Mercurial > repos > jjohnson > snpeff
diff snpEff.xml @ 7:0ad9733e22a4
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 29 Nov 2013 09:27:22 -0500 |
| parents | eb394dd65c98 |
| children | f981ba577f2b |
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--- a/snpEff.xml Thu Nov 28 08:16:11 2013 -0600 +++ b/snpEff.xml Fri Nov 29 09:27:22 2013 -0500 @@ -1,72 +1,73 @@ <tool id="snpEff" name="SnpEff" version="3.4"> <description>Variant effect and annotation</description> - <requirements> - <requirement type="package" version="3.4">snpEff</requirement> - </requirements> + <expand macro="requirements" /> + <macros> + <import>snpEff_macros.xml</import> + </macros> <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 -#if $filterIn and $filterIn.__str__ != 'no_filter': - $filterIn -#end if -#if $filterHomHet and $filterHomHet.__str__ != 'no_filter': - $filterHomHet -#end if -#if $annotations and $annotations.__str__ != '': - #echo " " - #echo ' '.join($annotations.__str__.split(',')) -#end if -#if $filterOut and $filterOut.__str__ != '': - #echo " " - #echo ' '.join($filterOut.__str__.split(',')) -#end if -#if str( $transcripts ) != 'None': - -onlyTr $transcripts -#end if -#if str( $intervals ) != 'None': ### fix this for multiple dataset input - -interval $intervals -#end if -#if $statsFile: - -stats $statsFile -#end if -#if $offset.__str__ != '': - ${offset} -#end if -#if $chr.__str__.strip() != '': - -chr "$chr" -#end if - $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> + 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 + #if $filterIn and $filterIn.__str__ != 'no_filter': + $filterIn + #end if + #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': + $filterHomHet + #end if + #if $annotations and $annotations.__str__ != '': + #echo " " + #echo ' '.join($annotations.__str__.split(',')) + #end if + #if $filterOut and $filterOut.__str__ != '': + #echo " " + #echo ' '.join($filterOut.__str__.split(',')) + #end if + #if str( $transcripts ) != 'None': + -onlyTr $transcripts + #end if + #if str( $intervals ) != 'None': ### fix this for multiple dataset input + -interval $intervals + #end if + #if $statsFile: + -stats $statsFile + #end if + #if $offset.__str__ != '': + ${offset} + #end if + #if $chr.__str__.strip() != '': + -chr "$chr" + #end if + $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)"/> @@ -85,10 +86,10 @@ </param> <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 name="genomeSrc" type="select" label="Genome source"> + <option value="cached">Locally installed reference genome</option> + <option value="history">Reference genome from your history</option> + <option value="named">Named on demand</option> </param> <when value="cached"> <param name="genomeVersion" type="select" label="Genome"> @@ -142,7 +143,7 @@ <option value="20000">20000 bases</option> </param> - <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases. Default: 2"> + <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2"> <option value="1">1 base</option> <option value="2">2 bases</option> <option value="3">3 bases</option> @@ -170,23 +171,23 @@ </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> + <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline)</option> + <option value="-canon" selected="true">Only use canonical transcripts</option> + <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> + <option value="-hgvs">Use HGVS annotations for amino acid sub-field</option> + <option value="-lof" selected="true">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option> + <option value="-oicr">Add OICR tag in VCF file</option> + <option value="-onlyReg" selected="true">Only use regulation tracks</option> + <option value="-sequenceOntolgy">Use Sequence Ontolgy terms.</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="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"> - <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> + <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"> @@ -195,12 +196,11 @@ <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> - + <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 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"/> @@ -214,15 +214,11 @@ <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> + <expand macro="stdio" /> <tests> <!-- Check that an effect was added in out VCF --> <!-- Check for a HTML header indicating that this was successful --> @@ -323,13 +319,9 @@ This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. -For details about this tool, please go to http://snpEff.sourceforge.net +@EXTERNAL_DOCUMENTATION@ -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. +@CITATION_SECTION@ </help> </tool>