diff snpSift_caseControl.xml @ 1:2c595fea585c

Add more doocumentation

--- a/snpSift_caseControl.xml	Thu Jan 17 16:31:12 2013 -0500
+++ b/snpSift_caseControl.xml	Wed Jan 30 16:20:32 2013 -0600
@@ -8,7 +8,7 @@
                 <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
+		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"/>
@@ -22,7 +22,12 @@
 			<option value="hom">Homozygous</option>
 			<option value="het">Heterozygous</option>
 		</param>
-		<param name="caseControStr" type="text" label="Case / Control" size="50"/>
+		<param name="caseControStr" type="text" label="Case / Control column designation" size="50">
+		<help>
+Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral
+		</help>
+		<validator type="regex" message="must be  only plus(+), minus(-), or zero(0) characters">[+-0]+</validator>
+                </param>
 	</inputs>
 	<outputs>
 		<data format="vcf" name="output" />
@@ -34,7 +39,32 @@
 
 	<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.
+**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 string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. 
+
+This command adds two annotations to the VCF file:
+
+ - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example: 
+
+  "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.*
+
+
+ - **CaseControlP**: A p-value (Fisher exact test) that the number of cases is N or more. Example:
+
+  "CaseControl=4,0;CaseControlP=3.030303e-02" *in this case the pValue of having 4 or more cases and zero controls is 0.03*
+
+
+For example, if we have ten samples (which means ten genotype columns in the VCF file), the first four are 'case' and the last six are 'control', so the description string would be "++++------".  Let's say we want to distinguish genotypes that are homozygous in 'case' and either homozygous or heterozygous in 'control'.  We would set:
+
+  - Hom/Het case = "hom"
+
+  - Hom/Het control = "any"  
+
+  - Case / Control column designation = ""++++------"
+
 
 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol