Mercurial > repos > jjohnson > snpeff_with_dep
comparison snpEff_download.xml @ 1:ebe280eca4a4
Add package requirement
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 13 Sep 2012 21:40:44 -0500 |
| parents | 388f178f9e13 |
| children | c641d515de2e |
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| 0:388f178f9e13 | 1:ebe280eca4a4 |
|---|---|
| 1 <tool id="snpEff_download" name="SnpEff Download" version="1.0"> | 1 <tool id="snpEff_download" name="SnpEff Download" version="1.0"> |
| 2 <description>Download a new database</description> | 2 <description>Download a new database</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="3.0f">snpEff</requirement> | |
| 4 <requirement type="set_environment">JAVA_JAR_PATH </requirement> | 5 <requirement type="set_environment">JAVA_JAR_PATH </requirement> |
| 5 </requirements> | 6 </requirements> |
| 6 <command>java -jar $JAVA_JAR_PATH/snpEff.jar download -c $JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> | 7 <command>java -jar $JAVA_JAR_PATH/snpEff.jar download -c $JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> |
| 7 <inputs> | 8 <inputs> |
| 8 <param name="genomeVersion" type="select" label="Genome"> | 9 <param name="genomeVersion" type="select" label="Genome"> |