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Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
author Jim Johnson <jj@umn.edu>
date Wed, 27 Nov 2013 09:11:32 -0600
parents 6ad9205c1307
children eb394dd65c98
comparison
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4:47ddc9f4d0b6 5:8952990fcab9
1 <tool id="snpEff" name="SnpEff" version="3.3"> 1 <tool id="snpEff" name="SnpEff" version="3.4">
2 <description>Variant effect and annotation</description> 2 <description>Variant effect and annotation</description>
3 <!-- 3 <requirements>
4 You will need to change the path to wherever your installation is. 4 <requirement type="package" version="3.4">snpEff</requirement>
5 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) 5 </requirements>
6 <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> 6 <command>
7 Options: 7 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff
8 -a , -around : Show N codons and amino acids around change (only in coding regions). Default is 0 codons. 8 -c \$SNPEFF_JAR_PATH/snpEff.config
9 -i <format> : Input format [ vcf, txt, pileup, bed ]. Default: VCF. 9 -i $inputFormat -o $outputFormat -upDownStreamLen $udLength
10 -o <format> : Ouput format [ txt, vcf, gatk, bed, bedAnn ]. Default: VCF.
11 -interval : Use a custom interval file (you may use this option many times)
12 -chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
13 -s, -stats : Name of stats file (summary). Default is 'snpEff_summary.html'
14 -t : Use multiple threads (implies '-noStats'). Default 'off'
15
16 Sequence change filter options:
17 -del : Analyze deletions only
18 -ins : Analyze insertions only
19 -hom : Analyze homozygous variants only
20 -het : Analyze heterozygous variants only
21 -minQ X, -minQuality X : Filter out variants with quality lower than X
22 -maxQ X, -maxQuality X : Filter out variants with quality higher than X
23 -minC X, -minCoverage X : Filter out variants with coverage lower than X
24 -maxC X, -maxCoverage X : Filter out variants with coverage higher than X
25 -nmp : Only MNPs (multiple nucleotide polymorphisms)
26 -snp : Only SNPs (single nucleotide polymorphisms)
27
28 Results filter options:
29 -fi <bedFile> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
30 -no-downstream : Do not show DOWNSTREAM changes
31 -no-intergenic : Do not show INTERGENIC changes
32 -no-intron : Do not show INTRON changes
33 -no-upstream : Do not show UPSTREAM changes
34 -no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
35
36 Annotations options:
37 -cancer : Perform 'cancer' comparissons (Somatic vs Germline). Default: false
38 -canon : Only use canonical transcripts.
39 -geneId : Use gene ID instead of gene name (VCF output). Default: false
40 -hgvs : Use HGVS annotations for amino acid sub-field. Default: false
41 -lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
42 -reg <name> : Regulation track to use (this option can be used add several times).
43 -oicr : Add OICR tag in VCF file. Default: false
44 -onlyReg : Only use regulation tracks.
45 -onlyTr <file.txt> : Only use the transcripts in this file. Format: One transcript ID per line.
