Mercurial > repos > jjohnson > snpeff
comparison snpSift_caseControl.xml @ 9:937367efb1da default tip
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 18 Sep 2013 10:49:56 -0500 |
| parents | 13b6ad2ddace |
| children |
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| 8:13b6ad2ddace | 9:937367efb1da |
|---|---|
| 6 --> | 6 --> |
| 7 <requirements> | 7 <requirements> |
| 8 <requirement type="package" version="3.2">snpEff</requirement> | 8 <requirement type="package" version="3.2">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' |