--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpSift_int.xml	Mon Apr 06 15:47:15 2015 -0400
@@ -0,0 +1,57 @@
+<tool id="snpSift_int" name="SnpSift Intervals" version="4.0.0">
+    <description>Filter variants using intervals</description>
+    <!-- 
+        You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
+    -->
+    <expand macro="requirements" />
+    <macros>
+        <import>snpSift_macros.xml</import>
+    </macros>
+    <command>
+        java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
+    </command>
+    <inputs>
+        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
+        <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" />
+    </outputs>
+    <expand macro="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" />
+                    <not_has_text text="1195966" />
+                </assert_contents>
+            </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>
+
+You can filter using intervals (BED file).
+
+@EXTERNAL_DOCUMENTATION@
+    http://snpeff.sourceforge.net/SnpSift.html#intervals
+
+@CITATION_SECTION@
+
+    </help>
+</tool>