Mercurial > repos > jjohnson > snpeff_with_dep
diff snpSift_annotate.xml @ 14:ef4598ea7179
Add SnpSift dependency
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 21 Sep 2012 16:00:25 -0500 |
| parents | e9e4ff80e72b |
| children | aab5e0adb26d |
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--- a/snpSift_annotate.xml Fri Sep 21 15:16:49 2012 -0500 +++ b/snpSift_annotate.xml Fri Sep 21 16:00:25 2012 -0500 @@ -5,10 +5,10 @@ You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) --> <requirements> - <requirement type="package" version="3.0">snpEff</requirement> + <requirement type="package" version="1.7">SnpSift</requirement> <requirement type="set_environment">JAVA_JAR_PATH </requirement> </requirements> - <command>java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command> + <command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command> <inputs> <param format="vcf" name="input" type="data" label="VCF input"/> <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/>