Mercurial > repos > saskia-hiltemann > annovar
diff tools/annovar/annovar.xml @ 0:d3a72e55deca draft
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author | saskia-hiltemann |
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date | Wed, 18 Sep 2013 10:51:20 -0400 |
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children | 7d9353127f8a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/annovar/annovar.xml Wed Sep 18 10:51:20 2013 -0400 @@ -0,0 +1,211 @@ +<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> + +