Mercurial > repos > iuc > snpeff
changeset 2:e09ce114d240 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff
| author | iuc |
|---|---|
| date | Fri, 19 Feb 2016 08:26:25 -0500 |
| parents | 500832f27cbc |
| children | b24873564cf6 |
| files | .shed.yml snpEff.xml |
| diffstat | 2 files changed, 88 insertions(+), 79 deletions(-) [+] |
line wrap: on
line diff
--- a/.shed.yml Thu Jan 22 08:28:37 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -# repository published to https://toolshed.g2.bx.psu.edu/repos/iuc/snpeff -owner: iuc -name: snpeff
--- a/snpEff.xml Thu Jan 22 08:28:37 2015 -0500 +++ b/snpEff.xml Fri Feb 19 08:26:25 2016 -0500 @@ -4,27 +4,28 @@ <macros> <import>snpEff_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> <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 $spliceSiteSize and str($spliceSiteSize) != '': + -spliceSiteSize "$spliceSiteSize" #end if - #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': - $filterHomHet + #if $annotations and str($annotations) != '': + #echo " " + #echo ' '.join(str($annotations).split(',')) #end if - #if $annotations and $annotations.__str__ != '': + #if $filterOut and str($filterOut) != '': #echo " " - #echo ' '.join($annotations.__str__.split(',')) + #echo ' '.join(str($filterOut).split(',')) #end if - #if $filterOut and $filterOut.__str__ != '': - #echo " " - #echo ' '.join($filterOut.__str__.split(',')) + #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 @@ -33,51 +34,51 @@ -interval $intervals #end if #if $statsFile: - -stats $statsFile + -stats $statsFile #end if - #if $offset.__str__ != 'default': - ${offset} + #if str($offset) != 'default': + ${offset} #end if - #if $chr.__str__.strip() != '': - -chr "$chr" + #if str($chr).strip() != '': + -chr "$chr" #end if - $noLog + $noLog #if $snpDb.genomeSrc == 'cached': -dataDir ${snpDb.genomeVersion.fields.path} - #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': + #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '': #echo " " - #echo ' '.join($snpDb.extra_annotations.__str__.split(',')) + #echo ' '.join(str($snpDb.extra_annotations).split(',')) #end if - #if $snpDb.regulation and $snpDb.regulation.__str__ != '': - -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# + #if $snpDb.regulation and str($snpDb.regulation) != '': + -reg #echo ' -reg '.join(str($snpDb.regulation).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 xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',') + #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '': + #set xannotations = [' '] + str($snpDb.extra_annotations).split(',') #echo " " #echo ' -'.join($xannotations) #end if - #if $snpDb.regulation and $snpDb.regulation.__str__ != '': - -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# + #if $snpDb.regulation and str($snpDb.regulation) != '': + -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))# #end if ${snpDb.snpeff_db.metadata.genome_version} - #else + #else -download $snpDb.genome_version #end if - $input > $snpeff_output ; + "$input" > "$snpeff_output"; #if $statsFile: #import os #set $genes_file = str($statsFile) + '.genes.txt' #set $genes_file_name = os.path.split($genes_file)[-1] mkdir $statsFile.files_path; - mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#; + mv "$genes_file" #echo os.path.join($statsFile.files_path, $genes_file_name)#; #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> @@ -159,7 +160,7 @@ </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 +190,6 @@ <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 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> @@ -224,6 +210,60 @@ <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> @@ -252,7 +292,6 @@ <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 --> @@ -271,8 +310,6 @@ <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"> @@ -290,29 +327,6 @@ <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=""/> --> @@ -336,8 +350,6 @@ <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">