Mercurial > repos > iuc > snpeff

comparison snpEff.xml @ 6:9ec1cb6f760d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e
author iuc
date Tue, 13 Oct 2015 17:30:57 -0400
parents 92b80578fa22
children aaa749ea91a2
comparison
equal deleted inserted replaced
5:92b80578fa22 6:9ec1cb6f760d
1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0"> 1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.1">
2 <description>Variant effect and annotation</description> 2 <description>Variant effect and annotation</description>
3 <macros> 3 <macros>
4 <import>snpEff_macros.xml</import> 4 <import>snpEff_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
11 -c \$SNPEFF_JAR_PATH/snpEff.config 11 -c \$SNPEFF_JAR_PATH/snpEff.config
12 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength 12 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
13 #if $spliceSiteSize and $spliceSiteSize.__str__ != '': 13 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
14 -spliceSiteSize $spliceSiteSize 14 -spliceSiteSize $spliceSiteSize
15 #end if 15 #end if
16 #if $filterIn and $filterIn.__str__ != 'no_filter':
17 $filterIn
18 #end if
19 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': 16 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
20 $filterHomHet 17 $filterHomHet
21 #end if 18 #end if
22 #if $annotations and $annotations.__str__ != '': 19 #if $annotations and $annotations.__str__ != '':
23 #echo " " 20 #echo " "
24 #echo ' '.join($annotations.__str__.split(',')) 21 #echo ' '.join($annotations.__str__.split(','))
25 #end if 22 #end if
26 #if $filterOut and $filterOut.__str__ != '': 23 #if $filterOut and $filterOut.__str__ != '':
27 #echo " " 24 #echo " "
28 #echo ' '.join($filterOut.__str__.split(',')) 25 #echo ' '.join($filterOut.__str__.split(','))
26 #end if
27 #if $filter.specificEffects == 'yes' and $filter.effects:
28 #for $eff in str($filter.effects).split(','):
29 -no $eff
30 #end for
29 #end if 31 #end if
30 #if str( $transcripts ) != 'None': 32 #if str( $transcripts ) != 'None':
31 -onlyTr $transcripts 33 -onlyTr $transcripts
32 #end if 34 #end if
33 #if str( $intervals ) != 'None': ### fix this for multiple dataset input 35 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
158 <filter type="data_meta" ref="snpeff_db" key="regulation" /> 160 <filter type="data_meta" ref="snpeff_db" key="regulation" />
159 </options> 161 </options>
160 </param> 162 </param>
161 </when> 163 </when>
162 <when value="named"> 164 <when value="named">
163 <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> 165 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
164 <help>@SNPEFF_DATABASE_URL@</help> 166 <help>@SNPEFF_DATABASE_URL@</help>
165 <validator type="regex" message="A genome version name is required">\S+</validator> 167 <validator type="regex" message="A genome version name is required">\S+</validator>
166 </param> 168 </param>
167 </when> 169 </when>
168 </conditional> 170 </conditional>
194 <option value="no_filter" selected="true">No filter (analyze everything)</option> 196 <option value="no_filter" selected="true">No filter (analyze everything)</option>
195 <option value="-hom">Analyze homozygous sequence changes only</option> 197 <option value="-hom">Analyze homozygous sequence changes only</option>
196 <option value="-het">Analyze heterozygous sequence changes only</option> 198 <option value="-het">Analyze heterozygous sequence changes only</option>
197 </param> 199 </param>
198 200
199 <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation -->
200 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
201 <option value="no_filter" selected="true">No filter (analyze everything)</option>
202 <option value="-del">Analyze deletions only</option>
203 <option value="-ins">Analyze insertions only</option>
204 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms)</option>
205 <option value="-snp">Only SNPs (single nucleotide polymorphisms)</option>
206 </param>
207
208 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> 201 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
