Mercurial > repos > jjohnson > snpeff
changeset 22:bb0797deab78 draft
Uploaded
| author | jjohnson |
|---|---|
| date | Wed, 09 Dec 2015 10:20:13 -0500 |
| parents | c780e3f75b3d |
| children | 924af057bbca |
| files | repository_dependencies.xml snpEff.xml snpEff_databases.xml snpEff_download.xml snpEff_genes.txt snpEff_macros.xml tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 8 files changed, 3589 insertions(+), 62 deletions(-) [+] |
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--- a/repository_dependencies.xml Wed Jan 14 12:03:21 2015 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="This requires the SnpEff datatype definitions."> - <repository name="snpeff_datatypes" owner="jjohnson" changeset_revision="5d6f3622b99d" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> -</repositories>
--- a/snpEff.xml Wed Jan 14 12:03:21 2015 -0600 +++ b/snpEff.xml Wed Dec 09 10:20:13 2015 -0500 @@ -1,22 +1,32 @@ -<tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.3"> +<tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0"> <description>Variant effect and annotation</description> - <expand macro="requirements" /> <macros> <import>snpEff_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> <command> <![CDATA[ - java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff - -c \$SNPEFF_JAR_PATH/snpEff.config + java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff + -c \$SNPEFF_JAR_PATH/snpEff.config -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength #if $spliceSiteSize and $spliceSiteSize.__str__ != '': -spliceSiteSize $spliceSiteSize #end if - #if $filterIn and $filterIn.__str__ != 'no_filter': - $filterIn + #if $spliceRegion.setSpliceRegions == 'yes': + #if $spliceRegion.spliceRegionExonSize and $spliceRegion.spliceRegionExonSize.__str__ != '': + -spliceRegionExonSize $spliceRegion.spliceRegionExonSize + #end if + #if $spliceRegion.spliceRegionIntronMin and $spliceRegion.spliceRegionIntronMin.__str__ != '': + -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin + #end if + #if $spliceRegion.spliceRegionIntronMax and $spliceRegion.spliceRegionIntronMax.__str__ != '': + -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax + #end if #end if #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': - $filterHomHet + $filterHomHet #end if #if $annotations and $annotations.__str__ != '': #echo " " @@ -26,6 +36,11 @@ #echo " " #echo ' '.join($filterOut.__str__.split(',')) #end if + #if $filter.specificEffects == 'yes' and $filter.effects: + #for $eff in str($filter.effects).split(','): + -no $eff + #end for + #end if #if str( $transcripts ) != 'None': -onlyTr $transcripts #end if @@ -33,15 +48,15 @@ -interval $intervals #end if #if $statsFile: - -stats $statsFile + -stats $statsFile #end if #if $offset.__str__ != 'default': - ${offset} + ${offset} #end if #if $chr.__str__.strip() != '': - -chr "$chr" + -chr "$chr" #end if - $noLog + $noLog #if $snpDb.genomeSrc == 'cached': -dataDir ${snpDb.genomeVersion.fields.path} #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': @@ -63,7 +78,7 @@ -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# #end if ${snpDb.snpeff_db.metadata.genome_version} - #else + #else -download $snpDb.genome_version #end if @@ -77,7 +92,7 @@ #end if #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]" - sed -i 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output + sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output #end if ]]> </command> @@ -86,8 +101,6 @@ <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> @@ -95,7 +108,6 @@ <param name="outputFormat" type="select" label="Output format"> <option value="vcf" selected="true">VCF (only if input is VCF)</option> <option value="gatk">GATK-compatible VCF (only if input is VCF)</option> - <option value="txt">Tabular</option> <option value="bed">BED</option> <option