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