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comparison snpEff.xml @ 12:6d429d880a75

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Update for snpeff version 4.0
author Jim Johnson <jj@umn.edu>
date Mon, 20 Oct 2014 08:37:01 -0500
parents c5288d5a446e
children 4be8e0068bc3
comparison
equal deleted inserted replaced
11:c5288d5a446e 12:6d429d880a75
1 <tool id="snpEff" name="SnpEff" version="3.6"> 1 <tool id="snpEff" name="SnpEff" version="4.0.0">
2 <description>Variant effect and annotation</description> 2 <description>Variant effect and annotation</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <macros> 4 <macros>
5 <import>snpEff_macros.xml</import> 5 <import>snpEff_macros.xml</import>
6 </macros> 6 </macros>
38 ${offset} 38 ${offset}
39 #end if 39 #end if
40 #if $chr.__str__.strip() != '': 40 #if $chr.__str__.strip() != '':
41 -chr "$chr" 41 -chr "$chr"
42 #end if 42 #end if
43 $noLog 43 $noLog
44 #if $snpDb.genomeSrc == 'cached': 44 #if $snpDb.genomeSrc == 'cached':
45 -dataDir ${snpDb.genomeVersion.fields.path} 45 -dataDir ${snpDb.genomeVersion.fields.path}
46 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': 46 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
47 #echo " " 47 #echo " "
48 #echo ' '.join($snpDb.extra_annotations.__str__.split(',')) 48 #echo ' '.join($snpDb.extra_annotations.__str__.split(','))
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">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>
180 <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option> 179 <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> 180 <option value="-oicr">Add OICR tag in VCF file</option>
182 <option value="-onlyReg">Only use regulation tracks</option> 181 <option value="-onlyReg">Only use regulation tracks</option>
183 <option value="-sequenceOntolgy">Use Sequence Ontolgy terms.</option> 182 <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option>
183 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
184 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
184 </param> 185 </param>
185 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/> 186 <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."/> 187 <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"> 188 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
188 <option value="-no-downstream">Do not show DOWNSTREAM changes</option> 189 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>