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comparison snpEff.xml @ 0:39bac90c773d draft

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author iuc
date Fri, 15 Aug 2014 06:00:47 -0400
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1 <tool id="snpEff" name="SnpEff" version="3.6">
2 <description>Variant effect and annotation</description>
3 <expand macro="requirements" />
4 <macros>
5 <import>snpEff_macros.xml</import>
6 </macros>
7 <command>
8 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff
9 -c \$SNPEFF_JAR_PATH/snpEff.config
10 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
11 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
12 -spliceSiteSize $spliceSiteSize
13 #end if
14 #if $filterIn and $filterIn.__str__ != 'no_filter':
15 $filterIn
16 #end if
17 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
18 $filterHomHet
19 #end if
20 #if $annotations and $annotations.__str__ != '':
21 #echo " "
22 #echo ' '.join($annotations.__str__.split(','))
23 #end if
24 #if $filterOut and $filterOut.__str__ != '':
25 #echo " "
26 #echo ' '.join($filterOut.__str__.split(','))
27 #end if
28 #if str( $transcripts ) != 'None':
29 -onlyTr $transcripts
30 #end if
31 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
32 -interval $intervals
33 #end if
34 #if $statsFile:
35 -stats $statsFile
36 #end if
37 #if $offset.__str__ != '':
38 ${offset}
39 #end if
40 #if $chr.__str__.strip() != '':
41 -chr "$chr"
42 #end if
43 $noLog
44 #if $snpDb.genomeSrc == 'cached':
45 -dataDir ${snpDb.genomeVersion.fields.path}
46 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
47 #echo " "
48 #echo ' '.join($snpDb.extra_annotations.__str__.split(','))
49 #end if
50 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
51 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
52 #end if
53 $snpDb.genomeVersion
54 #elif $snpDb.genomeSrc == 'history':
55 -dataDir ${snpDb.snpeff_db.files_path}
56 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
57 #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
58 #echo " "
59 #echo ' -'.join($xannotations)
60 #end if
61 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
62 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
63 #end if
64 ${snpDb.snpeff_db.metadata.genome_version}
65 #else
66 -download
67 $snpDb.genome_version
68 #end if
69 $input > $snpeff_output ;
70 #if $statsFile:
71 #import os
72 #set $genes_file = str($statsFile) + '.genes.txt'
73 #set $genes_file_name = os.path.split($genes_file)[-1]
74 mkdir $statsFile.files_path;
75 mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#;
76 #end if
77 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
78 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
79 sed -i 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output
80 #end if
81 </command>
82 <inputs>
83 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
84
85 <param name="inputFormat" type="select" label="Input format">
86 <option value="vcf" selected="true">VCF</option>
87 <option value="txt">Tabular (Deprecated)</option>
88 <option value="pileup">Pileup (Deprecated)</option>
89 <option value="bed">BED (Deprecated)</option>
90 </param>
91
92 <conditional name="outputConditional">
93 <param name="outputFormat" type="select" label="Output format">
94 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
95 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
96 <option value="txt">Tabular</option>
97 <option value="bed">BED</option>
98 <option value="bedAnn">BED annotations</option>
99 </param>
100 <when value="vcf" />
101 <when value="gatk">
102 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
103 </when>
104 <when value="txt" />
105 <when value="bed" />
106 <when value="bedAnn" />
107 </conditional>
108
109 <conditional name="snpDb">
110 <param name="genomeSrc" type="select" label="Genome source">
111 <option value="cached">Locally installed reference genome</option>
112 <option value="history">Reference genome from your history</option>
113 <option value="named">Named on demand</option>
114 </param>
115 <when value="cached">
116 <param name="genomeVersion" type="select" label="Genome">
117 <!--GENOME DESCRIPTION-->
118 <options from_data_table="snpeff_genomedb">
119 <filter type="unique_value" column="0" />
120 </options>
121 </param>
122 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
123 <help>These are available for only a few genomes</help>
124 <options from_data_table="snpeff_annotations">
125 <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
126 <filter type="unique_value" column="1" />
127 </options>
128 </param>
129 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
130 <help>These are available for only a few genomes</help>
131 <options from_data_table="snpeff_regulationdb">
132 <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
133 <filter type="unique_value" column="1" />
134 </options>
135 </param>
136 </when>
137 <when value="history">
138 <param format="snpeffdb" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/>
139 <!-- From metadata -->
140 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
141 <help>These are available for only a few genomes</help>
142 <options>
143 <filter type="data_meta" ref="snpeff_db" key="annotation" />
144 </options>
145 </param>
146 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
147 <help>These are available for only a few genomes</help>
148 <options>
149 <filter type="data_meta" ref="snpeff_db" key="regulation" />
150 </options>
151 </param>
152 </when>
153 <when value="named">
154 <param name="genome_version" type="text" value="GRCh37.68" label="Snpff Version Name"/>
155 </when>
156 </conditional>
157
158 <param name="udLength" type="select" label="Upstream / Downstream length">
159 <option value="0">No upstream / downstream intervals (0 bases)</option>
160 <option value="200">200 bases</option>
161 <option value="500">500 bases</option>
162 <option value="1000">1000 bases</option>
163 <option value="2000">2000 bases</option>
164 <option value="5000" selected="true">5000 bases</option>
165 <option value="10000">10000 bases</option>
166 <option value="20000">20000 bases</option>
167 </param>
168
169 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2">
170 <option value="1">1 base</option>
171 <option value="2" selected="true">2 bases</option>
172 <option value="3">3 bases</option>
173 <option value="4">4 bases</option>
174 <option value="5">5 bases</option>
