Mercurial > repos > jjohnson > snpeff
changeset 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 | 47ddc9f4d0b6 |
| children | eb394dd65c98 |
| files | README data_manager/data_manager_snpEff_databases.xml data_manager/data_manager_snpEff_download.py data_manager/data_manager_snpEff_download.xml datatypes_conf.xml lib/galaxy/datatypes/snpeff.py snpEff.xml snpEff_download.xml snpSift_annotate.xml snpSift_caseControl.xml snpSift_filter.xml snpSift_int.xml tool-data/snpeff_genomedb.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 15 files changed, 597 insertions(+), 408 deletions(-) [+] |
line wrap: on
line diff
--- a/README Mon Oct 07 10:59:44 2013 -0500 +++ b/README Wed Nov 27 09:11:32 2013 -0600 @@ -1,4 +1,6 @@ -These are galaxy tools for SnpEff ( http://snpeff.sourceforge.net/ ) +These are galaxy tools for SnpEff a variant annotation and effect prediction tool by Pablo Cingolani. +It annotates and predicts the effects of variants on genes (such as amino acid changes). +( http://snpeff.sourceforge.net/ ) This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift. @@ -15,4 +17,8 @@ data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc data_manager_snpeff_download - downloads a SnpEff genome database selected from: tool-data/snpeff_databases.loc and adds entries to snpeff_genomedb.loc,snpeff_regulationdb.loc,snpeff_annotations.loc +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.
--- a/data_manager/data_manager_snpEff_databases.xml Mon Oct 07 10:59:44 2013 -0500 +++ b/data_manager/data_manager_snpEff_databases.xml Wed Nov 27 09:11:32 2013 -0600 @@ -1,7 +1,7 @@ -<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="3.3" tool_type="manage_data"> +<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="3.4" tool_type="manage_data"> <description>Read the list of available snpEff databases</description> <requirements> - <requirement type="package" version="3.3">snpEff</requirement> + <requirement type="package" version="3.4">snpEff</requirement> </requirements> <command interpreter="python"> data_manager_snpEff_databases.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar "$out_file" @@ -33,6 +33,9 @@ For information about snpEff: http://snpEff.sourceforge.net +Please cite: +"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] + </help> </tool>
--- a/data_manager/data_manager_snpEff_download.py Mon Oct 07 10:59:44 2013 -0500 +++ b/data_manager/data_manager_snpEff_download.py Wed Nov 27 09:11:32 2013 -0600 @@ -39,24 +39,15 @@ ## Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory ##--- #data_dir = ~/snpEff/data/ - data_dir = None - try: - fh = open(config) - for i,line in enumerate(fh): - if line.strip().startswith('data_dir'): - (k,v) = line.split('=') - data_dir = os.path.expanduser(v.strip()) - break - except Exception, e: - stop_err( 'Error parsing %s %s\n' % (config,str( e )) ) - else: - fh.close() + data_dir = target_directory (snpEff_dir,snpEff_jar) = os.path.split(jar_path) args = [ 'java','-jar' ] args.append( jar_path ) args.append( 'download' ) - # args.append( '-c' ) - # args.append( 'config' ) + args.append( '-c' ) + args.append( config ) + args.append( '-dataDir' ) + args.append( data_dir ) args.append( '-v' ) args.append( genome_version ) proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir ) @@ -74,7 +65,7 @@ if fname.startswith('snpEffectPredictor'): # if snpEffectPredictor.bin download succeeded name = genome_version + (' : ' + organism if organism else '') - data_table_entry = dict(value=genome_version, name=name) + data_table_entry = dict(value=genome_version, name=name, path=data_dir) _add_data_table_entry( data_manager_dict, 'snpeff_genomedb', data_table_entry ) else: m = re.match(regulation_pattern,fname)
--- a/data_manager/data_manager_snpEff_download.xml Mon Oct 07 10:59:44 2013 -0500 +++ b/data_manager/data_manager_snpEff_download.xml Wed Nov 27 09:11:32 2013 -0600 @@ -1,7 +1,7 @@ -<tool id="data_manager_snpeff_download" name="SnpEff Download" version="3.3" tool_type="manage_data"> +<tool id="data_manager_snpeff_download" name="SnpEff Download" version="3.4" tool_type="manage_data"> <description>Download a new database</description> <requirements> - <requirement type="package" version="3.3">snpEff</requirement> + <requirement type="package" version="3.4">snpEff</requirement> </requirements> <command interpreter="python"> data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config @@ -11,7 +11,9 @@ </command> <inputs> <param name="genome_databases" type="select" label="Genome Version"> - <options from_data_table="snpeff_databases"/> + <options from_data_table="snpeff_databases"> + <filter type="sort_by" column="0" /> + </options> </param> </inputs> @@ -41,6 +43,9 @@ For details about this tool, please go to http://snpEff.sourceforge.net +Please cite: +"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] + </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Wed Nov 27 09:11:32 2013 -0600 @@ -0,0 +1,10 @@ +<?xml version="1.0"?