<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
    <description>Extracting variants from specific regions or genes</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">region</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        gemini @BINARY@

            #if $region.region_selector == '--reg':
                #if str($region.region).strip():
                    --reg "${region.region}"
                #end if
            #else:
                #if str($region.gene).strip():
                    --gene "${region.gene}"
                #end if
            #end if

            @COLUMN_SELECT@

            @CMDLN_SQL_FILTER_FILTER_OPTION@

            $show_samples


            $header
            "${ infile }"
            > "${ outfile }"
]]>
    </command>
    <inputs>
        <expand macro="infile" />

        <conditional name="region">
            <param name="region_selector" type="select" label="Select by ...?" help="">
                <option value="--reg">genomic coordinates</option>
                <option value="--gene">gene name</option>
            </param>
            <when value="--reg">
                <param name="region" type="text" label="Specify genomic region" help="e.g. chr1:100-200 (--reg)"/>
            </when>
            <when value="--gene">
                <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (--gene)" />
            </when>
        </conditional>

        <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False" label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/>

        <expand macro="column_filter" />
        <expand macro="filter" />
        <expand macro="add_header_column" />

    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
            <param name="region_selector" value="--reg" />
            <param name="region" value="chr3:187000000-187500000" />
            <param name="header" value="True" />
            <conditional name="report">
                <param name="report_selector" value="column_filter" />
                <param name="columns" value="chrom,start,gene" />
            </conditional>
            <output name="outfile">
                <assert_contents>
                    <has_line_matching expression="chrom&#009;start&#009;gene.*" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
**What it does**

One often is concerned with variants found solely in a particular gene or genomic region.

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