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comparison snpSift_int.xml @ 9:937367efb1da default tip

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Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
author Jim Johnson <jj@umn.edu>
date Wed, 18 Sep 2013 10:49:56 -0500
parents 13b6ad2ddace
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8:13b6ad2ddace 9:937367efb1da
6 --> 6 -->
7 <requirements> 7 <requirements>
8 <requirement type="package" version="3.2">snpEff</requirement> 8 <requirement type="package" version="3.2">snpEff</requirement>
9 </requirements> 9 </requirements>
10 <command> 10 <command>
11 java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output 11 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
12 </command> 12 </command>
13 <inputs> 13 <inputs>
14 <param format="vcf" name="input" type="data" label="VCF input"/> 14 <param format="vcf" name="input" type="data" label="VCF input"/>
15 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/> 15 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
16 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" 16 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals"