Mercurial > repos > jjohnson > snpeff
comparison snpSift_annotate.xml @ 0:c07c403fc470
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| author | jjohnson |
|---|---|
| date | Thu, 17 Jan 2013 16:31:12 -0500 |
| parents | |
| children | 192a236898f5 |
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| -1:000000000000 | 0:c07c403fc470 |
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| 1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="3.1"> | |
| 2 <description>Annotate SNPs from dbSnp</description> | |
| 3 <!-- | |
| 4 You will need to change the path to wherever your installation is. | |
| 5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
| 6 --> | |
| 7 <requirements> | |
| 8 <requirement type="package" version="3.1">snpEff</requirement> | |
| 9 </requirements> | |
| 10 <command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command> | |
| 11 <inputs> | |
| 12 <param format="vcf" name="input" type="data" label="VCF input"/> | |
| 13 <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."/> | |
| 14 </inputs> | |
| 15 <stdio> | |
| 16 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 17 <exit_code range="1:" level="fatal" description="Error" /> | |
| 18 </stdio> | |
| 19 | |
| 20 <outputs> | |
| 21 <data format="vcf" name="output" /> | |
| 22 </outputs> | |
| 23 | |
| 24 <help> | |
| 25 | |
| 26 This is typically used to annotate IDs from dbSnp. | |
| 27 | |
| 28 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate | |
| 29 | |
| 30 </help> | |
| 31 </tool> | |
| 32 |