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<tool id="fourgamete" name="Four Gamete Test" version="0.1">
    <requirements>
        <requirement type="package">pysam</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
    <description>Tests a VCF file for a subregion that passes four gamete test</description>
    <command>
        <![CDATA[
            python $__tool_directory__/four_gamete_pysam.py
            --vcfname $input
            --out $output
            --4gcompat
            --reti
            #if str($select_arg) == 'left':
            --left
            #elif str($select_arg) == 'right':
            --right
            #elif str($select_arg) == 'randomi':
            --rani
            #else:
            --ranb
            #end if
            --numinf $infsites
            #if  $input.is_of_type('vcf_bgzip')
                --tbi $input.metadata.tabix_index
            #end if

        ]]>

    </command>
    <inputs>
        <param format="vcf,vcf_bgzip,bcf" name="input" type="data" label="VCF input" />
        <param type="integer" name="infsites" label="Number of informative sites required in subregion" value="2" min="0" />
        <param name="select_arg" type="select" label="Subregion to Select">
            <option value="left">Left-most</option>
            <option value="right" selected="True">Right-most</option>
            <option value="randomi">Random (equal probability per region)</option>
            <option value="randomb">Random (probability equal to size)</option>
        </param>
    </inputs>
    <outputs>
        <data format="vcf" name="output"/>
    </outputs>
    <help>
    <![CDATA[

    Input VCF will be examined for regions that pass the four-gamete test, which indicates there have been no recombination in this region for this sample. For most cases, a failure of the four-gamete test occurs when two SNPs have four gametes between them. (00,01,10,11) Using selection criteria, a region with the target number of informative SNPs that passes the four-gamete criteria will be output to a VCF file.

    ]]>

    </help>
</tool>