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comparison snpEff.xml @ 3:3b0c657b852b

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Fix command in snpEff.xml
author Jim Johnson <jj@umn.edu>
date Wed, 06 Feb 2013 07:05:27 -0600
parents c07c403fc470
children b26a1aff7f81
comparison
equal deleted inserted replaced
2:a9bae7957c36 3:3b0c657b852b
7 --> 7 -->
8 <requirements> 8 <requirements>
9 <requirement type="package" version="3.1">snpEff</requirement> 9 <requirement type="package" version="3.1">snpEff</requirement>
10 </requirements> 10 </requirements>
11 <command> 11 <command>
12 export SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`; 12 SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
13 if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ; 13 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
14 then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ; 14 then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ;
15 fi; 15 fi";
16 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> 16 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>
17 <inputs> 17 <inputs>
18 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> 18 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
19 19
20 <param name="inputFormat" type="select" label="Input format"> 20 <param name="inputFormat" type="select" label="Input format">