<tool id="vcfbedintersect" name="VCF-BEDintersect:" version="@WRAPPER_VERSION@.0">
    <description>Intersect VCF and BED datasets</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio" />
    <command>
        #if str($bed_vs_interval.bed_vs_interval_selector) == "bed":
            vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}"
        #else:
            vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}"
        #end if
    </command>
    <inputs>
        <!-- selecting refernce source -->
        <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" />
        <conditional name="bed_vs_interval">
            <param name="bed_vs_interval_selector" type="select" label="BED dataset or an interval to intersect with">
                <option value="bed">BED</option>
                <option value="interval">Interval</option>
            </param>
            <when value="bed">
                <param name="bed_input" type="data" format="bed" label="Select BED dataset" />
            </when>
            <when value="interval">
                <param name="int_input" type="text" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" />
            </when>
        </conditional>
        <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert. Print entries that DO NOT intersect." />
    </inputs>
    <outputs>
        <data format="vcf" name="out_file1" />
    </outputs>
    <tests>
        <test>
            <param name="bed_vs_interval_selector" value="bed" />
            <param name="bed_input" value="vcfannotate.bed" ftype="bed" />
            <param name="invert" value="False" />
            <param name="vcf_input" value="vcflib.vcf"/>
            <output name="out_file1" file="vcfbedintersect-test1.vcf"/>
        </test>
        <test>
            <param name="bed_vs_interval_selector" value="interval" />
            <param name="int_input" value="20:1-30000" />
            <param name="invert" value="False" />
            <param name="vcf_input" value="vcflib.vcf"/>
            <output name="out_file1" file="vcfbedintersect-test2.vcf"/>
        </test>
    </tests>
    <help>
Computes intersection between a VCF dataset and a set of genomic intervals defined as either a BED dataset (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) or a manually typed interval (in the form of chr:start-end).

----

VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
    </help>
    <expand macro="citations" />
</tool>