<tool id="vcfbedintersect" name="VCF-BEDintersect:" version="0.0.1">
<requirements>
    <requirement type="package" version="86723982aa">vcflib</requirement>
    <!-- <requirement type="package" version="0.1.18">samtools</requirement> -->
</requirements>
  <description>Intersect VCF and BED datasets</description>
  <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="Intersect with BED dataset or an interval">
	 <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" size="20" 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" />
      <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>
</tool>