view gemini_de_novo.xml @ 4:ba3abde6775b draft default tip

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<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

            @CMDLN_SQL_FILTER_FILTER_OPTION@

            -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>