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comparison snpEff.xml @ 7:0ad9733e22a4

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Uploaded
author bgruening
date Fri, 29 Nov 2013 09:27:22 -0500
parents eb394dd65c98
children f981ba577f2b
comparison
equal deleted inserted replaced
6:eb394dd65c98 7:0ad9733e22a4
1 <tool id="snpEff" name="SnpEff" version="3.4"> 1 <tool id="snpEff" name="SnpEff" version="3.4">
2 <description>Variant effect and annotation</description> 2 <description>Variant effect and annotation</description>
3 <requirements> 3 <expand macro="requirements" />
4 <requirement type="package" version="3.4">snpEff</requirement> 4 <macros>
5 </requirements> 5 <import>snpEff_macros.xml</import>
6 </macros>
6 <command> 7 <command>
7 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff 8 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff
8 -c \$SNPEFF_JAR_PATH/snpEff.config 9 -c \$SNPEFF_JAR_PATH/snpEff.config
9 -i $inputFormat -o $outputFormat -upDownStreamLen $udLength 10 -i $inputFormat -o $outputFormat -upDownStreamLen $udLength
10 #if $spliceSiteSize and $spliceSiteSize.__str__ != '': 11 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
11 -spliceSiteSize $spliceSiteSize 12 -spliceSiteSize $spliceSiteSize
12 #end if 13 #end if
13 #if $filterIn and $filterIn.__str__ != 'no_filter': 14 #if $filterIn and $filterIn.__str__ != 'no_filter':
14 $filterIn 15 $filterIn
15 #end if 16 #end if
16 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': 17 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
17 $filterHomHet 18 $filterHomHet
18 #end if 19 #end if
19 #if $annotations and $annotations.__str__ != '': 20 #if $annotations and $annotations.__str__ != '':
20 #echo " " 21 #echo " "
21 #echo ' '.join($annotations.__str__.split(',')) 22 #echo ' '.join($annotations.__str__.split(','))
22 #end if 23 #end if
23 #if $filterOut and $filterOut.__str__ != '': 24 #if $filterOut and $filterOut.__str__ != '':
24 #echo " " 25 #echo " "
25 #echo ' '.join($filterOut.__str__.split(',')) 26 #echo ' '.join($filterOut.__str__.split(','))
26 #end if 27 #end if
27 #if str( $transcripts ) != 'None': 28 #if str( $transcripts ) != 'None':
28 -onlyTr $transcripts 29 -onlyTr $transcripts
29 #end if 30 #end if
30 #if str( $intervals ) != 'None': ### fix this for multiple dataset input 31 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
31 -interval $intervals 32 -interval $intervals
32 #end if 33 #end if
33 #if $statsFile: 34 #if $statsFile:
34 -stats $statsFile 35 -stats $statsFile
35 #end if 36 #end if
36 #if $offset.__str__ != '': 37 #if $offset.__str__ != '':
37 ${offset} 38 ${offset}
38 #end if 39 #end if
39 #if $chr.__str__.strip() != '': 40 #if $chr.__str__.strip() != '':
40 -chr "$chr" 41 -chr "$chr"
41 #end if 42 #end if
42 $noLog 43 $noLog
43 #if $snpDb.genomeSrc == 'cached': 44 #if $snpDb.genomeSrc == 'cached':
44 -dataDir ${snpDb.genomeVersion.fields.path} 45 -dataDir ${snpDb.genomeVersion.fields.path}
45 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': 46 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
46 #echo " " 47 #echo " "
47 #echo ' '.join($snpDb.extra_annotations.__str__.split(',')) 48 #echo ' '.join($snpDb.extra_annotations.__str__.split(','))
48 #end if 49 #end if
49 #if $snpDb.regulation and $snpDb.regulation.__str__ != '': 50 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
50 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# 51 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
51 #end if 52 #end if
52 $snpDb.genomeVersion 53 $snpDb.genomeVersion
53 #elif $snpDb.genomeSrc == 'history': 54 #elif $snpDb.genomeSrc == 'history':
54 -dataDir ${snpDb.snpeff_db.extra_files_path} 55 -dataDir ${snpDb.snpeff_db.extra_files_path}
55 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': 56 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
56 #set annotations = [' '] + $snpDb.extra_annotations.__str__.split(',') 57 #set annotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
57 #echo " " 58 #echo " "
58 #echo ' -'.join($annotations) 59 #echo ' -'.join($annotations)
59 #end if 60 #end if
60 #if $snpDb.regulation and $snpDb.regulation.__str__ != '': 61 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
61 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# 62 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
