--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpSift_caseControl.xml	Thu Jan 17 16:31:12 2013 -0500
@@ -0,0 +1,42 @@
+<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.1">
+	<description>Count samples are in 'case' and 'control' groups.</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>
+	</requirements>
+	<command>
+		java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output
+	</command>
+	<inputs>
+		<param format="vcf" name="input" type="data" label="VCF input"/>
+		<param name="hhCase" type="select" label="Hom/Het case">
+			<option value="any">Any</option>
+			<option value="hom">Homozygous</option>
+			<option value="het">Heterozygous</option>
+		</param>
+		<param name="hhControl" type="select" label="Hom/Het control">
+			<option value="any">Any</option>
+			<option value="hom">Homozygous</option>
+			<option value="het">Heterozygous</option>
+		</param>
+		<param name="caseControStr" type="text" label="Case / Control" size="50"/>
+	</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>
+
+	<help>
+
+Count samples are in 'case' and 'control' groups. You can count 'homozygous', 'heterozygous' or 'any' variants. Case and control are defined by a string containing plus and minus symbols ('+' and '-') where '+' is case and '-' is control. This command adds two annotations to the VCF file.
+
+For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol
+
+	</help>
+</tool>