46 -sequenceOntolgy : Use Sequence Ontolgy terms. Default: false
47 -ss, -spliceSiteSize <int> : Set size for splice sites (donor and acceptor) in bases. Default: 2
48 -ud, -upDownStreamLen <int> : Set upstream downstream interval length (in bases)
49
50 Generic options:
51 -0 : File positions are zero-based (same as '-inOffset 0 -outOffset 0')
52 -1 : File positions are one-based (same as '-inOffset 1 -outOffset 1')
53 -c , -config : Specify config file
54 -h , -help : Show this help and exit
55 -if, -inOffset : Offset input by a number of bases. E.g. '-inOffset 1' for one-based input files
56 -of, -outOffset : Offset output by a number of bases. E.g. '-outOffset 1' for one-based output files
57 -noLog : Do not report usage statistics to server
58 -noStats : Do not create stats (summary) file
59 -q , -quiet : Quiet mode (do not show any messages or errors)
60 -v , -verbose : Verbose mode
61
62 -->
63 <requirements>
64 <requirement type="package" version="3.3">snpEff</requirement>
65 </requirements>
66 <command>
67 SNPEFF_DATA_DIR=`grep '^data_dir' \$SNPEFF_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
68 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
69 then java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config $genomeVersion ;
70 fi";
71 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength
72 #if $spliceSiteSize and $spliceSiteSize.__str__ != '': 10 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
73 -spliceSiteSize $spliceSiteSize 11 -spliceSiteSize $spliceSiteSize
74 #end if 12 #end if
75 #if $filterIn and $filterIn.__str__ != 'no_filter': 13 #if $filterIn and $filterIn.__str__ != 'no_filter':
76 $filterIn 14 $filterIn
77 #end if 15 #end if
78 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': 16 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
79 $filterHomHet 17 $filterHomHet
80 #end if 18 #end if
81 #if $annotations and $annotations.__str__ != '': 19 #if $annotations and $annotations.__str__ != '':
20 #echo " "
82 #echo ' '.join($annotations.__str__.split(',')) 21 #echo ' '.join($annotations.__str__.split(','))
83 #end if 22 #end if
84 #if $extra_annotations and $extra_annotations.__str__ != '':
85 #echo ' '.join($extra_annotations.__str__.split(','))
86 #end if
87 #if $regulation and $regulation.__str__ != '':
88 -reg #echo ' -reg '.join($regulation.__str__.split(','))#
89 #end if
90 #if $filterOut and $filterOut.__str__ != '': 23 #if $filterOut and $filterOut.__str__ != '':
24 #echo " "
91 #echo ' '.join($filterOut.__str__.split(',')) 25 #echo ' '.join($filterOut.__str__.split(','))
92 #end if 26 #end if
93 #if str( $transcripts ) != 'None': 27 #if str( $transcripts ) != 'None':
94 -onlyTr $transcripts 28 -onlyTr $transcripts
95 #end if 29 #end if
103 ${offset} 37 ${offset}
104 #end if 38 #end if
105 #if $chr.__str__.strip() != '': 39 #if $chr.__str__.strip() != '':
106 -chr "$chr" 40 -chr "$chr"
107 #end if 41 #end if
108 $noLog $genomeVersion $input > $snpeff_output 42 $noLog
43 #if $snpDb.genomeSrc == 'cached':
44 -dataDir ${snpDb.genomeVersion.fields.path}
45 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
46 #echo " "
47 #echo ' '.join($snpDb.extra_annotations.__str__.split(','))
48 #end if
49 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
50 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
51 #end if
52 $snpDb.genomeVersion
53 #elif $snpDb.genomeSrc == 'history':
54 -dataDir ${snpDb.snpeff_db.extra_files_path}
55 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
56 #set annotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
57 #echo " "
58 #echo ' -'.join($annotations)
59 #end if
60 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
61 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
62 #end if
63 ${snpDb.snpeff_db.metadata.genome_version}
64 #else
65 -download
66 $snpDb.genome_version
67 #end if
68 $input > $snpeff_output
109 </command> 69 </command>
110 <inputs> 70 <inputs>
111 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> 71 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
112 72
113 <param name="inputFormat" type="select" label="Input format"> 73 <param name="inputFormat" type="select" label="Input format">
114 <option value="vcf" selected="true">VCF</option> 74 <option value="vcf" selected="true">VCF</option>
115 <option value="txt">Tabular (Deprecated)</option> 75 <option value="txt">Tabular (Deprecated)</option>
116 <option value="pileup">Pileup (Deprecated)</option> 76 <option value="pileup">Pileup (Deprecated)</option>
117 <option value="bed">BED (Deprecated)</option> 77 <option value="bed">BED (Deprecated)</option>
118 </param> 78 </param>
119 79
