annotate data_manager/data_manager_snpEff_download.xml @ 1:85a23e2dd92b draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584

<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.1.0" tool_type="manage_data">
    <description>Download a new database</description>
    <requirements>
        <requirement type="package" version="4.1">snpEff</requirement>
    </requirements>
    <stdio>
        <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
        <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <command interpreter="python">
        data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
          --genome_version "$genome_version" "$out_file"
        </command>
    <inputs>
        <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
            <help>https://snpeff-data.galaxyproject.org/databases/</help>
            <validator type="regex" message="A genome version name is required">\S+</validator>
        </param>
    </inputs>

    <outputs>
           <data name="out_file" format="data_manager_json" label="${tool.name}"/>
    </outputs>
    <tests>
        <test>
            <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="snpeffv_regulationdb" />
                    <has_text text="snpeffv_annotations" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

This tool downloads a SnpEff database and populates data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.

To see the list of available SnpEff genomes run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeff4_databases

The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/


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>
      <citations>
        <citation type="doi">10.4161/fly.19695</citation>
      </citations>
</tool>