Mercurial > repos > jjohnson > snpeff_with_dep

view snpSift_int.xml @ 2:5248f48fa4ee

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add debug actions to tool_dependencies
author Jim Johnson <jj@umn.edu>
date Thu, 13 Sep 2012 21:50:24 -0500
parents ebe280eca4a4
children c641d515de2e
line wrap: on
line source

<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>