120 <param name="outputFormat" type="select" label="Output format"> 80 <param name="outputFormat" type="select" label="Output format">
121 <option value="vcf" selected="true">VCF (only if input is VCF)</option> 81 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
122 <option value="txt">Tabular</option> 82 <option value="txt">Tabular</option>
123 <option value="bed">BED</option> 83 <option value="bed">BED</option>
124 <option value="bedAnn">BED Annotations</option> 84 <option value="bedAnn">BED Annotations</option>
125 </param> 85 </param>
126 86
127 <param name="genomeVersion" type="select" label="Genome"> 87 <conditional name="snpDb">
128 <!--GENOME DESCRIPTION--> 88 <param name="genomeSrc" type="select" label="">
129 <options from_data_table="snpeff_genomedb"/> 89 <option value="cached">Locally cached</option>
130 </param> 90 <option value="history">history</option>
131 91 <option value="named">named on demand</option>
132 <param name="udLength" type="select" label="Upstream / Downstream length"> 92 </param>
133 <option value="0">No upstream / downstream intervals (0 bases)</option> 93 <when value="cached">
134 <option value="200">200 bases</option> 94 <param name="genomeVersion" type="select" label="Genome">
135 <option value="500">500 bases</option> 95 <!--GENOME DESCRIPTION-->
136 <option value="1000">1000 bases</option> 96 <options from_data_table="snpeff_genomedb"/>
137 <option value="2000">2000 bases</option> 97 </param>
138 <option value="5000" selected="true">5000 bases</option> 98 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations">
139 <option value="10000">10000 bases</option>
140 <option value="20000">20000 bases</option>
141 </param>
142
143 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases. Default: 2">
144 <option value="1">1 base</option>
145 <option value="2">2 bases</option>
146 <option value="3">3 bases</option>
147 <option value="4">4 bases</option>
148 <option value="5">5 bases</option>
149 <option value="6">6 bases</option>
150 <option value="7">7 bases</option>
151 <option value="8">8 bases</option>
152 <option value="9">9 bases</option>
153 </param>
154
155 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
156 <option value="no_filter" selected="true">No filter (analyze everything)</option>
157 <option value="-hom">Analyze homozygous sequence changes only </option>
158 <option value="-het">Analyze heterozygous sequence changes only </option>
159 </param>
160
161 <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation -->
162 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
163 <option value="no_filter" selected="true">No filter (analyze everything)</option>
164 <option value="-del">Analyze deletions only </option>
165 <option value="-ins">Analyze insertions only </option>
166 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms) </option>
167 <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option>
168 </param>
169
170 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
171 <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline). Default: false</option>
172 <option value="-canon">Only use canonical transcripts.</option>
173 <option value="-geneId">Use gene ID instead of gene name (VCF output). Default: false</option>
174 <option value="-hgvs">Use HGVS annotations for amino acid sub-field. Default: false</option>
175 <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.</option>
176 <option value="-oicr">Add OICR tag in VCF file. Default: false</option>
177 <option value="-onlyReg">Only use regulation tracks.</option>
178 <option value="-sequenceOntolgy">Use Sequence Ontolgy terms. Default: false</option>
179 </param>
180
181 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations">
182 <help>These are available for only a few genomes</help> 99 <help>These are available for only a few genomes</help>
183 <!--GENOME REG_NAME -->
184 <options from_data_table="snpeff_annotations"> 100 <options from_data_table="snpeff_annotations">
185 <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> 101 <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
186 </options> 102 </options>
187 </param> 103 </param>
188 104 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation">
189 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation">
190 <help>These are available for only a few genomes</help> 105 <help>These are available for only a few genomes</help>
191 <!--GENOME REG_NAME -->
192 <options from_data_table="snpeff_regulationdb"> 106 <options from_data_table="snpeff_regulationdb">
193 <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> 107 <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
194 </options> 108 </options>
195 </param> 109 </param>
196 110 </when>