> +<datatypes> + <datatype_files> + <datatype_file name="snpeff.py"/> + </datatype_files> + <registration> + <datatype extension="snpeffdb" type="galaxy.datatypes.snpeff:SnpEffDb" display_in_upload="True"/> + </registration> +</datatypes> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/snpeff.py Wed Nov 27 09:11:32 2013 -0600 @@ -0,0 +1,46 @@ +""" +SnpEff datatypes +""" +import os,os.path,re,sys +import galaxy.datatypes.data +from galaxy.datatypes.data import Text +from galaxy.datatypes.metadata import MetadataElement + +class SnpEffDb( Text ): + """Class describing an IGV tiled data file (TDF) .tdf binary file""" + file_ext = "snpeffdb" + MetadataElement( name="genome_version", default=None, desc="Genome Version", readonly=True, visible=True, no_value=None ) + MetadataElement( name="regulation", default=[], desc="Regulation Names", readonly=True, visible=True, no_value=[] ) + MetadataElement( name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[] ) + + def __init__( self, **kwd ): + Text.__init__( self, **kwd ) + + def set_meta( self, dataset, **kwd ): + Text.set_meta(self, dataset, **kwd ) + data_dir = dataset.extra_files_path + ## search data_dir/genome_version for files + regulation_pattern = 'regulation_(.+).bin' + # annotation files that are included in snpEff by a flag + annotations_dict = {'nextProt.bin' : '-nextprot','motif.bin': '-motif'} + regulations = [] + annotations = [] + if data_dir and os.path.isdir(data_dir): + for root, dirs, files in os.walk(data_dir): + for fname in files: + if fname.startswith('snpEffectPredictor'): + # if snpEffectPredictor.bin download succeeded + genome_version = os.path.basename(root) + dataset.metadata.genome_version = genome_version + else: + m = re.match(regulation_pattern,fname) + if m: + name = m.groups()[0] + regulations.append(name) + elif fname in annotations_dict: + value = annotations_dict[fname] + name = value.lstrip('-') + annotations.append(name) + dataset.metadata.regulation = regulations + dataset.metadata.annotation = annotations +
--- 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_download.xml Wed Nov 27 09:11:32 2013 -0600 @@ -0,0 +1,34 @@ +<tool id="snpEff_download" name="SnpEff Download" version="3.4"> + <description>Download a new database</description> + <requirements> + <requirement type="package" version="3.4">snpEff</requirement> + </requirements> + <command> + echo $genomeVersion > $snpeff_db; + java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genomeVersion > $logfile + </command> + <inputs> + <param name="genomeVersion" type="select" label="Genome Version"> + <options from_data_table="snpeff_databases"/> + </param> + </inputs> + <outputs> + <data format="txt" name="logfile" /> + <data format="snpeffdb" name="snpeff_db" label="${genomeVersion}" /> + </outputs> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <help> + +This tool downloads a SnpEff database into the users history for use by snpEff. + +For details about this tool, please go to http://snpEff.sourceforge.net + +Please cite: +"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] + + </help> +</tool> +
--- a/snpSift_annotate.xml Mon Oct 07 10:59:44 2013 -0500 +++ b/snpSift_annotate.xml Wed Nov 27 09:11:32 2013 -0600 @@ -1,11 +1,11 @@ -<tool id="snpSift_annotate" name="SnpSift Annotate" version="3.3"> +<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="3.3">snpEff</requirement> + <requirement type="package" version="3.4">snpEff</requirement> </requirements> <command> java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd @@ -20,18 +20,22 @@ <param format="vcf" name="input" type="data" label="VCF input"/> <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/> - <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Annotate in Memory" - help="allows unsorted VCF files, but it loads the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files)"/> <conditional name="annotate"> <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> <when value="id"/> <when value="info"> - <param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs" + <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs" help="list is a comma separated list of fields. When blank, all INFO fields are included"> <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</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" /> @@ -60,6 +64,44 @@ 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>
