<tool id="snpSift_annotate" name="SnpSift Annotate" version="3.1">
	<description>Annotate SNPs from dbSnp</description>
	<!-- 
	    You will need to change the path to wherever your installation is.
		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
	-->
	<requirements>
                <requirement type="package" version="3.1">snpEff</requirement>
	</requirements>
	<command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command>
	<inputs>
		<param format="vcf" name="input" type="data" label="VCF input"/>
		<param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
	</inputs>
        <stdio>
          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
          <exit_code range="1:"  level="fatal"   description="Error" />
        </stdio>

	<outputs>
		<data format="vcf" name="output" />
	</outputs>
	<tests>
	    <test>
                <param name="input" ftype="vcf" value="annotate_1.vcf"/>
                <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
                <output name="output">
                    <assert_contents>
                        <has_text text="rs76166080" />
                    </assert_contents>
                </output>
	    </test>
	</tests>
	<help>

This is typically used to annotate IDs from dbSnp.

For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate

	</help>
</tool>