<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
    <description>Retrieve genes with actionable somatic mutations via COSMIC and DGIdb</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">actionable_mutations</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        gemini @BINARY@
            '$infile' | tr -s ' ' '\t'
            > '$outfile'
]]>
    </command>
    <inputs>
        <expand macro="infile" />
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <!-- Like in set_somatic this example is nonsensical because otherwise
                the testdata would be too big.-->
            <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
            <output name="outfile" file="gemini_actionable_mutations_result.tabular" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Retrieve genes with actionable somatic mutations via COSMIC and DGIdb. It checks for variants that have the somatic flag set (which can be done with GEMINI set_somatic) with high or medium impact severity. The results are then compared to entries in COSMIC and DGIdb

    ]]></help>
    <expand macro="citations"/>
</tool>