Mercurial > repos > devteam > snpeff_with_dep
diff snpeff_with_dep-244c09911d7a/snpSift_annotate.xml @ 0:d8bd4326dc3a draft
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| author | devteam |
|---|---|
| date | Thu, 27 Sep 2012 13:40:17 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpeff_with_dep-244c09911d7a/snpSift_annotate.xml Thu Sep 27 13:40:17 2012 -0400 @@ -0,0 +1,32 @@ +<tool id="snpSift_annotate" name="SnpSift Annotate" version="1.0"> + <description>Annotate SNPs from dbSnp</description> + <!-- + You will need to change the path to wherever your installation is. + 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="1.7">SnpSift</requirement> + </requirements> + <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."/> + </inputs> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + + <outputs> + <data format="vcf" name="output" /> + </outputs> + + <help> + +This is typically used to annotate IDs from dbSnp. + +For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate + + </help> +</tool> +