Mercurial > repos > devteam > snpeff_with_dep

comparison snpeff_with_dep-244c09911d7a/snpEff.xml @ 2:5e1d7c3f65c9 draft

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author devteam
date Thu, 27 Sep 2012 14:11:23 -0400
parents d8bd4326dc3a
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1:515163fbe70f 2:5e1d7c3f65c9
1 <tool id="snpEff" name="SnpEff" version="1.0"> 1 <tool id="snpEff" name="SnpEff" version="1.0">
2 <requirements>
3 <requirement type="package" version="3.0">snpEff</requirement>
4 </requirements>
2 <description>Variant effect and annotation</description> 5 <description>Variant effect and annotation</description>
3 <!-- 6 <!--
4 You will need to change the path to wherever your installation is. 7 You will need to change the path to wherever your installation is.
5 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) 8 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
6 <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> 9 <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
7 --> 10 -->
8 <requirements>
9 <requirement type="package" version="3.0">snpEff</requirement>
10 </requirements>
11 <command>java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> 11 <command>java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
12 <inputs> 12 <inputs>
13 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> 13 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
14 14
15 <param name="inputFormat" type="select" label="Input format"> 15 <param name="inputFormat" type="select" label="Input format">