value="bedAnn">BED annotations</option> </param> @@ -103,7 +115,6 @@ <when value="gatk"> <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" /> </when> - <when value="txt" /> <when value="bed" /> <when value="bedAnn" /> </conditional> @@ -159,7 +170,7 @@ </param> </when> <when value="named"> - <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> + <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> <help>@SNPEFF_DATABASE_URL@</help> <validator type="regex" message="A genome version name is required">\S+</validator> </param> @@ -189,21 +200,25 @@ <option value="9">9 bases</option> </param> + <conditional name="spliceRegion"> + <param name="setSpliceRegions" type="select" label="spliceRegion Settings"> + <option value="no">Use Defaults</option> + <option value="yes">Set Splice Region Parameters</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases"/> + <param name="spliceRegionIntronMin" type="integer" value="" min="1" max="10" optional="true" label="Set minimum number of bases for splice site region within intron. Default: 3 bases"/> + <param name="spliceRegionIntronMax" type="integer" value="" min="1" max="10" optional="true" label="Set maximum number of bases for splice site region within intron. Default: 8 bases"/> + </when> + </conditional> + <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 name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> <option value="-canon">Only use canonical transcripts</option> @@ -214,7 +229,13 @@ <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option> <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option> <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option> + <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN').</option> + <option value="-noHgvs">Do not add HGVS annotations.</option> + <option value="-noLof">Do not add LOF and NMD annotations.</option> + <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end).</option> + <option value="-oicr">Add OICR tag in VCF file. Default: false</option> </param> + <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. --> <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." help="Format is one transcript ID per line."/> <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output"> @@ -224,6 +245,60 @@ <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> + <conditional name="filter"> + <param name="specificEffects" type="select" label="Filter out specific Effects"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="effects" type="select" display="checkboxes" multiple="true" label="Filter output: do not report these Effects"> + <option value="CDS">CDS (coding_sequence_variant) The variant hits a CDS. MODIFIER</option> + <option value="CHROMOSOME_LARGE_DELETION">CHROMOSOME_LARGE_DELETION (chromosome) A large parte (over 1%) of the chromosome was deleted. HIGH</option> + <option value="CODON_CHANGE">CODON_CHANGE (coding_sequence_variant) One or many codons are changed e.g.: An MNP of size multiple of 3 MODERATE</option> + <option value="CODON_INSERTION">CODON_INSERTION (inframe_insertion) One or many codons are inserted e.g.: An insert multiple of three in a codon boundary MODERATE</option> + <option value="CODON_CHANGE_PLUS CODON_INSERTION">CODON_CHANGE_PLUS CODON_INSERTION (disruptive_inframe_insertion) One codon is changed and one or many codons are inserted e.g.: An insert of size multiple of three, not at codon boundary MODERATE</option> + <option value="CODON_DELETION">CODON_DELETION (inframe_deletion) One or many codons are deleted e.g.: A deletion multiple of three at codon boundary MODERATE</option> + <option value="CODON_CHANGE_PLUS CODON_DELETION">CODON_CHANGE_PLUS CODON_DELETION (disruptive_inframe_deletion) One codon is changed and one or more codons are deleted e.g.: A deletion of size multiple of three, not at codon boundary