="data_manager_snpeff_download" name="SnpEff Download" version="3.3" tool_type="manage_data">
    <description>Download a new database</description>
    <requirements>
        <requirement type="package" version="3.3">snpEff</requirement>
    </requirements>
    <command interpreter="python">
        data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config 
        --genome_version "${genome_databases.fields.value}"
        --organism "${genome_databases.fields.name}"
        "$out_file"
        </command>
    <inputs>
        <param name="genome_databases" type="select" label="Genome Version">
            <options from_data_table="snpeff_databases"/>
        </param>
    </inputs>

    <outputs>
           <data name="out_file" format="data_manager_json" label="${tool.name} : ${genome_databases.fields.value}"/>
    </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 go to http://snpEff.sourceforge.net

    </help>
</tool>