62 #end if 63 #end if
63 ${snpDb.snpeff_db.metadata.genome_version} 64 ${snpDb.snpeff_db.metadata.genome_version}
64 #else 65 #else
65 -download 66 -download
66 $snpDb.genome_version 67 $snpDb.genome_version
67 #end if 68 #end if
68 $input > $snpeff_output 69 $input > $snpeff_output
69 </command> 70 </command>
70 <inputs> 71 <inputs>
71 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> 72 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
72 73
73 <param name="inputFormat" type="select" label="Input format"> 74 <param name="inputFormat" type="select" label="Input format">
74 <option value="vcf" selected="true">VCF</option> 75 <option value="vcf" selected="true">VCF</option>
83 <option value="bed">BED</option> 84 <option value="bed">BED</option>
84 <option value="bedAnn">BED Annotations</option> 85 <option value="bedAnn">BED Annotations</option>
85 </param> 86 </param>
86 87
87 <conditional name="snpDb"> 88 <conditional name="snpDb">
88 <param name="genomeSrc" type="select" label=""> 89 <param name="genomeSrc" type="select" label="Genome source">
89 <option value="cached">Locally cached</option> 90 <option value="cached">Locally installed reference genome</option>
90 <option value="history">history</option> 91 <option value="history">Reference genome from your history</option>
91 <option value="named">named on demand</option> 92 <option value="named">Named on demand</option>
92 </param> 93 </param>
93 <when value="cached"> 94 <when value="cached">
94 <param name="genomeVersion" type="select" label="Genome"> 95 <param name="genomeVersion" type="select" label="Genome">
95 <!--GENOME DESCRIPTION--> 96 <!--GENOME DESCRIPTION-->
96 <options from_data_table="snpeff_genomedb"> 97 <options from_data_table="snpeff_genomedb">
140 <option value="5000" selected="true">5000 bases</option> 141 <option value="5000" selected="true">5000 bases</option>
141 <option value="10000">10000 bases</option> 142 <option value="10000">10000 bases</option>
142 <option value="20000">20000 bases</option> 143 <option value="20000">20000 bases</option>
143 </param> 144 </param>
144 145
145 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases. Default: 2"> 146 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2">
146 <option value="1">1 base</option> 147 <option value="1">1 base</option>
147 <option value="2">2 bases</option> 148 <option value="2">2 bases</option>
148 <option value="3">3 bases</option> 149 <option value="3">3 bases</option>
149 <option value="4">4 bases</option> 150 <option value="4">4 bases</option>
150 <option value="5">5 bases</option> 151 <option value="5">5 bases</option>
168 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms) </option> 169 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms) </option>
169 <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option> 170 <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option>
170 </param> 171 </param>
171 172
172 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> 173 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
173 <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline). Default: false</option> 174 <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline)</option>
174 <option value="-canon">Only use canonical transcripts.</option> 175 <option value="-canon" selected="true">Only use canonical transcripts</option>
175 <option value="-geneId">Use gene ID instead of gene name (VCF output). Default: false</option> 176 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
176 <option value="-hgvs">Use HGVS annotations for amino acid sub-field. Default: false</option> 177 <option value="-hgvs">Use HGVS annotations for amino acid sub-field</option>
177 <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.</option> 178 <option value="-lof" selected="true">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option>
178 <option value="-oicr">Add OICR tag in VCF file. Default: false</option> 179 <option value="-oicr">Add OICR tag in VCF file</option>
179 <option value="-onlyReg">Only use regulation tracks.</option> 180 <option value="-onlyReg" selected="true">Only use regulation tracks</option>
180 <option value="-sequenceOntolgy">Use Sequence Ontolgy terms. Default: false</option> 181 <option value="-sequenceOntolgy">Use Sequence Ontolgy terms.</option>
181 </param> 182 </param>
