view data_manager/data_manager_snpEff_download.xml @ 5:8952990fcab9

Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases

<tool id="data_manager_snpeff_download" name="SnpEff Download" version="3.4" tool_type="manage_data">
    <description>Download a new database</description>
    <requirements>
        <requirement type="package" version="3.4">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">
                <filter type="sort_by" column="0" />
            </options>
        </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>
    <tests>
        <test>
            <param name="genome_databases" value="GRCh37.71"/>
            <output name="out_file">
                <assert_contents>
                    <!-- Check that a genome was added -->
                    <has_text text="GRCh37.71" />
                    <has_text text="snpeff_regulationdb" />
                    <has_text text="snpeff_annotations" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

This tool downloads a SnpEff database.

For details about this tool, please go to http://snpEff.sourceforge.net

Please cite:
"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]

    </help>
</tool>