197 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/> 111 <when value="history">
198 <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file. Format: One transcript ID per line."/> 112 <param format="snpeffdb" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/>
199 113 <!-- From metadata -->
200 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output"> 114 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations">
201 <option value="-no-downstream">Do not show DOWNSTREAM changes </option> 115 <help>These are available for only a few genomes</help>
202 <option value="-no-intergenic">Do not show INTERGENIC changes </option> 116 <options>
203 <option value="-no-intron">Do not show INTRON changes </option> 117 <filter type="data_meta" ref="snpeff_db" key="annotation" />
204 <option value="-no-upstream">Do not show UPSTREAM changes </option> 118 </options>
205 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option> 119 </param>
206 </param> 120 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation">
207 121 <help>These are available for only a few genomes</help>
208 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> 122 <options>
209 <option value="" selected="true">Use default (based on input type)</option> 123 <filter type="data_meta" ref="snpeff_db" key="regulation" />
210 <option value="-0">Force zero-based positions (both input and output)</option> 124 </options>
211 <option value="-1">Force one-based positions (both input and output)</option> 125 </param>
212 </param> 126 </when>
213 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name" help="By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. You can prepend any string you want to the chromosome name."> 127 <when value="named">
214 <validator type="regex" message="No whitespace allows">^\S*$</validator> 128 <param name="genome_version" type="text" value="GRCh37.68" label="Snpff Version Name"/>
215 129 </when>
216 </param> 130 </conditional>
217 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/> 131
218 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/> 132 <param name="udLength" type="select" label="Upstream / Downstream length">
219 </inputs> 133 <option value="0">No upstream / downstream intervals (0 bases)</option>
220 <outputs> 134 <option value="200">200 bases</option>
221 <data format="vcf" name="snpeff_output" > 135 <option value="500">500 bases</option>
222 <change_format> 136 <option value="1000">1000 bases</option>
223 <when input="outputFormat" value="vcf" format="vcf" /> 137 <option value="2000">2000 bases</option>
224 <when input="outputFormat" value="txt" format="tabular" /> 138 <option value="5000" selected="true">5000 bases</option>
225 <when input="outputFormat" value="bed" format="bed" /> 139 <option value="10000">10000 bases</option>
226 <when input="outputFormat" value="bedAnn" format="bed" /> 140 <option value="20000">20000 bases</option>
227 </change_format> 141 </param>
228 </data> 142
229 143 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases. Default: 2">
230 <data format="html" name="statsFile"> 144 <option value="1">1 base</option>
231 <filter>generate_stats == True</filter> 145 <option value="2">2 bases</option>
232 </data> 146 <option value="3">3 bases</option>
233 </outputs> 147 <option value="4">4 bases</option>
234 <stdio> 148 <option value="5">5 bases</option>
235 <exit_code range="1:" level="fatal" description="Error" /> 149 <option value="6">6 bases</option>
236 <exit_code range="-1" level="fatal" description="Error: Cannot open file" /> 150 <option value="7">7 bases</option>
237 </stdio> 151 <option value="8">8 bases</option>
238 <tests> 152 <option value="9">9 bases</option>
239 <test> 153 </param>
240 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> 154
241 <param name="inputFormat" value="vcf"/> 155 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
242 <param name="outputFormat" value="vcf"/> 156 <option value="no_filter" selected="true">No filter (analyze everything)</option>
243 <param name="genomeVersion" value="testCase"/> 157 <option value="-hom">Analyze homozygous sequence changes only </option>
244 <param name="udLength" value="0"/> 158 <option value="-het">Analyze heterozygous sequence changes only </option>
245 <param name="filterHomHet" value="no_filter"/> 159 </param>
246 <param name="filterIn" value="no_filter"/> 160
247 <param name="generate_stats" value="False"/> 161 <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation -->
248 <param name="filterOut" value="+-no-upstream"/> 162 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
249 <output name="snpeff_output"> 163 <option value="no_filter" selected="true">No filter (analyze everything)</option>
