Mercurial > repos > jjohnson > snpeff
diff snpEff.xml @ 5:8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 27 Nov 2013 09:11:32 -0600 |
| parents | 6ad9205c1307 |
| children | eb394dd65c98 |
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--- a/snpEff.xml Mon Oct 07 10:59:44 2013 -0500 +++ b/snpEff.xml Wed Nov 27 09:11:32 2013 -0600 @@ -1,74 +1,12 @@ -<tool id="snpEff" name="SnpEff" version="3.3"> - <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="3.3">snpEff</requirement> - </requirements> - <command> -SNPEFF_DATA_DIR=`grep '^data_dir' \$SNPEFF_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`; -eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ; -then java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config $genomeVersion ; -fi"; -java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength +<tool id="snpEff" name="SnpEff" version="3.4"> + <description>Variant effect and annotation</description> + <requirements> + <requirement type="package" version="3.4">snpEff</requirement> + </requirements> + <command> +java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff +-c \$SNPEFF_JAR_PATH/snpEff.config +-i $inputFormat -o $outputFormat -upDownStreamLen $udLength #if $spliceSiteSize and $spliceSiteSize.__str__ != '': -spliceSiteSize $spliceSiteSize #end if @@ -79,15 +17,11 @@ $filterHomHet #end if #if $annotations and $annotations.__str__ != '': + #echo " " #echo ' '.join($annotations.__str__.split(',')) #end if -#if $extra_annotations and $extra_annotations.__str__ != '': - #echo ' '.join($extra_annotations.__str__.split(',')) -#end if -#if $regulation and $regulation.__str__ != '': - -reg #echo ' -reg '.join($regulation.__str__.split(','))# -#end if #if $filterOut and $filterOut.__str__ != '': + #echo " " #echo ' '.join($filterOut.__str__.split(',')) #end if #if str( $transcripts ) != 'None': @@ -105,228 +39,296 @@ #if $chr.__str__.strip() != '': -chr "$chr" #end if - $noLog $genomeVersion $input > $snpeff_output + $noLog +#if $snpDb.genomeSrc == 'cached': + -dataDir ${snpDb.genomeVersion.fields.path} + #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': + #echo " " + #echo ' '.join($snpDb.extra_annotations.__str__.split(',')) + #end if + #if $snpDb.regulation and $snpDb.regulation.__str__ != '': + -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# + #end if + $snpDb.genomeVersion +#elif $snpDb.genomeSrc == 'history': + -dataDir ${snpDb.snpeff_db.extra_files_path} + #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': + #set annotations = [' '] + $snpDb.extra_annotations.__str__.split(',') + #echo " " + #echo ' -'.join($annotations) + #end if + #if $snpDb.regulation and $snpDb.regulation.__str__ != '': + -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# + #end if + ${snpDb.snpeff_db.metadata.genome_version} +#else + -download + $snpDb.genome_version +#end if +$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_data_table="snpeff_genomedb"/> - </param> + <inputs> + <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> - <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="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="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> + <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> - <!-- The tool testing code can not handle select,radio,check boxes 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" 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="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> + <conditional name="snpDb"> + <param name="genomeSrc" type="select" label=""> + <option value="cached">Locally cached</option> + <option value="history">history</option> + <option value="named">named on demand</option> + </param> + <when value="cached"> + <param name="genomeVersion" type="select" label="Genome"> + <!--GENOME DESCRIPTION--> + <options from_data_table="snpeff_genomedb"/> + </param> + <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> <help>These are available for only a few genomes</help> - <!--GENOME REG_NAME --> <options from_data_table="snpeff_annotations"> - <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> + <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> + </options> + </param> + <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation"> + <help>These are available for only a few genomes</help> + <options from_data_table="snpeff_regulationdb"> + <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> </options> - </param> - - <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation"> - <help>These are available for only a few genomes</help> - <!--GENOME REG_NAME --> - <options from_data_table="snpeff_regulationdb"> - <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> - </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> + </when> + <when value="history"> + <param format="snpeffdb" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/> + <!-- From metadata --> + <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> + <help>These are available for only a few genomes</help> + <options> + <filter type="data_meta" ref="snpeff_db" key="annotation" /> + </options> + </param> + <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation"> + <help>These are available for only a few genomes</help> + <options> + <filter type="data_meta" ref="snpeff_db" key="regulation" /> + </options> + </param> + </when> + <when value="named"> + <param name="genome_version" type="text" value="GRCh37.68" label="Snpff Version Name"/> + </when> + </conditional> - <param name="filterOut" type="select" display="checkboxes" multiple="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="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="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 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,check boxes 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> - <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> + <param name="annotations" type="select" display="checkboxes" multiple="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="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" 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." + </help> + <validator type="regex" message="No whitespace allows">^\S*$</validator> - <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> + </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> + <!-- Check that an effect was added in out VCF --> + <!-- Check for a HTML header indicating that this was successful --> + <!-- + <output name="statsFile"> + <assert_contents> + <has_text text="SnpEff: Variant analysis" /> + </assert_contents> + </output> + --> + <!-- Setting filterOut throws exception in twilltestcase.py + <test> + <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> + <param name="inputFormat" value="vcf"/> + <param name="outputFormat" value="vcf"/> + <param name="genomeSrc" value="named"/> + <param name="genome_version" 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> + <has_text text="EFF=" /> + </assert_contents> + </output> + </test> + --> - </tests> - <help> + <test> + <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> + <param name="inputFormat" value="vcf"/> + <param name="outputFormat" value="vcf"/> + <param name="genomeSrc" value="named"/> + <param name="genome_version" 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="genomeSrc" value="named"/> + <param name="genome_version" 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> + + <!-- Check that NO UPSTREAM effect was added --> + <!-- Setting filterOut throws exception in twilltestcase.py + <test> + <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> + <param name="inputFormat" value="vcf"/> + <param name="outputFormat" value="vcf"/> + <param name="genomeSrc" value="named"/> + <param name="genome_version" 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> + <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> +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>