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view snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_caseControl.xml @ 3:c052639fa666 default tip
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author | pcingola |
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date | Fri, 20 Apr 2012 11:22:59 -0400 |
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<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) --> <command> java -Xmx1G -jar /home/pcingola/tools/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output </command> <inputs> <param format="Tabular" 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="tabular" name="output" /> </outputs> <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>