--- a/snpSift_caseControl.xml Mon Oct 07 10:59:44 2013 -0500 +++ b/snpSift_caseControl.xml Wed Nov 27 09:11:32 2013 -0600 @@ -1,11 +1,11 @@ -<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.3"> +<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.4"> <description>Count samples are in 'case' and 'control' groups.</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="3.3">snpEff</requirement> + <requirement type="package" version="3.4">snpEff</requirement> </requirements> <command> java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q @@ -121,5 +121,13 @@ For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol +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>
--- a/snpSift_filter.xml Mon Oct 07 10:59:44 2013 -0500 +++ b/snpSift_filter.xml Wed Nov 27 09:11:32 2013 -0600 @@ -1,98 +1,123 @@ -<tool id="snpSift_filter" name="SnpSift Filter" version="3.3"> - <options sanitize="False" /> - <description>Filter variants using arbitrary expressions</description> - <requirements> - <requirement type="package" version="3.3">snpEff</requirement> - </requirements> - <command> - java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse $pass - #if $filterId and len($filterId.__str__.strip()) > 0: - --filterId = "$filterId" - #end if - #if $addFilter and len($addFilter.__str__.strip()) > 0: - --addFilter = "$addFilter" - #end if - #if $rmFilter and len($rmFilter.__str__.strip()) > 0: - --rmFilter = "$rmFilter" +<tool id="snpSift_filter" name="SnpSift Filter" version="3.4"> + <options sanitize="False" /> + <description>Filter variants using arbitrary expressions</description> + <requirements> + <requirement type="package" version="3.4">snpEff</requirement> + </requirements> + <command> + java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse + #if $filtering.mode == 'field': + #if $filtering.replace.pass: + --pass + #if $filtering.replace.filterId and len($filtering.replace.filterId.__str__.strip()) > 0: + --filterId "$filtering.replace.filterId" #end if - > $output - </command> - <inputs> - <param format="vcf" name="input" type="data" label="VCF input"/> - <param name="expr" type="text" label="Expression" size="120"/> - <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse. Show lines that do not match filter expression"/> - <param name="pass" type="boolean" truevalue="--pass" falsevalue="" checked="false" label="Use 'PASS' field instead of filtering out VCF entries"/> - <param name="filterId" type="text" value="" optional="true" label="ID for this filter (##FILTER tag in header and FILTER VCF field)." size="10"/> - <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/> - <param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." size="10"/> - </inputs> - <configfiles> - <configfile name="exprFile"> - $expr - </configfile> - </configfiles> - - <outputs> - <data format="vcf" name="output" /> - </outputs> - <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> - - <tests> + #end if + #if $filtering.addFilter and len($filtering.addFilter.__str__.strip()) > 0: + --addFilter "$filtering.addFilter" + #end if + #if $filtering.rmFilter and len($filtering.rmFilter.__str__.strip()) > 0: + --rmFilter "$filtering.rmFilter" + #end if + #end if + > $output + </command> + <inputs> + <param format="vcf" name="input" type="data" label="VCF input"/> + <param name="expr" type="text" label="Expression" size="160"/> + <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse. Show lines that do not match filter expression"/> + <conditional name="filtering"> + <param name="mode" type="select" labael="Filter mode"> + <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option> + <option value="field">Change the FILTER field, but retain all entries</option> + </param> + <when value="entries"/> + <when value="field"> + <conditional name="replace"> + <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'" + help="appends an ID tag to non-matching entry FILTER "/> + <when value="no"/> + <when value="yes"> + <param name="filterId" type="text" value="" optional="true" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)." size="10" + help="Default ID is 'SnpSift'"/> + </when> + </conditional> + <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/> + <param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." size="10"/> + </when> + </conditional> + </inputs> + <configfiles> + <configfile name="exprFile"> + $expr + </configfile> + </configfiles> - <test> - <param name="input" ftype="vcf" value="test01.vcf"/> - <param name="expr" value="QUAL >= 50"/> - <output name="output"> - <assert_contents> - <has_text text="28837706" /> - <not_has_text text="NT_166464" /> - </assert_contents> - </output> - </test> + <outputs> + <data format="vcf" name="output" /> + </outputs> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + + <tests> - <test> - <param name="input" ftype="vcf" value="test01.vcf"/> - <param name="expr" value="(CHROM = '19')"/> - <output