--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfbedintersect.xml	Thu Mar 19 12:42:11 2015 -0400
@@ -0,0 +1,62 @@
+<tool id="vcfbedintersect" name="VCF-BEDintersect:" version="0.0.3">
+  <description>Intersect VCF and BED datasets</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <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" 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>
+  <expand macro="citations" />
+</tool>