--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpeff33/snpSift_int.xml	Mon Sep 30 00:59:41 2013 -0400
@@ -0,0 +1,66 @@
+<tool id="snpSift_int" name="SnpSift Intervals" version="3.3">
+    <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="3.3">snpEff</requirement>
+    </requirements>
+    <command>
+        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" />
+    </outputs>
+        <stdio>
+          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+          <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" />
+                        <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)
+
+For details about this tool, read the fine manual_ http://snpeff.sourceforge.net/SnpSift.html#intervals
+
+For details about this tool, please see the snpEff_ web site.
+
+.. _snpEff: http://snpEff.sourceforge.net
+.. _manual: http://snpeff.sourceforge.net/SnpSift.html#intervals
+.. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
+    </help>
+</tool>