<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
    <description>Identify candidate violations of Mendelian inheritance</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">mendel_errors</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        gemini @BINARY@

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

            @CMDLN_SQL_FILTER_FILTER_OPTION@

            #if int($min_kindreds) > 0:
                --min-kindreds $min_kindreds
            #end if

            #if str($families).strip():
                --families "$families"
            #end if

            $lenient
            $only_affected

            -d $d

            #if int($min_gq) > 0:
                --min-gq $min_gq
            #end if

            #if int($gt_pl_max) > -1:
                --gt-pl-max $gt_pl_max
            #end if


            "${ infile }"
            > "${ outfile }"
]]>
    </command>
    <inputs>
        <expand macro="infile" />
        <expand macro="column_filter" />
        <expand macro="filter" />
        <expand macro="min_kindreds" />
        <expand macro="family" />
        <expand macro="lenient" />
        <!-- this parameter should be allow-unaffected, but unfortunately it is not. -->
        <param name="only_affected" type="boolean" truevalue="--only-affected" falsevalue="" checked="False" label="Only consider candidates from affected samples." help="(--only-affected)"/>
        <expand macro="min_sequence_depth" />
        <expand macro="min_gq" />
        <expand macro="gt_pl_max" />
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
            <param name="columns" value="gene,ref,alt,impact" />
            <output name="outfile" file="gemini_mendel_errors_result.tabular" />
        </test>
    </tests>
    <help>
<![CDATA[

**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 mutations that violate the Mendelian inheritance scheme.

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