209 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> 202 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
210 <option value="-canon">Only use canonical transcripts</option> 203 <option value="-canon">Only use canonical transcripts</option>
211 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> 204 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
212 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option> 205 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
223 <option value="-no-intergenic">Do not show INTERGENIC changes</option> 216 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
224 <option value="-no-intron">Do not show INTRON changes</option> 217 <option value="-no-intron">Do not show INTRON changes</option>
225 <option value="-no-upstream">Do not show UPSTREAM changes</option> 218 <option value="-no-upstream">Do not show UPSTREAM changes</option>
226 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option> 219 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
227 </param> 220 </param>
221 <conditional name="filter">
222 <param name="specificEffects" type="select" label="Filter out specific Effects">
223 <option value="no">No</option>
224 <option value="yes">Yes</option>
225 </param>
226 <when value="no"/>
227 <when value="yes">
228 <param name="effects" type="select" display="checkboxes" multiple="true" label="Filter output: do not report these Effects">
229 <option value="CDS">CDS (coding_sequence_variant) The variant hits a CDS. MODIFIER</option>
230 <option value="CHROMOSOME_LARGE_DELETION">CHROMOSOME_LARGE_DELETION (chromosome) A large parte (over 1%) of the chromosome was deleted. HIGH</option>
231 <option value="CODON_CHANGE">CODON_CHANGE (coding_sequence_variant) One or many codons are changed e.g.: An MNP of size multiple of 3 MODERATE</option>
232 <option value="CODON_INSERTION">CODON_INSERTION (inframe_insertion) One or many codons are inserted e.g.: An insert multiple of three in a codon boundary MODERATE</option>
233 <option value="CODON_CHANGE_PLUS CODON_INSERTION">CODON_CHANGE_PLUS CODON_INSERTION (disruptive_inframe_insertion) One codon is changed and one or many codons are inserted e.g.: An insert of size multiple of three, not at codon boundary MODERATE</option>
234 <option value="CODON_DELETION">CODON_DELETION (inframe_deletion) One or many codons are deleted e.g.: A deletion multiple of three at codon boundary MODERATE</option>
235 <option value="CODON_CHANGE_PLUS CODON_DELETION">CODON_CHANGE_PLUS CODON_DELETION (disruptive_inframe_deletion) One codon is changed and one or more codons are deleted e.g.: A deletion of size multiple of three, not at codon boundary MODERATE</option>
236 <option value="DOWNSTREAM">DOWNSTREAM (downstream_gene_variant) Downstream of a gene (default length: 5K bases) MODIFIER</option>
237 <option value="EXON">EXON (exon_variant) The variant hits an exon (from a non-coding transcript) or a retained intron. MODIFIER</option>
238 <option value="EXON_DELETED">EXON_DELETED (exon_loss_variant) A deletion removes the whole exon. HIGH</option>
239 <option value="FRAME_SHIFT">FRAME_SHIFT (frameshift_variant) Insertion or deletion causes a frame shift e.g.: An indel size is not multple of 3 HIGH</option>
240 <option value="GENE">GENE (gene_variant) The variant hits a gene. MODIFIER</option>
241 <option value="INTERGENIC">INTERGENIC (intergenic_region) The variant is in an intergenic region MODIFIER</option>
242 <option value="INTERGENIC_CONSERVED">INTERGENIC_CONSERVED (conserved_intergenic_variant) The variant is in a highly conserved intergenic region MODIFIER</option>
243 <option value="INTRAGENIC">INTRAGENIC (intragenic_variant) The variant hits a gene, but no transcripts within the gene MODIFIER</option>
244 <option value="INTRON">INTRON (intron_variant) Variant hits and intron. Technically, hits no exon in the transcript. MODIFIER</option>
245 <option value="INTRON_CONSERVED">INTRON_CONSERVED (conserved_intron_variant) The variant is in a highly conserved intronic region MODIFIER</option>
