# HG changeset patch
# User devteam
# Date 1348769483 14400
# Node ID 5e1d7c3f65c94a7585a131ff04880479e5db73ee
# Parent  515163fbe70f8cf2bf3be6b7b31a1e05fb5f5b06
Uploaded

diff -r 515163fbe70f -r 5e1d7c3f65c9 snpeff_with_dep-244c09911d7a/snpEff.xml
--- a/snpeff_with_dep-244c09911d7a/snpEff.xml	Thu Sep 27 14:10:46 2012 -0400
+++ b/snpeff_with_dep-244c09911d7a/snpEff.xml	Thu Sep 27 14:11:23 2012 -0400
@@ -1,13 +1,13 @@
 <tool id="snpEff" name="SnpEff" version="1.0">
+    <requirements>
+        <requirement type="package" version="3.0">snpEff</requirement>
+    </requirements>
 	<description>Variant effect and annotation</description>
 	<!-- 
 	    You will need to change the path to wherever your installation is.
 		You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
 	<command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
 	-->
-	<requirements>
-		<requirement type="package" version="3.0">snpEff</requirement>
-	</requirements>
 	<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>
 	<inputs>
 		<param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>