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<tool id="snpEff" name="SnpEff" version="3.2">
	<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>
Options:
        -a , -around            : Show N codons and amino acids around change (only in coding regions). Default is 0 codons.
        -i <format>             : Input format [ vcf, txt, pileup, bed ]. Default: VCF.
        -o <format>             : Ouput format [ txt, vcf, gatk, bed, bedAnn ]. Default: VCF.
        -interval               : Use a custom interval file (you may use this option many times)
        -chr <string>           : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
        -s,  -stats             : Name of stats file (summary). Default is 'snpEff_summary.html'
        -t                      : Use multiple threads (implies '-noStats'). Default 'off'

Sequence change filter options:
        -del                    : Analyze deletions only
        -ins                    : Analyze insertions only
        -hom                    : Analyze homozygous variants only
        -het                    : Analyze heterozygous variants only
        -minQ X, -minQuality X  : Filter out variants with quality lower than X
        -maxQ X, -maxQuality X  : Filter out variants with quality higher than X
        -minC X, -minCoverage X : Filter out variants with coverage lower than X
        -maxC X, -maxCoverage X : Filter out variants with coverage higher than X
        -nmp                    : Only MNPs (multiple nucleotide polymorphisms)
        -snp                    : Only SNPs (single nucleotide polymorphisms)

Results filter options:
        -fi  <bedFile>                  : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
        -no-downstream                  : Do not show DOWNSTREAM changes
        -no-intergenic                  : Do not show INTERGENIC changes
        -no-intron                      : Do not show INTRON changes
        -no-upstream                    : Do not show UPSTREAM changes
        -no-utr                         : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes

Annotations options:
        -cancer                         : Perform 'cancer' comparissons (Somatic vs Germline). Default: false
        -canon                          : Only use canonical transcripts.
        -geneId                         : Use gene ID instead of gene name (VCF output). Default: false
        -hgvs                           : Use HGVS annotations for amino acid sub-field. Default: false
        -lof                            : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
        -reg <name>                     : Regulation track to use (this option can be used add several times).
        -oicr                           : Add OICR tag in VCF file. Default: false
        -onlyReg                        : Only use regulation tracks.
        -onlyTr <file.txt>              : Only use the transcripts in this file. Format: One transcript ID per line.
        -sequenceOntolgy                : Use Sequence Ontolgy terms. Default: false
        -ss, -spliceSiteSize <int>      : Set size for splice sites (donor and acceptor) in bases. Default: 2
        -ud, -upDownStreamLen <int>     : Set upstream downstream interval length (in bases)

Generic options:
        -0                      : File positions are zero-based (same as '-inOffset 0 -outOffset 0')
        -1                      : File positions are one-based (same as '-inOffset 1 -outOffset 1')
        -c , -config            : Specify config file
        -h , -help              : Show this help and exit
        -if, -inOffset          : Offset input by a number of bases. E.g. '-inOffset 1' for one-based input files
        -of, -outOffset         : Offset output by a number of bases. E.g. '-outOffset 1' for one-based output files
        -noLog                  : Do not report usage statistics to server
        -noStats                : Do not create stats (summary) file
        -q , -quiet             : Quiet mode (do not show any messages or errors)
        -v , -verbose           : Verbose mode

	-->
	<requirements>
		<requirement type="package" version="3.2">snpEff</requirement>
	</requirements>
	<command>
SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
eval "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 
#if $spliceSiteSize and $spliceSiteSize.__str__ != '':
  -spliceSiteSize $spliceSiteSize
#end if
#if $filterIn and $filterIn.__str__ != 'no_filter':
  -$filterIn 
#end if
#if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
  -$filterHomHet 
#end if
#if $annotations and $annotations.__str__ != '':
  -#slurp
  #echo ' -'.join($annotations.__str__.split(','))
#end if
#if $filterOut and $filterOut.__str__ != '':
  -#slurp
  #echo ' -'.join($filterOut.__str__.split(','))
#end if
#if str( $transcripts ) != 'None':
  -onlyTr $transcripts
#end if
#if str( $intervals ) != 'None':     ### fix this for multiple dataset input
  -interval $intervals
#end if
#if $statsFile:
  -stats $statsFile 
#end if
#if $offset.__str__ != '':
  -${offset} 
#end if
#if $chr.__str__.strip() != '':
  -chr "$chr" 
#end if
  $noLog $genomeVersion $input > $snpeff_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" selected="true">VCF</option>
			<option value="txt">Tabular (Deprecated)</option>
			<option value="pileup">Pileup (Deprecated)</option>
			<option value="bed">BED (Deprecated)</option>
		</param>

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

		<param name="genomeVersion" type="select" label="Genome">
                        <!--GENOME	DESCRIPTION-->
			<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="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases. Default: 2">
			<option value="1">1 base</option>
			<option value="2">2 bases</option>
			<option value="3">3 bases</option>
			<option value="4">4 bases</option>
			<option value="5">5 bases</option>
			<option value="6">6 bases</option>
			<option value="7">7 bases</option>
			<option value="8">8 bases</option>
			<option value="9">9 bases</option>
		</param>

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

                <!-- The tool testing code can not handle select,radio,checkbox values that start with '-', so the '-' is added in the command generation -->
        	<param name="filterIn" type="select" display="radio" label="Filter sequence changes">
			<option value="no_filter" selected="true">No filter (analyze everything)</option>
			<option value="del">Analyze deletions only </option>
			<option value="ins">Analyze insertions only </option>
			<option value="mnp">Only MNPs (multiple nucleotide polymorphisms) </option>
			<option value="snp">Only SNPs (single nucleotide polymorphisms) </option>
        	</param>

