<tool id="vcfrandomsample" name="VCFrandomSample:" version="@WRAPPER_VERSION@.0">
    <description>Randomly sample sites from VCF dataset</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio" />
    <command>
        vcfrandomsample
            #if $adv_options.adv_options_selector == "use_adv_controls":
                -s "${adv_options.scale_by}"
            #end if
            -p ${random_seed}
            -r ${rate}
            "${vcf_input}" > "${out_file1}" 
    </command>
    <inputs>
        <param format="vcf" name="vcf_input" type="data" label="Select random sites from"/>
        <param name="rate" type="float" value="0.1" label="base sampling probability per locus" help="-r, --rate"/>
        <param name="random_seed" type="integer" value="17823618326" label="use this random seed"
            help="-p, --random-seed; use this to make results reproducible" />
        <conditional name="adv_options">
            <param name="adv_options_selector" type="select" label="Advanced controls" help="Allows you to specify options that are not listed above">
                <option value="no">Don't use advanced options</option>
                <option value="use_adv_controls">Use advanced options</option>
            </param>
            <when value="" />
            <when value="use_adv_controls">
                <param name="scale_by" type="text" value="AF" label="scale sampling likelihood by this INFO field" help="-s, --scale-by; this only works for Float info fields such as AF" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="vcf" name="out_file1" />
    </outputs>
    <tests>
        <test>
            <param name="vcf_input" value="vcflib.vcf"/>
            <param name="rate" value="0.2" />
            <param name="random_seed" value="1" />
            <param name="adv_options_selector" value="no" />
            <output name="out_file1" file="vcfrandomsample-test1.vcf" lines_diff="2" />
        </test>
    </tests>
    <help>

Randomly sample sites from an input VCF dataset. Scale the sampling probability by the field specified by --scale-by (see advanced controls).  This may be
used to provide uniform sampling across allele frequencies, for instance (AF field in this case).

----

Vcfrandomsample @IS_PART_OF_VCFLIB@
    </help>
    <expand macro="citations" />
</tool>