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comparison snpSift_filter.xml @ 0:c07c403fc470

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author jjohnson
date Thu, 17 Jan 2013 16:31:12 -0500
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1 <tool id="snpSift_filter" name="SnpSift Filter" version="3.1">
2 <options sanitize="False" />
3 <description>Filter variants using arbitrary expressions</description>
4 <!--
5 You will need to change the path to wherever your installation is.
6 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
7 java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
8 -->
9 <requirements>
10 <requirement type="package" version="3.1">snpEff</requirement>
11 </requirements>
12 <command>
13 java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
14 </command>
15 <inputs>
16 <param format="vcf" name="input" type="data" label="VCF input"/>
17 <param name="expr" type="text" label="Expression" size="50"/>
18 </inputs>
19 <configfiles>
20 <configfile name="exprFile">
21 $expr
22 </configfile>
23 </configfiles>
24
25 <outputs>
26 <data format="vcf" name="output" />
27 </outputs>
28 <stdio>
29 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
30 <exit_code range="1:" level="fatal" description="Error" />
31 </stdio>
32 <help>
33
34 You can filter using arbitrary expressions.
35
36 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#filter
37
38 </help>
39 </tool>