<tool id="snpEff" name="SnpEff" version="3.1">
	<description>Variant effect and annotation</description>
	<!-- 
	    You will need to change the path to wherever your installation is.
		You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
	<command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
	-->
	<requirements>
		<requirement type="package" version="3.1">snpEff</requirement>
	</requirements>
	<command>
export SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download  -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ;
fi;
java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
	<inputs>
		<param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>

		<param name="inputFormat" type="select" label="Input format">
			<option value="vcf">VCF</option>
			<option value="txt">Tabular</option>
			<option value="pileup">Pileup</option>
			<option value="bed">BED</option>
		</param>

		<param name="outputFormat" type="select" label="Output format">
			<option value="txt">Tabular</option>
			<option value="vcf">VCF (only if input is VCF)</option>
			<option value="bed">BED</option>
			<option value="bedAnn">BED Annotations</option>
		</param>

		<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>

		<param name="udLength" type="select" label="Upstream / Downstream length">
			<option value="0">No upstream / downstream intervals (0 bases)</option>
			<option value="200">200 bases</option>
			<option value="500">500 bases</option>
			<option value="1000">1000 bases</option>
			<option value="2000">2000 bases</option>
			<option value="5000" selected="true">5000 bases</option>
			<option value="10000">10000 bases</option>
			<option value="20000">20000 bases</option>
		</param>

        <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
			<option value="">No filter (analyze everything)</option>
			<option value="-hom">Analyze homozygous sequence changes only </option>
			<option value="-het">Analyze heterozygous sequence changes only </option>
        </param>

        <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
			<option value="">No filter (analyze everything)</option>
			<option value="-del">Analyze deletions only </option>
			<option value="-ins">Analyze insertions only </option>
			<option value="-nmp">Only MNPs (multiple nucleotide polymorphisms) </option>
			<option value="-snp">Only SNPs (single nucleotide polymorphisms) </option>
        </param>

        <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="false" value="None" label="Filter output">
			<option value="None" selected="true">None</option>
			<option value="downstream">Do not show DOWNSTREAM changes </option>
			<option value="intergenic">Do not show INTERGENIC changes </option>
			<option value="intron">Do not show INTRON changes </option>
			<option value="upstream">Do not show UPSTREAM changes </option>
			<option value="utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option>
        </param>

        <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
			<option value="">Use default (based on input type)</option>
			<option value="-0">Force zero-based positions (both input and output)</option>
			<option value="-1">Force one-based positions (both input and output)</option>
		</param>
	</inputs>
	<outputs>
		<data format="tabular" name="output" >
			<change_format>
				<when input="outputFormat" value="txt" format="tabular" />
				<when input="outputFormat" value="vcf" format="vcf" />
				<when input="outputFormat" value="bed" format="bed" />
				<when input="outputFormat" value="bedAnn" format="bed" />
			</change_format>
		</data>
		<data format="html" name="statsFile" />
	</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 calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.

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

	</help>
</tool>