<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
    <description>Map genes and variants to KEGG pathways</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">pathways</token>
    </macros>
    <command>
<![CDATA[
        gemini 
            --annotation-dir ${annotation_databases.fields.path}
            @BINARY@
            -v $ensembl
            $lof
            "${ infile }"
            > "${ outfile }"
]]>
    </command>
    <expand macro="stdio" />
    <inputs>
        <param name="infile" type="data" format="sqlite" label="GEMINI database" />

        <param name="ensembl" type="integer" value="68" size="5" label="Version of ensembl genes to use" 
            help="Supported versions: 66 to 71. use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)">
            <validator type="in_range" min="66" max="71"/>
        </param>

        <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False" 
            label="Report only pathways with loss-of-function variants" help="(--lof)"/>
        <expand macro="annotation_dir" />
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>
**What it does**

Mapping genes to biological pathways is useful in understanding the function/role played by a gene. 
Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases. 
We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation. 

This requires your VCF be annotated with either snpEff/VEP.

@CITATION@
    </help>
    <expand macro="citations"/>
</tool>