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comparison snpSift_caseControl.xml @ 2:6ad9205c1307

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Update to SnpEff version 3.3
author Jim Johnson <jj@umn.edu>
date Fri, 04 Oct 2013 09:09:29 -0500
parents e1d9f6a0ad53
children 8952990fcab9
comparison
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1:bea875f081e8 2:6ad9205c1307
1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.2"> 1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.3">
2 <description>Count samples are in 'case' and 'control' groups.</description> 2 <description>Count samples are in 'case' and 'control' groups.</description>
3 <!-- 3 <!--
4 You will need to change the path to wherever your installation is. 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) 5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
6 --> 6 -->
7 <requirements> 7 <requirements>
8 <requirement type="package" version="3.2">snpEff</requirement> 8 <requirement type="package" version="3.3">snpEff</requirement>
9 </requirements> 9 </requirements>
10 <command> 10 <command>
11 java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar caseControl -q 11 java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q
12 #if $name.__str__.strip() != '': 12 #if $name.__str__.strip() != '':
13 -name $name 13 -name $name
14 #end if 14 #end if
15 #if $ctrl.ctrl_src == 'caseString': 15 #if $ctrl.ctrl_src == 'caseString':
16 '$ctrl.caseControlStr' 16 '$ctrl.caseControlStr'