250 <assert_contents> 164 <option value="-del">Analyze deletions only </option>
251 <!-- Check that an effect was added --> 165 <option value="-ins">Analyze insertions only </option>
252 <has_text text="EFF=" /> 166 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms) </option>
253 </assert_contents> 167 <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option>
254 </output> 168 </param>
255 <!-- Check for a HTML header indicating that this was successful --> 169
256 <!-- 170 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
257 <output name="statsFile"> 171 <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline). Default: false</option>
258 <assert_contents> 172 <option value="-canon">Only use canonical transcripts.</option>
259 <has_text text="SnpEff: Variant analysis" /> 173 <option value="-geneId">Use gene ID instead of gene name (VCF output). Default: false</option>
260 </assert_contents> 174 <option value="-hgvs">Use HGVS annotations for amino acid sub-field. Default: false</option>
261 </output> 175 <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.</option>
262 --> 176 <option value="-oicr">Add OICR tag in VCF file. Default: false</option>
263 </test> 177 <option value="-onlyReg">Only use regulation tracks.</option>
264 178 <option value="-sequenceOntolgy">Use Sequence Ontolgy terms. Default: false</option>
265 <test> 179 </param>
266 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> 180 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
267 <param name="inputFormat" value="vcf"/> 181 <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file. Format: One transcript ID per line."/>
268 <param name="outputFormat" value="vcf"/> 182 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
269 <param name="genomeVersion" value="testCase"/> 183 <option value="-no-downstream">Do not show DOWNSTREAM changes </option>
270 <param name="udLength" value="0"/> 184 <option value="-no-intergenic">Do not show INTERGENIC changes </option>
271 <param name="filterHomHet" value="+-het"/> 185 <option value="-no-intron">Do not show INTRON changes </option>
272 <param name="filterIn" value="no_filter"/> 186 <option value="-no-upstream">Do not show UPSTREAM changes </option>
273 <!-- 187 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option>
274 <param name="filterOut" value=""/> 188 </param>
275 --> 189
276 <param name="generate_stats" value="False"/> 190 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
277 <output name="snpeff_output"> 191 <option value="" selected="true">Use default (based on input type)</option>
278 <assert_contents> 192 <option value="-0">Force zero-based positions (both input and output)</option>
279 <!-- Check that NO effects were added since -het is set --> 193 <option value="-1">Force one-based positions (both input and output)</option>
280 <not_has_text text="EFF=NON_SYNONYMOUS_CODING" /> 194 </param>
281 </assert_contents> 195 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
282 </output> 196 <help>
283 </test> 197 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
284 <test> 198 You can prepend any string you want to the chromosome name."
285 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> 199 </help>
286 <param name="inputFormat" value="vcf"/> 200 <validator type="regex" message="No whitespace allows">^\S*$</validator>
287 <param name="outputFormat" value="vcf"/> 201
288 <param name="genomeVersion" value="testCase"/> 202 </param>
289 <param name="udLength" value="0"/> 203 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
290 <param name="filterHomHet" value="no_filter"/> 204 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
291 <param name="filterIn" value="del"/> 205 </inputs>
292 <!-- 206 <outputs>
293 <param name="filterOut" value=""/> 207 <data format="vcf" name="snpeff_output" >
294 --> 208 <change_format>
295 <param name="generate_stats" value="False"/> 209 <when input="outputFormat" value="vcf" format="vcf" />
296 <output name="snpeff_output"> 210 <when input="outputFormat" value="txt" format="tabular" />
297 <assert_contents> 211 <when input="outputFormat" value="bed" format="bed" />
298 <!-- Check that deleletions were evaluated --> 212 <when input="outputFormat" value="bedAnn" format="bed" />
299 <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" /> 213 </change_format>
300 <!-- Check that insertion on last line was NOT evaluated --> 214 </data>
301 <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" /> 215
302 </assert_contents> 216 <data format="html" name="statsFile">
303 </output> 217 <filter>generate_stats == True</filter>
304 </test> 218 </data>
305 <test> 219 </outputs>