MODERATE</option> + <option value="DOWNSTREAM">DOWNSTREAM (downstream_gene_variant) Downstream of a gene (default length: 5K bases) MODIFIER</option> + <option value="EXON">EXON (exon_variant) The variant hits an exon (from a non-coding transcript) or a retained intron. MODIFIER</option> + <option value="EXON_DELETED">EXON_DELETED (exon_loss_variant) A deletion removes the whole exon. HIGH</option> + <option value="FRAME_SHIFT">FRAME_SHIFT (frameshift_variant) Insertion or deletion causes a frame shift e.g.: An indel size is not multple of 3 HIGH</option> + <option value="GENE">GENE (gene_variant) The variant hits a gene. MODIFIER</option> + <option value="INTERGENIC">INTERGENIC (intergenic_region) The variant is in an intergenic region MODIFIER</option> + <option value="INTERGENIC_CONSERVED">INTERGENIC_CONSERVED (conserved_intergenic_variant) The variant is in a highly conserved intergenic region MODIFIER</option> + <option value="INTRAGENIC">INTRAGENIC (intragenic_variant) The variant hits a gene, but no transcripts within the gene MODIFIER</option> + <option value="INTRON">INTRON (intron_variant) Variant hits and intron. Technically, hits no exon in the transcript. MODIFIER</option> + <option value="INTRON_CONSERVED">INTRON_CONSERVED (conserved_intron_variant) The variant is in a highly conserved intronic region MODIFIER</option> + <option value="MICRO_RNA">MICRO_RNA (miRNA) Variant affects an miRNA MODIFIER</option> + <option value="NON_SYNONYMOUS_CODING">NON_SYNONYMOUS_CODING (missense_variant) Variant causes a codon that produces a different amino acid e.g.: Tgg/Cgg, W/R MODERATE</option> + <option value="NON_SYNONYMOUS_START">NON_SYNONYMOUS_START (initiator_codon_variant) Variant causes start codon to be mutated into another start codon (the new codon produces a different AA). e.g.: Atg/Ctg, M/L (ATG and CTG can be START codons) LOW</option> + <option value="NON_SYNONYMOUS_STOP">NON_SYNONYMOUS_STOP (stop_retained_variant) Variant causes stop codon to be mutated into another stop codon (the new codon produces a different AA). e.g.: Atg/Ctg, M/L (ATG and CTG can be START codons) LOW</option> + <option value="RARE_AMINO_ACID">RARE_AMINO_ACID (rare_amino_acid_variant) The variant hits a rare amino acid thus is likely to produce protein loss of function HIGH</option> + <option value="SPLICE_SITE_ACCEPTOR">SPLICE_SITE_ACCEPTOR (splice_acceptor_variant) The variant hits a splice acceptor site (defined as two bases before exon start, except for the first exon). HIGH</option> + <option value="SPLICE_SITE_DONOR">SPLICE_SITE_DONOR (splice_donor_variant) The variant hits a Splice donor site (defined as two bases after coding exon end, except for the last exon). HIGH</option> + <option value="SPLICE_SITE_REGION">SPLICE_SITE_REGION (splice_region_variant) A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. LOW</option> + <option value="SPLICE_SITE_BRANCH">SPLICE_SITE_BRANCH (splice_region_variant) A varaint affective putative (Lariat) branch point, located in the intron. LOW</option> + <option value="SPLICE_SITE_BRANCH_U12">SPLICE_SITE_BRANCH_U12 (splice_region_variant) A varaint affective putative (Lariat) branch point from U12 splicing machinery, located in the intron. MODERATE</option> + <option value="STOP_LOST">STOP_LOST (stop_lost) Variant causes stop codon to be mutated into a non-stop codon e.g.: Tga/Cga, */R HIGH</option> + <option value="START_GAINED">START_GAINED (5_prime_UTR_premature start_codon_gain_variant) A variant in 5'UTR region produces a three base sequence that can be a START codon. LOW</option> + <option value="START_LOST">START_LOST (start_lost) Variant causes start codon to be mutated into a non-start codon. e.g.: aTg/aGg, M/R HIGH</option> + <option value="STOP_GAINED">STOP_GAINED (stop_gained) Variant causes a STOP codon e.g.: Cag/Tag, Q/* HIGH</option> + <option