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1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="1.0">
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2 <description>Count samples are in 'case' and 'control' groups.</description>
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3 <!--
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4 You will need to change the path to wherever your installation is.
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5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
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6 -->
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7 <requirements>
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8 <requirement type="package" version="3.0">snpEff</requirement>
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9 <requirement type="set_environment">JAVA_JAR_PATH </requirement>
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10 </requirements>
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11 <command>
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12 java -Xmx1G -jar $JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output
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13 </command>
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14 <inputs>
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15 <param format="vcf" name="input" type="data" label="VCF input"/>
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16 <param name="hhCase" type="select" label="Hom/Het case">
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17 <option value="any">Any</option>
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18 <option value="hom">Homozygous</option>
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19 <option value="het">Heterozygous</option>
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20 </param>
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21 <param name="hhControl" type="select" label="Hom/Het control">
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22 <option value="any">Any</option>
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23 <option value="hom">Homozygous</option>
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24 <option value="het">Heterozygous</option>
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25 </param>
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26 <param name="caseControStr" type="text" label="Case / Control" size="50"/>
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27 </inputs>
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28 <outputs>
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29 <data format="vcf" name="output" />
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30 </outputs>
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31 <stdio>
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32 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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33 <exit_code range="1:" level="fatal" description="Error" />
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34 </stdio>
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35
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36 <help>
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37
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38 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.
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39
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40 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol
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41
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42 </help>
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43 </tool>
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