name="output"> - <assert_contents> - <has_text text="3205820" /> - <not_has_text text="NT_16" /> - </assert_contents> - </output> - </test> + <test> + <param name="input" ftype="vcf" value="test01.vcf"/> + <param name="expr" value="QUAL >= 50"/> + <param name="mode" value="entries"/> + <output name="output"> + <assert_contents> + <has_text text="28837706" /> + <not_has_text text="NT_166464" /> + </assert_contents> + </output> + </test> - <test> - <param name="input" ftype="vcf" value="test01.vcf"/> - <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/> - <output name="output"> - <assert_contents> - <has_text text="20175" /> - <has_text text="35549" /> - <has_text text="22256" /> - <not_has_text text="18933" /> - <not_has_text text="37567" /> - </assert_contents> - </output> - </test> + <test> + <param name="input" ftype="vcf" value="test01.vcf"/> + <param name="expr" value="(CHROM = '19')"/> + <param name="mode" value="entries"/> + <output name="output"> + <assert_contents> + <has_text text="3205820" /> + <not_has_text text="NT_16" /> + </assert_contents> + </output> + </test> - <test> - <param name="input" ftype="vcf" value="test01.vcf"/> - <param name="expr" value="( DP >= 5 )"/> - <output name="output"> - <assert_contents> - <has_text text="DP=5;" /> - <has_text text="DP=6;" /> - <not_has_text text="DP=1;" /> - </assert_contents> - </output> - </test> + <test> + <param name="input" ftype="vcf" value="test01.vcf"/> + <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/> + <param name="mode" value="entries"/> + <output name="output"> + <assert_contents> + <has_text text="20175" /> + <has_text text="35549" /> + <has_text text="22256" /> + <not_has_text text="18933" /> + <not_has_text text="37567" /> + </assert_contents> + </output> + </test> - </tests> + <test> + <param name="input" ftype="vcf" value="test01.vcf"/> + <param name="expr" value="( DP >= 5 )"/> + <param name="mode" value="entries"/> + <output name="output"> + <assert_contents> + <has_text text="DP=5;" /> + <has_text text="DP=6;" /> + <not_has_text text="DP=1;" /> + </assert_contents> + </output> + </test> - <help> + </tests> + + <help> **SnpSift filter** @@ -123,5 +148,12 @@ For complete details about this tool and epressions that can be used, please go to http://snpeff.sourceforge.net/SnpSift.html#filter - </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>
--- a/snpSift_int.xml Mon Oct 07 10:59:44 2013 -0500 +++ b/snpSift_int.xml Wed Nov 27 09:11:32 2013 -0600 @@ -1,11 +1,11 @@ -<tool id="snpSift_int" name="SnpSift Intervals" version="3.3"> +<tool id="snpSift_int" name="SnpSift Intervals" version="3.4"> <description>Filter variants using intervals </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="3.3">snpEff</requirement> + <requirement type="package" version="3.4">snpEff</requirement> </requirements> <command> java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output @@ -57,5 +57,11 @@ For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals +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>
--- a/tool-data/snpeff_genomedb.loc.sample Mon Oct 07 10:59:44 2013 -0500 +++ b/tool-data/snpeff_genomedb.loc.sample Wed Nov 27 09:11:32 2013 -0600 @@ -1,5 +1,5 @@ ## Downloaded Databases for SnpEff ## These are from the list on: http://snpeff.sourceforge.net/download.html ## the Description field in this sample is "Genome : Version" -#Version Description -#GRCh37.68 Homo sapiens : GRCh37.68 +#Version Description data_dir path +#GRCh37.68 Homo sapiens : GRCh37.68 /home/galaxy/snpEff/data
--- a/tool_data_table_conf.xml.sample Mon Oct 07 10:59:44 2013 -0500 +++ b/tool_data_table_conf.xml.sample Wed Nov 27 09:11:32 2013 -0600 @@ -4,12 +4,16 @@ <file path="tool-data/snpeff_databases.loc" /> </table> <table name="snpeff_genomedb" comment_char="#"> - <columns>value, name</columns> + <columns>value, name, path</columns> <file path="tool-data/snpeff_genomedb.loc" /> </table> <table name="snpeff_regulationdb" comment_char="#"> - <columns>value, name</columns> + <columns>genome, value, name</columns> <file path="tool-data/snpeff_regulationdb.loc" /> </table> + <table name="snpeff_annotations" comment_char="#"> + <columns>genome, value, name</columns> + <file path="tool-data/snpeff_annotations.loc" /> + </table> </tables>
--- a/tool_dependencies.xml Mon Oct 07 10:59:44 2013 -0500 +++ b/tool_dependencies.xml Wed Nov 27 09:11:32 2013 -0600 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> - <package name="snpEff" version="3.3"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_snpeff_3_3" owner="jjohnson" changeset_revision="a462177619be" /> + <package name="snpEff" version="3.4"> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_snpeff_3_4" owner="jjohnson" changeset_revision="7fb1061d905a" /> </package> </tool_dependency>