value="SYNONYMOUS_CODING">SYNONYMOUS_CODING (synonymous_variant) Variant causes a codon that produces the same amino acid e.g.: Ttg/Ctg, L/L LOW</option> + <option value="SYNONYMOUS_START">SYNONYMOUS_START (start_retained) Variant causes start codon to be mutated into another start codon. e.g.: Ttg/Ctg, L/L (TTG and CTG can be START codons) LOW</option> + <option value="SYNONYMOUS_STOP">SYNONYMOUS_STOP (stop_retained_variant) Variant causes stop codon to be mutated into another stop codon. e.g.: taA/taG, */* LOW</option> + <option value="TRANSCRIPT">TRANSCRIPT (transcript_variant) The variant hits a transcript. MODIFIER</option> + <option value="REGULATION">REGULATION (regulatory_region_variant) The variant hits a known regulatory feature (non-coding). MODIFIER</option> + <option value="UPSTREAM">UPSTREAM (upstream_gene_variant) Upstream of a gene (default length: 5K bases) MODIFIER</option> + <option value="UTR_3_PRIME">UTR_3_PRIME (3_prime_UTR_variant) Variant hits 3'UTR region MODIFIER</option> + <option value="UTR_3_DELETED">UTR_3_DELETED (3_prime_UTR_truncation + exon_loss) The variant deletes an exon which is in the 3'UTR of the transcript MODERATE</option> + <option value="UTR_5_PRIME">UTR_5_PRIME (5_prime_UTR_variant) Variant hits 5'UTR region MODIFIER</option> + <option value="UTR_5_DELETED">UTR_5_DELETED (5_prime_UTR_truncation + exon_loss_variant) The variant deletes an exon which is in the 5'UTR of the transcript MODERATE</option> + <option value="NEXT_PROT">NEXT_PROT (sequence_feature + exon_loss_variant) A 'NextProt' based annotation. Details are provided in the 'feature type' sub-field (ANN), or in the effect details (EFF). MODERATE </option> + + </param> + </when> + </conditional> <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> <option value="default" selected="true">Use default (based on input type)</option> @@ -243,7 +318,6 @@ <outputs> <data format="vcf" name="snpeff_output" > <change_format> - <when input="outputConditional.outputFormat" value="txt" format="tabular" /> <when input="outputConditional.outputFormat" value="bed" format="bed" /> <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> </change_format> @@ -252,7 +326,6 @@ <filter>generate_stats == True</filter> </data> </outputs> - <expand macro="stdio" /> <tests> <!-- Check that an effect was added in out VCF --> <!-- Check for a HTML header indicating that this was successful --> @@ -262,7 +335,7 @@ <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"/> @@ -272,7 +345,6 @@ <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"> @@ -281,7 +353,7 @@ </assert_contents> </output> </test> - --> + --> <test> <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> @@ -291,7 +363,6 @@ <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=""/> --> @@ -312,7 +383,6 @@ <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=""/> --> @@ -337,7 +407,6 @@ <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"> @@ -349,7 +418,7 @@ --> </tests> - <help> + <help><![CDATA[ This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. @@ -357,6 +426,7 @@ @CITATION_SECTION@ +]]> </help> <expand macro="citations" /> </tool>
--- a/snpEff_databases.xml Wed Jan 14 12:03:21 2015 -0600 +++ b/snpEff_databases.xml Wed Dec 09 10:20:13 2015 -0500 @@ -1,26 +1,28 @@ <tool id="snpEff_databases" name="SnpEff Available Databases" version="@WRAPPER_VERSION@.0"> <description></description> - <expand macro="requirements" /> <macros> <import>snpEff_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> <command> <![CDATA[ - java -jar \$SNPEFF_JAR_PATH/snpEff.jar databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > $snpeff_dbs + java -jar \$SNPEFF_JAR_PATH/snpEff.jar databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > $snpeff_dbs ]]> </command> <inputs> </inputs> <outputs> - <data format="tabular" name="snpeff_dbs" label="${tool.name} available databases" /> + <data format="tabular" name="snpeff_dbs" label="${tool.name} @SNPEFF_VERSION@ available databases" /> </outputs> - <expand macro="stdio" /> - <help> + <help><![CDATA[ @EXTERNAL_DOCUMENTATION@ @CITATION_SECTION@ +]]> </help> </tool>
