Mercurial > repos > iuc > snpeff
diff snpEff_download.xml @ 1:500832f27cbc draft
Uploaded
author | iuc |
---|---|
date | Thu, 22 Jan 2015 08:28:37 -0500 |
parents | e8adfc4c0a6b |
children | b24873564cf6 |
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--- a/snpEff_download.xml Wed Dec 11 08:53:32 2013 -0500 +++ b/snpEff_download.xml Thu Jan 22 08:28:37 2015 -0500 @@ -1,23 +1,22 @@ -<tool id="snpEff_download" name="SnpEff Download" version="3.4"> +<tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0"> <description>Download a new database</description> <expand macro="requirements" /> <macros> <import>snpEff_macros.xml</import> </macros> <command> - echo $genomeVersion > $snpeff_db; - java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genomeVersion > $logfile +<![CDATA[ + java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.files_path -v $genome_version +]]> </command> <inputs> - <param name="genomeVersion" type="select" label="Select the genome version you want to download"> - <options from_data_table="snpeff_databases"> - <filter type="sort_by" column="0" /> - </options> + <param name="genome_version" type="text" size="40" value="" label="Select the genome version you want to download (e.g. GRCh37.74)"> + <help>@SNPEFF_DATABASE_URL@</help> + <validator type="regex" message="A genome version name is required">\S+</validator> </param> </inputs> <outputs> - <data format="txt" name="logfile" /> - <data format="snpeffdb" name="snpeff_db" label="${genomeVersion}" /> + <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" /> </outputs> <expand macro="stdio" /> <help> @@ -27,5 +26,6 @@ @CITATION_SECTION@ </help> + <expand macro="citations" /> </tool>