Mercurial > repos > jjohnson > snpeff

comparison snpEff.xml @ 10:39cb913568ec

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Do not select any annotations by default
author Jim Johnson <jj@umn.edu>
date Tue, 10 Dec 2013 14:28:37 -0600
parents f981ba577f2b
children c5288d5a446e
comparison
equal deleted inserted replaced
9:f981ba577f2b 10:39cb913568ec
52 #end if 52 #end if
53 $snpDb.genomeVersion 53 $snpDb.genomeVersion
54 #elif $snpDb.genomeSrc == 'history': 54 #elif $snpDb.genomeSrc == 'history':
55 -dataDir ${snpDb.snpeff_db.extra_files_path} 55 -dataDir ${snpDb.snpeff_db.extra_files_path}
56 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': 56 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
57 #set annotations = [' '] + $snpDb.extra_annotations.__str__.split(',') 57 #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
58 #echo " " 58 #echo " "
59 #echo ' -'.join($annotations) 59 #echo ' -'.join($xannotations)
60 #end if 60 #end if
61 #if $snpDb.regulation and $snpDb.regulation.__str__ != '': 61 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
62 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# 62 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
63 #end if 63 #end if
64 ${snpDb.snpeff_db.metadata.genome_version} 64 ${snpDb.snpeff_db.metadata.genome_version}
172 <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option> 172 <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option>
173 </param> 173 </param>
174 174
175 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> 175 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
176 <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline)</option> 176 <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline)</option>
177 <option value="-canon" selected="true">Only use canonical transcripts</option> 177 <option value="-canon">Only use canonical transcripts</option>
178 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> 178 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
179 <option value="-hgvs">Use HGVS annotations for amino acid sub-field</option> 179 <option value="-hgvs">Use HGVS annotations for amino acid sub-field</option>
180 <option value="-lof" selected="true">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option> 180 <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option>
181 <option value="-oicr">Add OICR tag in VCF file</option> 181 <option value="-oicr">Add OICR tag in VCF file</option>
182 <option value="-onlyReg" selected="true">Only use regulation tracks</option> 182 <option value="-onlyReg">Only use regulation tracks</option>
183 <option value="-sequenceOntolgy">Use Sequence Ontolgy terms.</option> 183 <option value="-sequenceOntolgy">Use Sequence Ontolgy terms.</option>
184 </param> 184 </param>
185 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/> 185 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
186 <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."/> 186 <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."/>
187 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output"> 187 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">