<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
    <description>Identify somatic fusion genes from a GEMINI database</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">fusions</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[

        gemini
        #if $annotation_databases:
            --annotation-dir "${ annotation_databases.fields.path }"
        #end if
        @BINARY@
        $in_cosmic_census
        
        #if float($min_quality) >= 0:
            --min-qual $min_quality
        #end if

        #if str($evidence_type):
            --evidence_type $evidence_type
        #end if 
        
        "${ infile }" | tr -s ' ' '\t'
        > "${ outfile }" 
]]>
    </command>
    <inputs>

        <expand macro="infile" />
        <expand macro="annotation_dir" />

        <param argument="--in_cosmic_census" type="boolean" truevalue="--in_cosmic_census" falsevalue="" checked="False" label="One or both genes in fusion is in COSMIC cancer census" />

        <param name="min_quality" type="float" value="-1" label="The min variant quality (VCF QUAL)" help="default: -1 (not set) (--min_qual)"/>

        <param argument="--evidence_type" type="select" label="The supporting evidence types for the variant" >
            <option value="" selected="True">select one (optional)</option>
            <option value="PE">PE</option>
            <option value="SR">SR</option>
            <option value="PE,SR">PE,SR</option>
        </param>

    </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. The resulting output should be empty.-->
            <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
            <output name="outfile" file="gemini_fusions_result.tabular" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Identifies somatic fusion genes from a GEMINI database.
]]>
    </help>
    <expand macro="citations"/>
</tool>