Mercurial > repos > jjohnson > snpeff
annotate 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 |
| rev | line source |
|---|---|
| 8 | 1 <tool id="snpEff_download" name="SnpEff Download" version="3.2"> |
| 0 | 2 <description>Download a new database</description> |
| 3 <requirements> | |
| 8 | 4 <requirement type="package" version="3.2">snpEff</requirement> |
| 0 | 5 </requirements> |
|
9
937367efb1da
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
Jim Johnson <jj@umn.edu>
parents:
8
diff
changeset
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6 <command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> |
| 0 | 7 <inputs> |
| 8 <param name="genomeVersion" type="select" label="Genome"> | |
| 9 <options from_file="snpeffect_genomedb.loc"> | |
| 10 <column name="name" index="1"/> | |
| 11 <column name="value" index="0"/> | |
| 12 </options> | |
| 13 </param> | |
| 14 </inputs> | |
| 15 | |
| 16 <outputs> | |
| 17 <data format="txt" name="logfile" /> | |
| 18 </outputs> | |
| 19 <stdio> | |
| 20 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 21 <exit_code range="1:" level="fatal" description="Error" /> | |
| 22 </stdio> | |
| 23 | |
| 24 <help> | |
| 25 | |
| 26 This tool downloads a SnpEff database. | |
| 27 | |
| 28 For details about this tool, please go to http://snpEff.sourceforge.net | |
| 29 | |
| 30 </help> | |
| 31 </tool> | |
| 32 |