Mercurial > repos > jjohnson > snpeff
comparison snpEff_download.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 |
|---|---|
| 1 <tool id="snpEff_download" name="SnpEff Download" version="3.2"> | 1 <tool id="snpEff_download" name="SnpEff Download" version="3.2"> |
| 2 <description>Download a new database</description> | 2 <description>Download a new database</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="3.2">snpEff</requirement> | 4 <requirement type="package" version="3.2">snpEff</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> | 6 <command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> |
| 7 <inputs> | 7 <inputs> |
| 8 <param name="genomeVersion" type="select" label="Genome"> | 8 <param name="genomeVersion" type="select" label="Genome"> |
| 9 <options from_file="snpeffect_genomedb.loc"> | 9 <options from_file="snpeffect_genomedb.loc"> |
| 10 <column name="name" index="1"/> | 10 <column name="name" index="1"/> |
| 11 <column name="value" index="0"/> | 11 <column name="value" index="0"/> |