annotate data_manager/data_manager_snpEff_download.xml @ 5:3d9dd4b9fb09 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty

<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3k" tool_type="manage_data">
    <description>Download a new database</description>
    <requirements>
        <requirement type="package" version="4.3k">snpeff</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/data_manager_snpEff_download.py'
--genome_version '$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/">
            <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><![CDATA[
This tool downloads a SnpEff database and populates the 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
    ]]></help>
    <citations>
        <citation type="doi">10.4161/fly.19695</citation>
    </citations>
</tool>