<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>