<tool id="snpSift_annotate" name="SnpSift Annotate" version="3.4">
	<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="3.4">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 > $output 
        </command>
	<inputs>
		<param format="vcf" name="input" type="data" label="VCF input"/>
		<param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 
                       help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
                <conditional name="annotate">
			<param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
			<when value="id"/>
			<when value="info">
				<param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs"
                                       help="list is a comma separated list of fields. When blank, all INFO fields are included">	
					<validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
				</param>
			</when>
                </conditional>
		<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).
                       Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). 
                       </help>
                </param>
	</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

Annotatating only the ID field from dbSnp137.vcf ::

    Input VCF:
    CHROM  POS         ID           REF  ALT  QUAL   FILTER  INFO
    22      16157571    .            T    G    0.0    FAIL    NS=53
    22      16346045    .            T    C    0.0    FAIL    NS=244
    22      16350245    .            C    A    0.0    FAIL    NS=192

    Annotated Output VCF:
    #CHROM  POS         ID           REF  ALT  QUAL   FILTER  INFO
    22      16157571    .            T    G    0.0    FAIL    NS=53
    22      16346045    rs56234788   T    C    0.0    FAIL    NS=244
    22      16350245    rs2905295    C    A    0.0    FAIL    NS=192



Annotatating both the ID and INFO fields from dbSnp137.vcf ::

    Input VCF:
    #CHROM  POS         ID           REF  ALT  QUAL   FILTER  INFO
    22      16157571    .            T    G    0.0    FAIL    NS=53
    22      16346045    .            T    C    0.0    FAIL    NS=244
    22      16350245    .            C    A    0.0    FAIL    NS=192

    Annotated Output VCF:
    #CHROM  POS         ID           REF  ALT  QUAL   FILTER  INFO
    22      16157571    .            T    G    0.0    FAIL    NS=53
    22      16346045    rs56234788   T    C    0.0    FAIL    NS=244;RSPOS=16346045;GMAF=0.162248628884826;dbSNPBuildID=129;SSR=0;SAO=0;VP=050100000000000100000100;WGT=0;VC=SNV;SLO;GNO
    22      16350245    rs2905295    C    A    0.0    FAIL    NS=192;RSPOS=16350245;GMAF=0.230804387568556;dbSNPBuildID=101;SSR=1;SAO=0;VP=050000000000000100000140;WGT=0;VC=SNV;GNO


SnpEff citation:
"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]

SnpSift citation:
"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.


	</help>
</tool>