Mercurial > repos > jjohnson > snpeff

comparison snpSift_filter.xml @ 9:937367efb1da default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
children
comparison
equal deleted inserted replaced
8:13b6ad2ddace 9:937367efb1da
3 <description>Filter variants using arbitrary expressions</description> 3 <description>Filter variants using arbitrary expressions</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.2">snpEff</requirement> 5 <requirement type="package" version="3.2">snpEff</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command>
8 java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse $pass 8 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse $pass
9 #if $filterId and len($filterId.__str__.strip()) > 0: 9 #if $filterId and len($filterId.__str__.strip()) > 0:
10 --filterId = "$filterId" 10 --filterId = "$filterId"
11 #end if 11 #end if
12 #if $addFilter and len($addFilter.__str__.strip()) > 0: 12 #if $addFilter and len($addFilter.__str__.strip()) > 0:
13 --addFilter = "$addFilter" 13 --addFilter = "$addFilter"