<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.1.0" tool_type="manage_data">
	<description>Read the list of available snpEff databases</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_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>
      <citations>
        <citation type="doi">10.4161/fly.19695</citation>
      </citations>
</tool>