Mercurial > repos > saskia-hiltemann > annovar
view tools/annovar/annovar.xml @ 0:d3a72e55deca draft
Uploaded
author | saskia-hiltemann |
---|---|
date | Wed, 18 Sep 2013 10:51:20 -0400 |
parents | |
children | 7d9353127f8a |
line wrap: on
line source
<tool id="Annovar" name="ANNOVAR" version="2013aug"> <description> Annotate a file using ANNOVAR </description> <requirements> <requirement type="package" version="1">cgatools17</requirement> </requirements> <command interpreter="bash"> annovar.sh --impactscores ${impactscores} --esp ${esp} --gerp ${gerp} --cosmic61 ${cosmic61} --cosmic63 ${cosmic63} --cosmic64 ${cosmic64} --cosmic65 ${cosmic65} --outall ${annotated} --outinvalid ${invalid} --dorunannovar ${dorun} --inputfile ${infile} --buildver ${reference.fields.dbkey} --humandb ${reference.fields.ANNOVAR_humandb} --scriptsdir ${reference.fields.ANNOVAR_scripts} --verdbsnp ${verdbsnp} --geneanno ${geneanno} --tfbs ${tfbs} --mce ${mce} --cytoband ${cytoband} --segdup ${segdup} --dgv ${dgv} --gwas ${gwas} #if $filetype.type == "other" --varfile N --VCF N --chrcol ${filetype.col_chr} --startcol ${filetype.col_start} --endcol ${filetype.col_end} --obscol ${filetype.col_obs} --refcol ${filetype.col_ref} #if $filetype.convertcoords.convert == "Y" --vartypecol ${filetype.convertcoords.col_vartype} --convertcoords Y #else --convertcoords N #end if #end if #if $filetype.type == "vcf" --varfile N --VCF Y --convertcoords N #end if #if $filetype.type == "varfile" --varfile Y --VCF N #end if --cg46 ${cgfortysix} --cg69 ${cgsixtynine} --ver1000g ${ver1000g} </command> <inputs> <param name="dorun" type="hidden" value="Y"/> <!-- will add tool in future to filter on annovar columns, then will call annovar.sh with dorun==N --> <param name="reference" type="select" label="Reference"> <options from_data_table="annovar_loc" /> </param> <param name="infile" type="data" label="Select file to annotate" help="Must be CG varfile or a tab-separated file with a 1 line header"/> <conditional name="filetype"> <param name="type" type="select" label="Select filetype" > <option value="vcf" selected="false"> VCF4 file </option> <option value="varfile" selected="false"> CG varfile </option> <option value="other" selected="false"> Other </option> </param> <when value="other"> <param name="col_chr" type="data_column" data_ref="infile" multiple="False" label="Chromosome Column" /> <param name="col_start" type="data_column" data_ref="infile" multiple="False" label="Start Column" /> <param name="col_end" type="data_column" data_ref="infile" multiple="False" label="End Column" /> <param name="col_ref" type="data_column" data_ref="infile" multiple="False" label="Reference Allele Column" /> <param name="col_obs" type="data_column" data_ref="infile" multiple="False" label="Observed Allele Column" /> <conditional name="convertcoords"> <param name="convert" type="select" label="Is this file using Complete Genomics (0-based half-open) cooridinates?" > <option value="Y"> Yes </option> <option value="N" selected="True"> No </option> </param> <when value="Y"> <param name="col_vartype" type="data_column" data_ref="infile" multiple="False" label="varType Column" /> </when> </conditional> </when> </conditional> <param name="geneanno" type="select" label="Select Gene Annotation(s)" multiple="true" optional="true" display="checkboxes"> <option value="refSeq" selected="true" > RefSeq </option> <option value="knowngene"> UCSC KnownGene </option> <option value="ensgene" > Ensembl </option> </param> <!-- region-based annotation --> <param name="cytoband" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Cytogenic band Annotation?" help="This option identifies Giemsa-stained chromosomes bands, (e.g. 1q21.1-q23.3)."/> <param name="tfbs" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Transcription Factor Binding Site Annotation?"/> <param name="mce" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Most Conserved Elements Annotation?" help="This option phastCons 44-way alignments to annotate variants that fall within conserved genomic regions."/> <param name="segdup" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Segmental Duplication Annotation?" help="Genetic variants that are mapped to segmental duplications are most likely sequence alignment errors and should be treated with extreme caution."/> <param name="dgv" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="DGV (Database of Genomic Variants) Annotation?" help="Identify previously reported structural variants in DGV (Database of Genomic Variants) "/> <param name="gwas" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="GWAS studies Annotation?" help="Identify variants reported in previously published GWAS (Genome-wide association studies) "/> <!