Mercurial > repos > jjohnson > snpeff_with_dep
view snpSift_int.xml @ 3:458d28b65750
Correct name for tool_dependencies.xml
author | Jim Johnson <jj@umn.edu> |
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date | Fri, 14 Sep 2012 07:26:01 -0500 |
parents | ebe280eca4a4 |
children | c641d515de2e |
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<tool id="snpSift_int" name="SnpSift Intervals" version="1.0"> <description>Filter variants using intervals </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="3.0f">snpEff</requirement> <requirement type="set_environment">JAVA_JAR_PATH </requirement> </requirements> <command> cat $input | java -Xmx2G -jar $JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output </command> <inputs> <param format="vcf" name="input" type="data" label="VCF input"/> <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/> </inputs> <outputs> <data format="vcf" name="output" /> </outputs> <help> You can filter using intervals (BED file) For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals </help> </tool>