Mercurial > repos > jjohnson > snpeff
comparison snpSift_caseControl.xml @ 0:c07c403fc470
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| author | jjohnson |
|---|---|
| date | Thu, 17 Jan 2013 16:31:12 -0500 |
| parents | |
| children | 2c595fea585c |
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| -1:000000000000 | 0:c07c403fc470 |
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| 1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.1"> | |
| 2 <description>Count samples are in 'case' and 'control' groups.</description> | |
| 3 <!-- | |
| 4 You will need to change the path to wherever your installation is. | |
| 5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
| 6 --> | |
| 7 <requirements> | |
| 8 <requirement type="package" version="3.1">snpEff</requirement> | |
| 9 </requirements> | |
| 10 <command> | |
| 11 java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output | |
| 12 </command> | |
| 13 <inputs> | |
| 14 <param format="vcf" name="input" type="data" label="VCF input"/> | |
| 15 <param name="hhCase" type="select" label="Hom/Het case"> | |
| 16 <option value="any">Any</option> | |
| 17 <option value="hom">Homozygous</option> | |
| 18 <option value="het">Heterozygous</option> | |
| 19 </param> | |
| 20 <param name="hhControl" type="select" label="Hom/Het control"> | |
| 21 <option value="any">Any</option> | |
| 22 <option value="hom">Homozygous</option> | |
| 23 <option value="het">Heterozygous</option> | |
| 24 </param> | |
| 25 <param name="caseControStr" type="text" label="Case / Control" size="50"/> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data format="vcf" name="output" /> | |
| 29 </outputs> | |
| 30 <stdio> | |
| 31 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 32 <exit_code range="1:" level="fatal" description="Error" /> | |
| 33 </stdio> | |
| 34 | |
| 35 <help> | |
| 36 | |
| 37 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. | |
| 38 | |
| 39 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol | |
| 40 | |
| 41 </help> | |
| 42 </tool> |