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comparison snpSift_caseControl.xml @ 0:388f178f9e13

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author jjohnson
date Thu, 13 Sep 2012 22:33:33 -0400
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1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="1.0">
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="set_environment">JAVA_JAR_PATH </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
31 <help>
32
33 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.
34
35 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol
36
37 </help>
38 </tool>