<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
    <description>Find genes among variants that are interacting partners</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">interactions</token>
    </macros>
    <command>
<![CDATA[
        gemini 
            --annotation-dir ${annotation_databases.fields.path}
            #if $gene.gene_selector == 'lof':
                ## lof interactions is a separate program
                lof_interactions
            #else:
                ## use normal gemini interactions program
                @BINARY@
                -g "${gene.gene}"
            #end if

            -r "${radius}"
            $variant_mode
            "${ infile }"
            > "${ outfile }"
]]>
    </command>
    <expand macro="stdio" />
    <inputs>
        <expand macro="infile" />

        <conditional name="gene">
            <param name="gene_selector" type="select" label="Studying" help="">
                <option value="gene">Interesting gene</option>
                <option value="lof">All loss-of-function variants</option>
            </param>
            <when value="gene">
                <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (-g)" />
            </when>
            <when value="lof"/>
        </conditional>
        <expand macro="annotation_dir" />
        <expand macro="radius" />
        <expand macro="variant_mode" />
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>
**What it does**

Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data.
Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the
protein itself. We have used the HPRD_ binary interaction data to build a p-p network graph which can be explored by GEMINI.

.. _HPRD: http://www.ncbi.nlm.nih.gov/pubmed/18988627


@CITATION@
    </help>
    <expand macro="citations">
        <citation type="doi">10.1093/nar/gkn892</citation><!-- HPRD citation -->
    </expand>
</tool>