--- a/snpEff_download.xml Wed Jan 14 12:03:21 2015 -0600 +++ b/snpEff_download.xml Wed Dec 09 10:20:13 2015 -0500 @@ -1,16 +1,18 @@ -<tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.3"> +<tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0"> <description>Download a new database</description> - <expand macro="requirements" /> <macros> <import>snpEff_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> <command> <![CDATA[ - java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.files_path -v $genome_version + java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.files_path -v $genome_version ]]> </command> <inputs> - <param name="genome_version" type="text" size="40" value="" label="Select the genome version you want to download (e.g. GRCh37.74)"> + <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)"> <help>@SNPEFF_DATABASE_URL@</help> <validator type="regex" message="A genome version name is required">\S+</validator> </param> @@ -18,13 +20,13 @@ <outputs> <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" /> </outputs> - <expand macro="stdio" /> - <help> + <help><![CDATA[ @EXTERNAL_DOCUMENTATION@ @CITATION_SECTION@ +]]> </help> <expand macro="citations" /> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_genes.txt Wed Dec 09 10:20:13 2015 -0500 @@ -0,0 +1,3455 @@ +# The following table is formatted as tab separated values. +#GeneName GeneId TranscriptId BioType variants_impact_HIGH variants_impact_LOW variants_impact_MODERATE variants_impact_MODIFIER variants_effect_3_prime_UTR_variant variants_effect_5_prime_UTR_premature_start_codon_gain_variant variants_effect_5_prime_UTR_variant variants_effect_disruptive_inframe_deletion variants_effect_disruptive_inframe_deletion+splice_region_variant variants_effect_disruptive_inframe_insertion variants_effect_downstream_gene_variant variants_effect_frameshift_variant variants_effect_frameshift_variant+splice_acceptor_variant+splice_region_variant+intron_variant variants_effect_frameshift_variant+splice_region_variant variants_effect_frameshift_variant+start_lost variants_effect_frameshift_variant+stop_gained variants_effect_frameshift_variant+stop_lost variants_effect_inframe_deletion variants_effect_inframe_deletion+splice_region_variant variants_effect_inframe_insertion variants_effect_intron_variant variants_effect_missense_variant variants_effect_missense_variant+splice_region_variant variants_effect_non_coding_exon_variant variants_effect_sequence_feature variants_effect_splice_acceptor_variant+intron_variant variants_effect_splice_acceptor_variant+splice_region_variant+intron_variant variants_effect_splice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant variants_effect_splice_donor_variant+intron_variant variants_effect_splice_region_variant variants_effect_splice_region_variant+intron_variant variants_effect_splice_region_variant+non_coding_exon_variant variants_effect_splice_region_variant+stop_retained_variant variants_effect_splice_region_variant+synonymous_variant variants_effect_start_lost variants_effect_stop_gained variants_effect_stop_gained+splice_region_variant variants_effect_stop_lost variants_effect_stop_retained_variant variants_effect_synonymous_variant variants_effect_upstream_gene_variant bases_affected_DOWNSTREAM total_score_DOWNSTREAM length_DOWNSTREAM bases_affected_EXON total_score_EXON length_EXON bases_affected_INTRON total_score_INTRON length_INTRON bases_affected_NONE total_score_NONE length_NONE bases_affected_SPLICE_SITE_ACCEPTOR total_score_SPLICE_SITE_ACCEPTOR length_SPLICE_SITE_ACCEPTOR