<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
    <description>Identifying potential de novo mutations</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">de_novo</token>
    </macros>
    <command>
<![CDATA[
        gemini @BINARY@

            #if $report.report_selector != 'all':
                --columns "${report.columns}"
            #end if

            #if $filter.filter_selector == 'yes':
                --filter "${filter.filter}"
            #end if
            -d $d
            "${ infile }"
            > "${ outfile }"
]]>
    </command>
    <expand macro="stdio" />
    <inputs>
        <expand macro="infile" />

        <expand macro="column_filter" />
        <expand macro="filter" />
        <expand macro="min_sequence_depth" />
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>
**What it does**

Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI, 
you can use this tool for identifying de novo (a.k.a spontaneous) mutations that arise in offspring.

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