comparison snpSift_filter.xml @ 9:937367efb1da default tip

Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.

8:13b6ad2ddace

	<description>Filter variants using arbitrary expressions</description>
	<requirements>
                <requirement type="package" version="3.2">snpEff</requirement>
	</requirements>
	<command>
		java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse $pass 
                #if $filterId and len($filterId.__str__.strip()) > 0:
			--filterId = "$filterId"
                #end if
                #if $addFilter and len($addFilter.__str__.strip()) > 0:
			--addFilter = "$addFilter"

9:937367efb1da

	<description>Filter variants using arbitrary expressions</description>
	<requirements>
                <requirement type="package" version="3.2">snpEff</requirement>
	</requirements>
	<command>
		java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse $pass 
                #if $filterId and len($filterId.__str__.strip()) > 0:
			--filterId = "$filterId"
                #end if
                #if $addFilter and len($addFilter.__str__.strip()) > 0:
			--addFilter = "$addFilter"