<tool id="snpSift_annotate" name="SnpSift Annotate" version="3.2">
	<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="3.2">snpEff</requirement>
	</requirements>
	<command>
        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd 
        #if $annotate.id :
          -id
        #elif $annotate.info_ids.__str__.strip() != '' :
          -info "$annotate.info_ids"
        #end if          
        -q $dbSnp $input > $output 
        </command>
	<inputs>
		<param format="vcf" name="input" type="data" label="VCF input"/>
		<param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 
                       help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
		<param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Annotate in Memory" 
                       help="allows unsorted VCF files, but it loads the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files)"/>
                <conditional name="annotate">
			<param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
			<when value="id"/>
			<when value="info">
				<param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs"
                                       help="list is a comma separated list of fields. When blank, all INFO fields are included">	
					<validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
				</param>
			</when>
                </conditional>
	</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"/>
                <param name="annotate_cmd" value="False"/>
                <param name="id" value="True"/>
                <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>