bases_affected_SPLICE_SITE_DONOR total_score_SPLICE_SITE_DONOR length_SPLICE_SITE_DONOR bases_affected_SPLICE_SITE_REGION total_score_SPLICE_SITE_REGION length_SPLICE_SITE_REGION bases_affected_TRANSCRIPT total_score_TRANSCRIPT length_TRANSCRIPT bases_affected_UPSTREAM total_score_UPSTREAM length_UPSTREAM bases_affected_UTR_3_PRIME total_score_UTR_3_PRIME length_UTR_3_PRIME bases_affected_UTR_5_PRIME total_score_UTR_5_PRIME length_UTR_5_PRIME +A4GALT ENSG00000128274 ENST00000249005 protein_coding 1 10 9 3 2 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 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0 0 0 +ZC3H7B ENSG00000100403 ENST00000486331 retained_intron 0 0 0 33 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 5 0 0 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 5000 14 0 4673 5 0 2658 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ZDHHC8 ENSG00000099904 ENST00000320602 protein_coding 0 19 18 14 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 18 0 0 3 0 0 0 0 0 2 0 0 0 0 0 0 0 0 14 4 0 0 0 32 0 1222 8 0 1225 3 0 63 0 0 0 0 0 0 2 0 6 0 0 0 4 0 5000 2 0 1050 0 0 0 +ZDHHC8 ENSG00000099904 ENST00000334554 protein_coding 0 61 20 11 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 20 0 0 44 0 0 0 0 0 2 0 0 0 0 0 0 0 0 15 4 0 0 0 35 0 2779 5 0 1225 44 0 5207 0 0 0 0 0 0 2 0 6 0 0 0 4 0 5000 2 0 2607 0 0 0 +ZDHHC8 ENSG00000099904 ENST00000405930 protein_coding 0 26 17 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 17 0 0 11 0 0 0 0 0 1 0 0 0 0 0 0 0 0 14 4 0 0 0 31 0 1001 12 0 3264 11 0 285 0 0 0 0 0 0 1 0 6 0 0 0 4 0 5000 0 0 0 0 0 0 +ZDHHC8 ENSG00000099904 ENST00000436518 protein_coding 0 4 3 40 0 0 0 0 0 0 28 0 0 0 0 0 0 0 0 0 2 3 0 0 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2589 0 0 0 4 0 72 0 0 0 0 0 0 0 0 0 0 0 0 3 0 5000 0 0 0 1 0 68 +ZNF70 ENSG00000187792 ENST00000341976 protein_coding 1 23 9 19 1 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 10 0 0 0 0 0 0 0 0 0 0 1 0 0 0 12 15 0 0 0 22 0 3638 0 0 0 10 0 69 0 0 0 0 0 0 0 0 0 0 0 0 15 0 5000 1 0 2218 4 0 79 +ZNF74 ENSG00000185252 ENST00000356671 protein_coding 0 22 18 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 18 0 0 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 24 0 1948 9 0 4004 16 0 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ZNF74 ENSG00000185252 ENST00000357502 protein_coding 0 0 5 28 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 2305 10 0 4004 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 2025 0 0 0 +ZNF74 ENSG00000185252 ENST00000400451 protein_coding 0 6 18 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 24 0 2302 9 0 4004 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ZNF74 ENSG00000185252 ENST00000403682 protein_coding 0 0 5 28 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 2031 10 0 4004 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 1751 0 0 0 +ZNF74 ENSG00000185252 ENST00000405993 protein_coding 0 15 17 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 17 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 23 0 1592 10 0 4618 9 0 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ZNF74 ENSG00000185252 ENST00000420626 protein_coding 0 0 2 31 0 0 0 0 0 0 20 0 0 0 0 0 0 0 0 0 11 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 5000 2 0 117 11 0 10714 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ZNF74 ENSG00000185252 ENST00000437275 nonsense_mediated_decay 0 0 0 55 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 0 3079 9 0 4004 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 0 3079 0 0 0 +ZNF74 ENSG00000185252 ENST00000476678 retained_intron 0 0 0 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 29 0 2017 1 0 4004 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 5000 0 0 0 0 0 0 +ZNF74 ENSG00000185252 ENST00000493734 retained_intron 0 