Mercurial > repos > jjohnson > snpeff_with_dep

comparison snpEff.xml @ 14:ef4598ea7179

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Add SnpSift dependency
author Jim Johnson <jj@umn.edu>
date Fri, 21 Sep 2012 16:00:25 -0500
parents e9e4ff80e72b
children aab5e0adb26d
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13:d57983929080 14:ef4598ea7179
7 --> 7 -->
8 <requirements> 8 <requirements>
9 <requirement type="package" version="3.0">snpEff</requirement> 9 <requirement type="package" version="3.0">snpEff</requirement>
10 <requirement type="set_environment">JAVA_JAR_PATH </requirement> 10 <requirement type="set_environment">JAVA_JAR_PATH </requirement>
11 </requirements> 11 </requirements>
12 <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 <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>
13 <inputs> 13 <inputs>
14 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> 14 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
15 15
16 <param name="inputFormat" type="select" label="Input format"> 16 <param name="inputFormat" type="select" label="Input format">
17 <option value="vcf">VCF</option> 17 <option value="vcf">VCF</option>