306 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> 220 <stdio>
307 <param name="inputFormat" value="vcf"/> 221 <exit_code range="1:" level="fatal" description="Error" />
308 <param name="outputFormat" value="vcf"/> 222 <exit_code range="-1" level="fatal" description="Error: Cannot open file" />
309 <param name="genomeVersion" value="testCase"/> 223 </stdio>
310 <param name="udLength" value="0"/> 224 <tests>
311 <param name="filterHomHet" value="no_filter"/> 225 <!-- Check that an effect was added in out VCF -->
312 <param name="filterIn" value="no_filter"/> 226 <!-- Check for a HTML header indicating that this was successful -->
313 <param name="filterOut" value="+-no-upstream"/> 227 <!--
314 <param name="generate_stats" value="False"/> 228 <output name="statsFile">
315 <output name="snpeff_output"> 229 <assert_contents>
316 <assert_contents> 230 <has_text text="SnpEff: Variant analysis" />
317 <!-- Check that NO UPSTREAM effect was added --> 231 </assert_contents>
318 <not_has_text text="UPSTREAM" /> 232 </output>
319 </assert_contents> 233 -->
320 </output> 234 <!-- Setting filterOut throws exception in twilltestcase.py
321 </test> 235 <test>
322 236 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
323 </tests> 237 <param name="inputFormat" value="vcf"/>
324 <help> 238 <param name="outputFormat" value="vcf"/>
239 <param name="genomeSrc" value="named"/>
240 <param name="genome_version" value="testCase"/>
241 <param name="udLength" value="0"/>
242 <param name="filterHomHet" value="no_filter"/>
243 <param name="filterIn" value="no_filter"/>
244 <param name="generate_stats" value="False"/>
245 <param name="filterOut" value="+-no-upstream"/>
246 <output name="snpeff_output">
247 <assert_contents>
248 <has_text text="EFF=" />
249 </assert_contents>
250 </output>
251 </test>
252 -->
253
254 <test>
255 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
256 <param name="inputFormat" value="vcf"/>
257 <param name="outputFormat" value="vcf"/>
258 <param name="genomeSrc" value="named"/>
259 <param name="genome_version" value="testCase"/>
260 <param name="udLength" value="0"/>
261 <param name="filterHomHet" value="+-het"/>
262 <param name="filterIn" value="no_filter"/>
263 <!--
264 <param name="filterOut" value=""/>
265 -->
266 <param name="generate_stats" value="False"/>
267 <output name="snpeff_output">
268 <assert_contents>
269 <!-- Check that NO effects were added since -het is set -->
270 <not_has_text text="EFF=NON_SYNONYMOUS_CODING" />
271 </assert_contents>
272 </output>
273 </test>
274
275 <test>
276 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
277 <param name="inputFormat" value="vcf"/>
278 <param name="outputFormat" value="vcf"/>
279 <param name="genomeSrc" value="named"/>
280 <param name="genome_version" value="testCase"/>
281 <param name="udLength" value="0"/>
282 <param name="filterHomHet" value="no_filter"/>
283 <param name="filterIn" value="del"/>
284 <!--
285 <param name="filterOut" value=""/>
286 -->
287 <param name="generate_stats" value="False"/>
288 <output name="snpeff_output">
289 <assert_contents>
290 <!-- Check that deleletions were evaluated -->
291 <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" />
292 <!-- Check that insertion on last line was NOT evaluated -->
293 <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" />
294 </assert_contents>
295 </output>
296 </test>
297
298 <!-- Check that NO UPSTREAM effect was added -->
299 <!-- Setting filterOut throws exception in twilltestcase.py
300 <test>
301 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
302 <param name="inputFormat" value="vcf"/>
303 <param name="outputFormat" value="vcf"/>
304 <param name="genomeSrc" value="named"/>
305 <param name="genome_version" value="testCase"/>
306 <param name="udLength" value="0"/>
307 <param name="filterHomHet" value="no_filter"/>
308 <param name="filterIn" value="no_filter"/>
309 <param name="filterOut" value="+-no-upstream"/>
310 <param name="generate_stats" value="False"/>
311 <output name="snpeff_output">
312 <assert_contents>
313 <not_has_text text="UPSTREAM" />
314 </assert_contents>
315 </output>
316 </test>
317 -->
318
319 </tests>
320 <help>
325 321
326 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. 322 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
327 323
328 For details about this tool, please go to http://snpEff.sourceforge.net 324 For details about this tool, please go to http://snpEff.sourceforge.net
329 325
330 </help> 326 SnpEff citation:
327 "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]
328
329 SnpSift citation:
330 "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.
331
332 </help>
331 </tool> 333 </tool>
332 334