<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="latest">
	<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="latest">snpEff</requirement>
	</requirements>
	<command interpreter="perl">snpSiftWrapper.pl caseControl -q -tfam $tfam $input > $output </command>
	<inputs>
		<param format="vcf" name="input" type="data" label="VCF input"/>
		<param format="tfam" name="tfam" type="data" label="TFAM file"/>
	</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>

**SnpSift CaseControl**

Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. 

Case and control are defined by a TFAM file (phenotype column)

This command adds two annotations to the VCF file:

 - **Cases**: Three comma separated numbers numbers representing the number of homozygous (ALT), heterozygous (ALT) and allele count in Case group

 - **Controls**: Three comma separated numbers numbers representing the number of homozygous (ALT), heterozygous (ALT) and allele count in Control group

 - **CC_DOM**: p-value under Dominant model

 - **CC_REC**: p-value under Recesive model

 - **CC_ALL**: p-value using allele counts

 - **CC_GEN**: p-value using Genotypic (co-dominant) model

For details about this tool, please go to https://pcingola.github.io/SnpEff/SnpSift.html#casecontrol

	</help>
</tool>
