<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="@WRAPPER_VERSION@.0" tool_type="manage_data">
    <description>Read the list of available snpEff databases</description>
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @CONDA_SNPEFF_JAR_PATH@ &&
        python '$__tool_directory__/data_manager_snpEff_databases.py' 
            --jar_path '\$SNPEFF_JAR_PATH/snpEff.jar'
            '$out_file'
        ]]>
    </command>
    <inputs>
    </inputs>
    <outputs>
           <data name="out_file" format="data_manager_json"/>
    </outputs>
        <tests>
            <test>
                <output name="out_file">
                    <assert_contents>
                        <!-- Check that a genome was added -->
                        <has_text text="GRCh38.76" />
                    </assert_contents>
                </output>
            </test>
        </tests>
    <help>

This tool updatess the list of SnpEff databases for the SnpEff Download data manager.
It should only need to be run once for a snpEff version, 
since it populates the SnpEff Download data manager from the snpEff config file.

For information about snpEff:    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>
    <expand macro="citations" />
</tool>