Mercurial > repos > devteam > snpeff_with_dep
diff snpeff_with_dep-244c09911d7a/snpSift_caseControl.xml @ 0:d8bd4326dc3a draft
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| author | devteam |
|---|---|
| date | Thu, 27 Sep 2012 13:40:17 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpeff_with_dep-244c09911d7a/snpSift_caseControl.xml Thu Sep 27 13:40:17 2012 -0400 @@ -0,0 +1,42 @@ +<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="1.0"> + <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="1.7">SnpSift</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>