Mercurial > repos > iuc > snpeff
changeset 7:aaa749ea91a2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
| author | iuc |
|---|---|
| date | Tue, 07 Jun 2016 09:40:10 -0400 |
| parents | 9ec1cb6f760d |
| children | 1501e66908de |
| files | snpEff.xml snpEff_databases.xml snpEff_download.xml snpEff_macros.xml tool_dependencies.xml |
| diffstat | 5 files changed, 93 insertions(+), 77 deletions(-) [+] |
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--- a/snpEff.xml Tue Oct 13 17:30:57 2015 -0400 +++ b/snpEff.xml Tue Jun 07 09:40:10 2016 -0400 @@ -1,28 +1,37 @@ -<tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.1"> +<tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0"> <description>Variant effect and annotation</description> <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 + #if $spliceSiteSize and str($spliceSiteSize) != '': + -spliceSiteSize "$spliceSiteSize" #end if - #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': - $filterHomHet + #if $spliceRegion.setSpliceRegions == 'yes': + #if $spliceRegion.spliceRegionExonSize and str($spliceRegion.spliceRegionExonSize) != '': + -spliceRegionExonSize $spliceRegion.spliceRegionExonSize + #end if + #if $spliceRegion.spliceRegionIntronMin and str($spliceRegion.spliceRegionIntronMin) != '': + -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin + #end if + #if $spliceRegion.spliceRegionIntronMax and str($spliceRegion.spliceRegionIntronMax) != '': + -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax + #end if #end if - #if $annotations and $annotations.__str__ != '': + #if $annotations and str($annotations) != '': #echo " " - #echo ' '.join($annotations.__str__.split(',')) + #echo ' '.join(str($annotations).split(',')) #end if - #if $filterOut and $filterOut.__str__ != '': + #if $filterOut and str($filterOut) != '': #echo " " - #echo ' '.join($filterOut.__str__.split(',')) + #echo ' '.join(str($filterOut).split(',')) #end if #if $filter.specificEffects == 'yes' and $filter.effects: #for $eff in str($filter.effects).split(','): @@ -38,49 +47,49 @@ #if $statsFile: -stats $statsFile #end if - #if $offset.__str__ != 'default': + #if str($offset) != 'default': ${offset} #end if - #if $chr.__str__.strip() != '': + #if str($chr).strip() != '': -chr "$chr" #end if $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 -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 -e '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> @@ -89,8 +98,6 @@ <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> @@ -98,7 +105,6 @@ <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> @@ -106,7 +112,6 @@ <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> @@ -192,11 +197,18 @@ <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> + <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="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> @@ -208,7 +220,13 @@ <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"> @@ -230,9 +248,9 @@ <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_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="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> @@ -286,12 +304,11 @@ <validator type="regex" message="No whitespace allowed">^\S*$</validator> </param> <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/> - <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/> + <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server"/> </inputs> <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> @@ -318,7 +335,6 @@ <param name="genomeSrc" value="named"/> <param name="genome_version" value="testCase"/> <param name="udLength" value="0"/> - <param name="filterHomHet" value="no_filter"/> <param name="generate_stats" value="False"/> <param name="filterOut" value="+-no-upstream"/> <output name="snpeff_output"> @@ -336,27 +352,6 @@ <param name="genomeSrc" value="named"/> <param name="genome_version" value="testCase"/> <param name="udLength" value="0"/> - <param name="filterHomHet" value="+-het"/> - <!-- - <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="filterOut" value=""/> --> @@ -380,7 +375,6 @@ <param name="genomeSrc" value="named"/> <param name="genome_version" value="testCase"/> <param name="udLength" value="0"/> - <param name="filterHomHet" value="no_filter"/> <param name="filterOut" value="+-no-upstream"/> <param name="generate_stats" value="False"/> <output name="snpeff_output"> @@ -392,14 +386,13 @@ --> </tests> - <help> + <help><![CDATA[ This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. @EXTERNAL_DOCUMENTATION@ -@CITATION_SECTION@ - +]]> </help> <expand macro="citations" /> </tool>
--- a/snpEff_databases.xml Tue Oct 13 17:30:57 2015 -0400 +++ b/snpEff_databases.xml Tue Jun 07 09:40:10 2016 -0400 @@ -5,9 +5,10 @@ </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> @@ -15,12 +16,21 @@ <outputs> <data format="tabular" name="snpeff_dbs" label="${tool.name} @SNPEFF_VERSION@ available databases" /> </outputs> - <help> + <tests> + <test> + <output name="snpeff_dbs"> + <assert_contents> + <has_text text="ebola_zaire" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ @EXTERNAL_DOCUMENTATION@ -@CITATION_SECTION@ - +]]> </help> + <expand macro="citations" /> </tool>
--- a/snpEff_download.xml Tue Oct 13 17:30:57 2015 -0400 +++ b/snpEff_download.xml Tue Jun 07 09:40:10 2016 -0400 @@ -5,9 +5,10 @@ </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 "$genome_version" ]]> </command> <inputs> @@ -19,12 +20,21 @@ <outputs> <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" /> </outputs> - <help> + <tests> + <test> + <param name="genome_version" value="ebola_zaire"/> + <output name="snpeff_db"> + <assert_contents> + <has_text text="ebola_zaire" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ @EXTERNAL_DOCUMENTATION@ -@CITATION_SECTION@ - +]]> </help> <expand macro="citations" /> </tool>
--- a/snpEff_macros.xml Tue Oct 13 17:30:57 2015 -0400 +++ b/snpEff_macros.xml Tue Jun 07 09:40:10 2016 -0400 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="4.0">snpEff</requirement> + <requirement type="package" version="4.1">snpEff</requirement> </requirements> </xml> <xml name="stdio"> @@ -10,9 +10,12 @@ <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> - <token name="@WRAPPER_VERSION@">4.0</token> - <token name="@SNPEFF_VERSION@">SnpEff4.0</token> - <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_0/</token> + <xml name="version_command"> + <version_command>java -jar "$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_dependencies.xml Tue Oct 13 17:30:57 2015 -0400 +++ b/tool_dependencies.xml Tue Jun 07 09:40:10 2016 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="snpEff" version="4.0"> - <repository changeset_revision="15d3951f1517" name="package_snpeff_4_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="snpEff" version="4.1"> + <repository changeset_revision="733a2dcb9853" name="package_snpeff_4_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>