Mercurial > repos > jjohnson > snpeff
diff snpEff.xml @ 23:924af057bbca draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
| author | jjohnson |
|---|---|
| date | Sat, 09 Apr 2016 11:51:40 -0400 |
| parents | bb0797deab78 |
| children |
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--- a/snpEff.xml Wed Dec 09 10:20:13 2015 -0500 +++ b/snpEff.xml Sat Apr 09 11:51:40 2016 -0400 @@ -8,33 +8,30 @@ <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 $spliceRegion.setSpliceRegions == 'yes': - #if $spliceRegion.spliceRegionExonSize and $spliceRegion.spliceRegionExonSize.__str__ != '': + #if $spliceRegion.spliceRegionExonSize and str($spliceRegion.spliceRegionExonSize) != '': -spliceRegionExonSize $spliceRegion.spliceRegionExonSize #end if - #if $spliceRegion.spliceRegionIntronMin and $spliceRegion.spliceRegionIntronMin.__str__ != '': + #if $spliceRegion.spliceRegionIntronMin and str($spliceRegion.spliceRegionIntronMin) != '': -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin #end if - #if $spliceRegion.spliceRegionIntronMax and $spliceRegion.spliceRegionIntronMax.__str__ != '': + #if $spliceRegion.spliceRegionIntronMax and str($spliceRegion.spliceRegionIntronMax) != '': -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax #end if #end if - #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': - $filterHomHet - #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(','): @@ -50,49 +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> @@ -213,12 +210,6 @@ </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> - <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> @@ -257,9 +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> @@ -313,7 +304,7 @@ <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" > @@ -344,7 +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"> @@ -362,27 +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=""/> --> @@ -406,7 +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"> @@ -424,8 +392,6 @@ @EXTERNAL_DOCUMENTATION@ -@CITATION_SECTION@ - ]]> </help> <expand macro="citations" />