--- a/snpSift_int.xml	Thu Mar 28 12:29:45 2013 -0500
+++ b/snpSift_int.xml	Mon May 13 12:45:07 2013 -0500
@@ -1,18 +1,20 @@
-<tool id="snpSift_int" name="SnpSift Intervals" version="3.1">
+<tool id="snpSift_int" name="SnpSift Intervals" version="3.2">
 	<description>Filter variants using intervals </description>
 	<!-- 
 	    You will need to change the path to wherever your installation is.
 		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
 	-->
 	<requirements>
-                <requirement type="package" version="3.1">snpEff</requirement>
+                <requirement type="package" version="3.2">snpEff</requirement>
 	</requirements>
 	<command>
-		cat $input | java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output
+		java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
 	</command>
 	<inputs>
 		<param format="vcf" name="input" type="data" label="VCF input"/>
 		<param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
+		<param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" 
+                       help="Filter out (exclude) VCF entries that match any interval in the BED files"/>
 	</inputs>
 	<outputs>
 		<data format="vcf" name="output" />
@@ -22,9 +24,11 @@
           <exit_code range="1:"  level="fatal"   description="Error" />
         </stdio>
         <tests>
+
             <test>
                 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
                 <param name="bedFile" ftype="bed" value="interval.bed"/>
+                <param name="exclude" value="False"/>
                 <output name="output">
                     <assert_contents>
                         <has_text text="872687" />
@@ -33,6 +37,18 @@
                 </output>
             </test>
 
+            <test>
+                <param name="input" ftype="vcf" value="annotate_5.vcf"/>
+                <param name="bedFile" ftype="bed" value="interval.bed"/>
+                <param name="exclude" value="True"/>
+                <output name="output">
+                    <assert_contents>
+                        <has_text text="1195966" />
+                        <not_has_text text="872687" />
+                    </assert_contents>
+                </output>
+            </test>
+
         </tests>
 
 	<help>