view 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.

<tool id="snpEff_download" name="SnpEff Download" version="3.2">
	<description>Download a new database</description>
	<requirements>
		<requirement type="package" version="3.2">snpEff</requirement>
	</requirements>
	<command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
	<inputs>
		<param name="genomeVersion" type="select" label="Genome">
			<options from_file="snpeffect_genomedb.loc">
				<column name="name" index="1"/>
				<column name="value" index="0"/>
			</options>
		</param>
	</inputs>

	<outputs>
		<data format="txt" name="logfile" />
	</outputs>
        <stdio>
          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
          <exit_code range="1:"  level="fatal"   description="Error" />
        </stdio>

	<help>

This tool downloads a SnpEff database.

For details about this tool, please go to http://snpEff.sourceforge.net

	</help>
</tool>