0 0 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 2304 8 0 4004 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ZNRF3 ENSG00000183579 ENST00000332811 protein_coding 0 13 11 31 0 0 0 0 0 0 23 0 0 0 0 0 0 0 0 0 8 11 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 11 0 23 0 5000 22 0 1752 8 0 2630 0 0 0 0 0 0 0 0 0 2 0 6 0 0 0 0 0 0 0 0 0 0 0 0 +ZNRF3 ENSG00000183579 ENST00000402174 protein_coding 0 43 11 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 11 0 0 30 0 0 0 0 0 2 0 0 0 0 0 0 0 0 11 0 0 0 0 22 0 1752 8 0 2630 30 0 8753 0 0 0 0 0 0 2 0 6 0 0 0 0 0 0 0 0 0 0 0 0 +ZNRF3 ENSG00000183579 ENST00000406323 protein_coding 0 13 11 11 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 8 11 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 11 0 3 0 5000 22 0 1752 8 0 2630 0 0 0 0 0 0 0 0 0 2 0 6 0 0 0 0 0 0 0 0 0 0 0 0 +ZNRF3 ENSG00000183579 ENST00000544604 protein_coding 0 48 11 31 0 0 0 0 0 0 23 0 0 0 0 0 0 0 0 0 8 11 0 0 35 0 0 0 0 0 2 0 0 0 0 0 0 0 0 11 0 23 0 5000 22 0 1752 8 0 2630 35 0 8753 0 0 0 0 0 0 2 0 6 0 0 0 0 0 0 0 0 0 0 0 0 +snoU13 ENSG00000238498 ENST00000458891 snoRNA 0 0 0 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 0 5000 0 0 0 0 0 0 +snoU13 ENSG00000238887 ENST00000459164 snoRNA 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 5000 0 0 0 0 0 0 +snoU13 ENSG00000238910 ENST00000459049 snoRNA 0 0 0 3 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 5000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +snoU13 ENSG00000239066 ENST00000459485 snoRNA 0 0 0 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 0 5000 0 0 0 0 0 0
--- a/snpEff_macros.xml Wed Jan 14 12:03:21 2015 -0600 +++ b/snpEff_macros.xml Wed Dec 09 10:20:13 2015 -0500 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="4.0">snpEff</requirement> + <requirement type="package" version="4.1">snpEff</requirement> </requirements> </xml> <xml name="stdio"> @@ -10,9 +10,12 @@ <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> - <token name="@WRAPPER_VERSION@">4.0</token> - <token name="@SNPEFF_VERSION@">SnpEff4.0</token> - <token name="@SNPEFF_DATABASE_URL@">http://sourceforge.net/projects/snpeff/files/databases/v4_0/</token> + <xml name="version_command"> + <version_command>java -jar $SNPEFF_JAR_PATH/SnpEff.jar -version</version_command> + </xml> + <token name="@WRAPPER_VERSION@">4.1</token> + <token name="@SNPEFF_VERSION@">SnpEff4.1</token> + <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_1/</token> <token name="@EXTERNAL_DOCUMENTATION@"> For details about this tool, please go to:
--- a/tool_data_table_conf.xml.sample Wed Jan 14 12:03:21 2015 -0600 +++ b/tool_data_table_conf.xml.sample Wed Dec 09 10:20:13 2015 -0500 @@ -1,8 +1,4 @@ <tables> - <table name="snpeffv_databases" comment_char="#"> - <columns>key, version, value, name</columns> - <file path="tool-data/snpeffv_databases.loc" /> - </table> <table name="snpeffv_genomedb" comment_char="#"> <columns>key, version, value, name, path</columns> <file path="tool-data/snpeffv_genomedb.loc" /> @@ -15,5 +11,9 @@ <columns>key, version, genome, value, name</columns> <file path="tool-data/snpeffv_annotations.loc" /> </table> + <table name="snpeffv_databases" comment_char="#"> + <columns>key, version, value, name</columns> + <file path="tool-data/snpeffv_databases.loc" /> + </table> </tables>
--- a/tool_dependencies.xml Wed Jan 14 12:03:21 2015 -0600 +++ b/tool_dependencies.xml Wed Dec 09 10:20:13 2015 -0500 @@ -1,7 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="snpEff" version="4.0"> - <repository name="package_snpeff_4_0" owner="jjohnson" changeset_revision="4ac635fc1781" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <package name="snpEff" version="4.1"> + <repository changeset_revision="02a5e07a4121" name="package_snpeff_4_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency> -