175 <option value="6">6 bases</option>
176 <option value="7">7 bases</option>
177 <option value="8">8 bases</option>
178 <option value="9">9 bases</option>
179 </param>
180
181 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
182 <option value="no_filter" selected="true">No filter (analyze everything)</option>
183 <option value="-hom">Analyze homozygous sequence changes only</option>
184 <option value="-het">Analyze heterozygous sequence changes only</option>
185 </param>
186
187 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
188 <option value="no_filter" selected="true">No filter (analyze everything)</option>
189 <option value="-del">Analyze deletions only</option>
190 <option value="-ins">Analyze insertions only</option>
191 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms)</option>
192 <option value="-snp">Only SNPs (single nucleotide polymorphisms)</option>
193 </param>
194
195 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
196 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
197 <option value="-canon">Only use canonical transcripts</option>
198 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
199 <option value="-hgvs">Use HGVS annotations for amino acid sub-field</option>
200 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
201 <option value="-oicr">Add OICR tag in VCF file</option>
202 <option value="-onlyReg">Only use regulation tracks</option>
203 <option value="-sequenceOntolgy">Use Sequence Ontology terms</option>
204 </param>
205 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
206 <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."/>
207 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
208 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
209 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
210 <option value="-no-intron">Do not show INTRON changes</option>
211 <option value="-no-upstream">Do not show UPSTREAM changes</option>
212 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
213 </param>
214
215 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
216 <option value="" selected="true">Use default (based on input type)</option>
217 <option value="-0">Force zero-based positions (both input and output)</option>
218 <option value="-1">Force one-based positions (both input and output)</option>
219 </param>
220 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
221 <help>
222 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
223 You can prepend any string you want to the chromosome name.
224 </help>
225 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
226 </param>
227 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
228 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
229 </inputs>
230 <outputs>
231 <data format="vcf" name="snpeff_output" >
232 <change_format>
233 <when input="outputConditional.outputFormat" value="txt" format="tabular" />
234 <when input="outputConditional.outputFormat" value="bed" format="bed" />
235 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
236 </change_format>
237 </data>
238 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">
239 <filter>generate_stats == True</filter>
240 </data>
241 </outputs>
242 <expand macro="stdio" />
243 <tests>
244 <!-- Check that an effect was added in out VCF -->
245 <!-- Check for a HTML header indicating that this was successful -->
246 <!--
247 <output name="statsFile">
248 <assert_contents>
249 <has_text text="SnpEff: Variant analysis" />
250 </assert_contents>
251 </output>
252 -->
253 <!-- Setting filterOut throws exception in twilltestcase.py
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="no_filter"/>
262 <param name="filterIn" value="no_filter"/>
263 <param name="generate_stats" value="False"/>
264 <param name="filterOut" value="+-no-upstream"/>
265 <output name="snpeff_output">
266 <assert_contents>
267 <has_text text="EFF=" />
268 </assert_contents>
269 </output>
270 </test>
271 -->
272
273 <test>
274 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
275 <param name="inputFormat" value="vcf"/>
276 <param name="outputFormat" value="vcf"/>
277 <param name="genomeSrc" value="named"/>
278 <param name="genome_version" value="testCase"/>
279 <param name="udLength" value="0"/>
280 <param name="filterHomHet" value="+-het"/>
281 <param name="filterIn" value="no_filter"/>
282 <!--
283 <param name="filterOut" value=""/>
284 -->
285 <param name="generate_stats" value="False"/>
286 <output name="snpeff_output">
287 <assert_contents>
288 <!-- Check that NO effects were added since -het is set -->
289 <not_has_text text="EFF=NON_SYNONYMOUS_CODING" />
290 </assert_contents>
291 </output>
292 </test>
293
294 <test>
295 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
296 <param name="inputFormat" value="vcf"/>
297 <param name="outputFormat" value="vcf"/>
298 <param name="genomeSrc" value="named"/>
299 <param name="genome_version" value="testCase"/>
300 <param name="udLength" value="0"/>
301 <param name="filterHomHet" value="no_filter"/>
302 <param name="filterIn" value="+-del"/>
303 <!--
304 <param name="filterOut" value=""/>
305 -->
306 <param name="generate_stats" value="False"/>
307 <output name="snpeff_output">
308 <assert_contents>
309 <!-- Check that deleletions were evaluated -->
310 <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" />
311 <!-- Check that insertion on last line was NOT evaluated -->
312 <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" />
313 </assert_contents>
314 </output>
315 </test>
316
317 <!-- Check that NO UPSTREAM effect was added -->
318 <!-- Setting filterOut throws exception in twilltestcase.py
319 <test>
320 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
321 <param name="inputFormat" value="vcf"/>
322 <param name="outputFormat" value="vcf"/>
323 <param name="genomeSrc" value="named"/>
324 <param name="genome_version" value="testCase"/>
325 <param name="udLength" value="0"/>
326 <param name="filterHomHet" value="no_filter"/>
327 <param name="filterIn" value="no_filter"/>
328 <param name="filterOut" value="+-no-upstream"/>
329 <param name="generate_stats" value="False"/>
330 <output name="snpeff_output">
331 <assert_contents>
332 <not_has_text text="UPSTREAM" />
333 </assert_contents>
334 </output>
335 </test>
336 -->
337
338 </tests>
339 <help>
340 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
341
342 @EXTERNAL_DOCUMENTATION@
343
344 </help>
345 <expand macro="citations" />
346 </tool>
347