        	<param name="annotations" type="select" display="checkboxes" multiple="true" optional="true" label="Annotation options">
			<option value="cancer">Perform 'cancer' comparissons (Somatic vs Germline). Default: false</option>
                        <option value="canon">Only use canonical transcripts.</option>
                        <option value="geneId">Use gene ID instead of gene name (VCF output). Default: false</option>
                        <option value="hgvs">Use HGVS annotations for amino acid sub-field. Default: false</option>
                        <option value="lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.</option>
                        <option value="oicr">Add OICR tag in VCF file. Default: false</option>
                        <option value="onlyReg">Only use regulation tracks.</option>
                        <option value="sequenceOntolgy">Use Sequence Ontolgy terms. Default: false</option>
        	</param>

        	<param name="regulation" type="select" display="checkboxes" multiple="true" optional="true" label="Non-coding and regulatory Annotation">
                       <help>These are available for only a few genomes</help>
                       <!--GENOME	REG_NAME  -->
                       <options from_file="snpeffect_regulationdb.loc">
                                <column name="name" index="1"/>
                                <column name="value" index="0"/>
				<filter type="param_value" ref="genomeVersion" key="name" column="1" />
                        </options>
        	</param>

        	<param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
        	<param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file. Format: One transcript ID per line."/>

        	<param name="filterOut" type="select" display="checkboxes" multiple="true" optional="true" label="Filter output">
			<option value="no-downstream">Do not show DOWNSTREAM changes </option>
			<option value="no-intergenic">Do not show INTERGENIC changes </option>
			<option value="no-intron">Do not show INTRON changes </option>
			<option value="no-upstream">Do not show UPSTREAM changes </option>
			<option value="no-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="" selected="true">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>
        	<param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name" help="By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.  You can prepend any string you want to the chromosome name.">
                                       <validator type="regex" message="No whitespace allows">^\S*$</validator>
 
		</param>
        	<param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
        	<param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
	</inputs>
	<outputs>
		<data format="vcf" name="snpeff_output" >
			<change_format>
				<when input="outputFormat" value="vcf" format="vcf" />
				<when input="outputFormat" value="txt" format="tabular" />
				<when input="outputFormat" value="bed" format="bed" />
				<when input="outputFormat" value="bedAnn" format="bed" />
			</change_format>
		</data>
                
		<data format="html" name="statsFile">
                    <filter>generate_stats == True</filter>
                </data>
	</outputs>
        <stdio>
          <exit_code range="1:"  level="fatal"   description="Error" />
          <exit_code range="-1"  level="fatal"   description="Error: Cannot open file" />
        </stdio>
        <tests>
            <test>
                <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
                <param name="inputFormat" value="vcf"/>
                <param name="outputFormat" value="vcf"/>
                <param name="genomeVersion" value="testCase"/>
                <param name="udLength" value="0"/>
                <param name="filterHomHet" value="no_filter"/>
                <param name="filterIn" value="no_filter"/>
                <param name="generate_stats" value="False"/>
                <!--
                <param name="filterOut" value="no-upstream"/>
                -->
                <output name="snpeff_output">
                    <assert_contents>
                        <!-- Check that an effect was added -->
                        <has_text text="EFF=" />
                    </assert_contents>
                </output>
                        <!-- Check for a HTML header indicating that this was successful -->
                <!--
                <output name="statsFile">
                    <assert_contents>
                        <has_text text="SnpEff: Variant analysis" />
                    </assert_contents>
                </output>
                --> 
            </test>

            <test>
                <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
                <param name="inputFormat" value="vcf"/>
                <param name="outputFormat" value="vcf"/>
                <param name="genomeVersion" value="testCase"/>
                <param name="udLength" value="0"/>
                <param name="filterHomHet" value="het"/>
                <param name="filterIn" value="no_filter"/>
                <!--
                <param name="filterOut" value=""/>
                -->
                <param name="generate_stats" value="False"/>
                <output name="snpeff_output">
                    <assert_contents>
                        <!-- Check that NO effects were added since -het is set -->
                        <not_has_text text="EFF=NON_SYNONYMOUS_CODING" />
                    </assert_contents>
                </output>
            </test>
            <test>
                <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
                <param name="inputFormat" value="vcf"/>
                <param name="outputFormat" value="vcf"/>
                <param name="genomeVersion" value="testCase"/>
                <param name="udLength" value="0"/>
                <param name="filterHomHet" value="no_filter"/>
                <param name="filterIn" value="del"/>
                <!--
                <param name="filterOut" value=""/>
                -->
                <param name="generate_stats" value="False"/>
                <output name="snpeff_output">
                    <assert_contents>
                        <!-- Check that deleletions were evaluated -->
                        <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" />
                        <!-- Check that insertion on last line was NOT evaluated -->
                        <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" />
                    </assert_contents>
                </output>
            </test>
            <test>
                <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
                <param name="inputFormat" value="vcf"/>
                <param name="outputFormat" value="vcf"/>
                <param name="genomeVersion" value="testCase"/>
                <param name="udLength" value="0"/>
                <param name="filterHomHet" value="no_filter"/>
                <param name="filterIn" value="no_filter"/>
                <param name="filterOut" value="no-upstream"/>
                <param name="generate_stats" value="False"/>
                <output name="snpeff_output">
                    <assert_contents>
                        <!-- Check that NO UPSTREAM  effect was added -->
                        <not_has_text text="UPSTREAM" />
                    </assert_contents>
                </output>
            </test>

        </tests>
	<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>