Mercurial > repos > devteam > snpeff_with_dep
diff snpeff_with_dep-244c09911d7a/snpEff.xml @ 2:5e1d7c3f65c9 draft
Uploaded
| author | devteam |
|---|---|
| date | Thu, 27 Sep 2012 14:11:23 -0400 |
| parents | d8bd4326dc3a |
| children |
line wrap: on
line diff
--- 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)"/>