Mercurial > repos > iuc > snpeff
comparison snpEff_download.xml @ 1:500832f27cbc draft
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author | iuc |
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date | Thu, 22 Jan 2015 08:28:37 -0500 |
parents | e8adfc4c0a6b |
children | b24873564cf6 |
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0:e8adfc4c0a6b | 1:500832f27cbc |
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1 <tool id="snpEff_download" name="SnpEff Download" version="3.4"> | 1 <tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0"> |
2 <description>Download a new database</description> | 2 <description>Download a new database</description> |
3 <expand macro="requirements" /> | 3 <expand macro="requirements" /> |
4 <macros> | 4 <macros> |
5 <import>snpEff_macros.xml</import> | 5 <import>snpEff_macros.xml</import> |
6 </macros> | 6 </macros> |
7 <command> | 7 <command> |
8 echo $genomeVersion > $snpeff_db; | 8 <![CDATA[ |
9 java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genomeVersion > $logfile | 9 java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.files_path -v $genome_version |
10 ]]> | |
10 </command> | 11 </command> |
11 <inputs> | 12 <inputs> |
12 <param name="genomeVersion" type="select" label="Select the genome version you want to download"> | 13 <param name="genome_version" type="text" size="40" value="" label="Select the genome version you want to download (e.g. GRCh37.74)"> |
13 <options from_data_table="snpeff_databases"> | 14 <help>@SNPEFF_DATABASE_URL@</help> |
14 <filter type="sort_by" column="0" /> | 15 <validator type="regex" message="A genome version name is required">\S+</validator> |
15 </options> | |
16 </param> | 16 </param> |
17 </inputs> | 17 </inputs> |
18 <outputs> | 18 <outputs> |
19 <data format="txt" name="logfile" /> | 19 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" /> |
20 <data format="snpeffdb" name="snpeff_db" label="${genomeVersion}" /> | |
21 </outputs> | 20 </outputs> |
22 <expand macro="stdio" /> | 21 <expand macro="stdio" /> |
23 <help> | 22 <help> |
24 | 23 |
25 @EXTERNAL_DOCUMENTATION@ | 24 @EXTERNAL_DOCUMENTATION@ |
26 | 25 |
27 @CITATION_SECTION@ | 26 @CITATION_SECTION@ |
28 | 27 |
29 </help> | 28 </help> |
29 <expand macro="citations" /> | |
30 </tool> | 30 </tool> |
31 | 31 |