view data_manager/data_manager_snpEff_download.xml @ 3:c6769a700e55

Update loc data to separate version 4 databases

<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.0" tool_type="manage_data">
    <description>Download a new database</description>
    <requirements>
        <requirement type="package" version="4.0">snpEff</requirement>
    </requirements>
    <command interpreter="python">
        data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config 
        #if $snpDb.genomeSrc == "named":
          --genome_version "${snpDb.genome_version}"
        #else
          --genome_version "${snpDb.genome_databases.fields.value}"
          --organism "${snpDb.genome_databases.fields.name}"
        #end if
        "$out_file"
        </command>
    <inputs>
        <conditional name="snpDb">
            <param name="genomeSrc" type="select" label="Select Genome Version">
                <help>The list is very large and may take some time to display on your browser</help>
                <option value="named">By Genome Version Name</option>
                <option value="cached">Select from list</option>
            </param>
            <when value="named">
                <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>
            </when>
            <when value="cached">
                <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version">
                    <options from_data_table="snpeff4_databases">
                        <filter type="sort_by" column="0" />
                    </options>
                </param>
            </when>
        </conditional>
    </inputs>

    <outputs>
           <data name="out_file" format="data_manager_json" label="${tool.name}"/>
    </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="genomeSrc"  value="named"/>
            <param name="genome_version" value="GRCh38.76"/>
            <output name="out_file">
                <assert_contents>
                    <!-- Check that a genome was added -->
                    <has_text text="GRCh38.76" />
                    <has_text text="snpeff4_regulationdb" />
                    <has_text text="snpeff4_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>