182 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/> 183 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
183 <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file. Format: One transcript ID per line."/> 184 <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."/>
184 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output"> 185 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
185 <option value="-no-downstream">Do not show DOWNSTREAM changes </option> 186 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
186 <option value="-no-intergenic">Do not show INTERGENIC changes </option> 187 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
187 <option value="-no-intron">Do not show INTRON changes </option> 188 <option value="-no-intron">Do not show INTRON changes</option>
188 <option value="-no-upstream">Do not show UPSTREAM changes </option> 189 <option value="-no-upstream">Do not show UPSTREAM changes</option>
189 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option> 190 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
190 </param> 191 </param>
191 192
192 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> 193 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
193 <option value="" selected="true">Use default (based on input type)</option> 194 <option value="" selected="true">Use default (based on input type)</option>
194 <option value="-0">Force zero-based positions (both input and output)</option> 195 <option value="-0">Force zero-based positions (both input and output)</option>
195 <option value="-1">Force one-based positions (both input and output)</option> 196 <option value="-1">Force one-based positions (both input and output)</option>
196 </param> 197 </param>
197 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name"> 198 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
198 <help> 199 <help>
199 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. 200 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
200 You can prepend any string you want to the chromosome name." 201 You can prepend any string you want to the chromosome name.
201 </help> 202 </help>
202 <validator type="regex" message="No whitespace allows">^\S*$</validator> 203 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
203
204 </param> 204 </param>
205 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/> 205 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
206 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/> 206 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
207 </inputs> 207 </inputs>
208 <outputs> 208 <outputs>
212 <when input="outputFormat" value="txt" format="tabular" /> 212 <when input="outputFormat" value="txt" format="tabular" />
213 <when input="outputFormat" value="bed" format="bed" /> 213 <when input="outputFormat" value="bed" format="bed" />
214 <when input="outputFormat" value="bedAnn" format="bed" /> 214 <when input="outputFormat" value="bedAnn" format="bed" />
215 </change_format> 215 </change_format>
216 </data> 216 </data>
217
218 <data format="html" name="statsFile"> 217 <data format="html" name="statsFile">
219 <filter>generate_stats == True</filter> 218 <filter>generate_stats == True</filter>
220 </data> 219 </data>
221 </outputs> 220 </outputs>
222 <stdio> 221 <expand macro="stdio" />
223 <exit_code range="1:" level="fatal" description="Error" />
224 <exit_code range="-1" level="fatal" description="Error: Cannot open file" />
225 </stdio>
226 <tests> 222 <tests>
227 <!-- Check that an effect was added in out VCF --> 223 <!-- Check that an effect was added in out VCF -->
228 <!-- Check for a HTML header indicating that this was successful --> 224 <!-- Check for a HTML header indicating that this was successful -->
229 <!-- 225 <!--
230 <output name="statsFile"> 226 <output name="statsFile">
321 </tests> 317 </tests>
322 <help> 318 <help>
323 319
324 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. 320 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
325 321
326 For details about this tool, please go to http://snpEff.sourceforge.net 322 @EXTERNAL_DOCUMENTATION@
327 323
328 SnpEff citation: 324 @CITATION_SECTION@
329 "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]
330
331 SnpSift citation:
332 "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.
333 325
334 </help> 326 </help>
335 </tool> 327 </tool>
336 328