-- filter-based annotation --> <param name="verdbsnp" type="select" label="Select dbSNP version(s) to annotate with" multiple="true" display="checkboxes" optional="true" help="SNPs in dbSNP may be flagged as Clinically Associated, Select the NonFlagged version if you do not wish to annotate with these SNPs "> <option value="snp128" > 128 (hg18/hg19) </option> <option value="snp128NonFlagged"> 128 NonFlagged </option> <option value="snp129" > 129 (hg18/hg19) </option> <option value="snp129NonFlagged"> 129 NonFlagged </option> <option value="snp130" > 130 (hg18/hg19) </option> <option value="snp130NonFlagged"> 130 NonFlagged </option> <option value="snp131" > 131 (hg18/hg19) </option> <option value="snp131NonFlagged"> 131 NonFlagged </option> <option value="snp132" > 132 (hg18/hg19) </option> <option value="snp132NonFlagged"> 132 NonFlagged </option> <option value="snp135" > 135 (hg19 only) </option> <option value="snp135NonFlagged"> 135 NonFlagged </option> <option value="snp137" > 137 (hg19 only) </option> <option value="snp137NonFlagged"> 137 NonFlagged </option> </param> <param name="ver1000g" type="select" label="Select 1000Genomes Annotation(s)" multiple="true" display="checkboxes" optional="true" help="2012april database for ALL populations was converted to hg18 using the UCSC liftover program"> <option value="1000g2012apr"> 2012apr (hg18/hg19) (5 populations: AMR,AFR,ASN,CEU,ALL) </option> <option value="1000g2012feb"> 2012feb (hg19) (1 population: ALL) </option> <option value="1000g2010nov"> 2010nov (hg19) (1 population: ALL) </option> <option value="1000g2010jul"> 2010jul (hg18) (4 populations: YRI,JPT,CHB,CEU)</option> </param> <!-- <param name="g1000" type="boolean" checked="True" truevalue="Y" falsevalue="N" label="Annotate with 1000genomes project? (version 2012april)"/> --> <param name="esp" type="select" label="Select Exome Variant Server version(s) to annotate with" multiple="true" display="checkboxes" optional="true" help="si versions of databases contain indels and chrY calls"> <option value="esp6500si_all" > ESP6500si ALL </option> <option value="esp6500si_ea" > ESP6500si European Americans </option> <option value="esp6500si_aa" > ESP6500si African Americans </option> <option value="esp6500_all" > ESP6500 ALL </option> <option value="esp6500_ea" > ESP6500 European Americans </option> <option value="esp6500_aa" > ESP6500 African Americans </option> <option value="esp5400_all" > ESP5400 ALL </option> <option value="esp5400_ea" > ESP5400 European Americans </option> <option value="esp5400_aa" > ESP5400 African Americans </option> </param> <param name="gerp" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="GERP++ Annotation?" help="GERP identifies constrained elements in multiple alignments by quantifying substitution deficits (see http://mendel.stanford.edu/SidowLab/downloads/gerp/ for details) This option annotates those variants having GERP++>2 in human genome, as this threshold is typically regarded as evolutionarily conserved and potentially functional"/> <param name="cgfortysix" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 46 Genomes?" help="Diversity Panel; 46 unrelated individuals"/> <param name="cgsixtynine" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 69 Genomes?" help="Diversity Panel, Pedigree, YRI trio and PUR trio"/> <param name="cosmic61" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC61? (hg19 only)"/> <param name="cosmic63" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC63? (hg19 only)"/> <param name="cosmic64" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC64? (hg19 only)"/> <param name="cosmic65" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC65? (hg19 only)"/> <param name="impactscores" type="select" label="Select functional impact scores annotate with" multiple="true" display="checkboxes" optional="true" help="LJB refers to Liu, Jian, Boerwinkle paper in Human Mutation, pubmed ID 21520341."> <option value="avsift"> AV SIFT </option> <option value="ljbsift"> LJB SIFT (corresponds to 1-SIFT)</option> <option value="pp2"> PolyPhen2 </option> <option value="mutationtaster" > MutationTaster </option> <option value="lrt"> LRT (Likelihood Ratio Test) </option> <option value="phylop"> PhyloP </option> </param> <!-- prefix for output file so you dont have to manually rename history items --> <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/> </inputs> <outputs> <data format="tabular" name="invalid" label="$fname ANNOVAR Invalid input on ${on_string}"/> <data format="tabular" name="annotated" label="$fname ANNOVAR Annotated variants on ${on_string}"/> </outputs> <help> **What it does** This tool will annotate a file using ANNOVAR. **ANNOVAR Website and Documentation** Website: http://www.openbioinformatics.org/annovar/ Paper: http://nar.oxfordjournals.org/content/38/16/e164 **Input Formats** Input Formats may be one of the following: VCF file Complete Genomics varfile Custom tab-delimited file (specify chromosome, start, end, reference allele, observed allele columns) Custom tab-delimited CG-derived file (specify chromosome, start, end, reference allele, observed allele, varType columns) </help> </tool>