Mercurial > repos > iuc > snpeff
comparison snpEff_download.xml @ 0:e8adfc4c0a6b draft
Uploaded
| author | iuc |
|---|---|
| date | Wed, 11 Dec 2013 08:53:32 -0500 |
| parents | |
| children | 500832f27cbc |
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| -1:000000000000 | 0:e8adfc4c0a6b |
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| 1 <tool id="snpEff_download" name="SnpEff Download" version="3.4"> | |
| 2 <description>Download a new database</description> | |
| 3 <expand macro="requirements" /> | |
| 4 <macros> | |
| 5 <import>snpEff_macros.xml</import> | |
| 6 </macros> | |
| 7 <command> | |
| 8 echo $genomeVersion > $snpeff_db; | |
| 9 java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genomeVersion > $logfile | |
| 10 </command> | |
| 11 <inputs> | |
| 12 <param name="genomeVersion" type="select" label="Select the genome version you want to download"> | |
| 13 <options from_data_table="snpeff_databases"> | |
| 14 <filter type="sort_by" column="0" /> | |
| 15 </options> | |
| 16 </param> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format="txt" name="logfile" /> | |
| 20 <data format="snpeffdb" name="snpeff_db" label="${genomeVersion}" /> | |
| 21 </outputs> | |
| 22 <expand macro="stdio" /> | |
| 23 <help> | |
| 24 | |
| 25 @EXTERNAL_DOCUMENTATION@ | |
| 26 | |
| 27 @CITATION_SECTION@ | |
| 28 | |
| 29 </help> | |
| 30 </tool> | |
| 31 |