246 <option value="MICRO_RNA">MICRO_RNA (miRNA) Variant affects an miRNA MODIFIER</option>
247 <option value="NON_SYNONYMOUS_CODING">NON_SYNONYMOUS_CODING (missense_variant) Variant causes a codon that produces a different amino acid e.g.: Tgg/Cgg, W/R MODERATE</option>
248 <option value="NON_SYNONYMOUS_START">NON_SYNONYMOUS_START (initiator_codon_variant) Variant causes start codon to be mutated into another start codon (the new codon produces a different AA). e.g.: Atg/Ctg, M/L (ATG and CTG can be START codons) LOW</option>
249 <option value="NON_SYNONYMOUS_STOP">NON_SYNONYMOUS_STOP (stop_retained_variant) Variant causes stop codon to be mutated into another stop codon (the new codon produces a different AA). e.g.: Atg/Ctg, M/L (ATG and CTG can be START codons) LOW</option>
250 <option value="RARE_AMINO_ACID">RARE_AMINO_ACID (rare_amino_acid_variant) The variant hits a rare amino acid thus is likely to produce protein loss of function HIGH</option>
251 <option value="SPLICE_SITE_ACCEPTOR">SPLICE_SITE_ACCEPTOR (splice_acceptor_variant) The variant hits a splice acceptor site (defined as two bases before exon start, except for the first exon). HIGH</option>
252 <option value="SPLICE_SITE_DONOR">SPLICE_SITE_DONOR (splice_donor_variant) The variant hits a Splice donor site (defined as two bases after coding exon end, except for the last exon). HIGH</option>
253 <option value="SPLICE_SITE_REGION">SPLICE_SITE_REGION (splice_region_variant) A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. LOW</option>
254 <option value="SPLICE_SITE_BRANCH">SPLICE_SITE_BRANCH (splice_region_variant) A varaint affective putative (Lariat) branch point, located in the intron. LOW</option>
255 <option value="SPLICE_SITE_BRANCH_U12">SPLICE_SITE_BRANCH_U12 (splice_region_variant) A varaint affective putative (Lariat) branch point from U12 splicing machinery, located in the intron. MODERATE</option>
256 <option value="STOP_LOST">STOP_LOST (stop_lost) Variant causes stop codon to be mutated into a non-stop codon e.g.: Tga/Cga, */R HIGH</option>
257 <option value="START_GAINED">START_GAINED (5_prime_UTR_premature start_codon_gain_variant) A variant in 5'UTR region produces a three base sequence that can be a START codon. LOW</option>
258 <option value="START_LOST">START_LOST (start_lost) Variant causes start codon to be mutated into a non-start codon. e.g.: aTg/aGg, M/R HIGH</option>
259 <option value="STOP_GAINED">STOP_GAINED (stop_gained) Variant causes a STOP codon e.g.: Cag/Tag, Q/* HIGH</option>
260 <option value="SYNONYMOUS_CODING">SYNONYMOUS_CODING (synonymous_variant) Variant causes a codon that produces the same amino acid e.g.: Ttg/Ctg, L/L LOW</option>
261 <option value="SYNONYMOUS_START">SYNONYMOUS_START (start_retained) Variant causes start codon to be mutated into another start codon. e.g.: Ttg/Ctg, L/L (TTG and CTG can be START codons) LOW</option>
262 <option value="SYNONYMOUS_STOP">SYNONYMOUS_STOP (stop_retained_variant) Variant causes stop codon to be mutated into another stop codon. e.g.: taA/taG, */* LOW</option>
263 <option value="TRANSCRIPT">TRANSCRIPT (transcript_variant) The variant hits a transcript. MODIFIER</option>
264 <option value="REGULATION">REGULATION (regulatory_region_variant) The variant hits a known regulatory feature (non-coding). MODIFIER</option>
265 <option value="UPSTREAM">UPSTREAM (upstream_gene_variant) Upstream of a gene (default length: 5K bases) MODIFIER</option>
266 <option value="UTR_3_PRIME">UTR_3_PRIME (3_prime_UTR_variant) Variant hits 3'UTR region MODIFIER</option>
267 <option value="UTR_3_DELETED">UTR_3_DELETED (3_prime_UTR_truncation + exon_loss) The variant deletes an exon which is in the 3'UTR of the transcript MODERATE</option>
268 <option value="UTR_5_PRIME">UTR_5_PRIME (5_prime_UTR_variant) Variant hits 5'UTR region MODIFIER</option>
269 <option value="UTR_5_DELETED">UTR_5_DELETED (5_prime_UTR_truncation + exon_loss_variant) The variant deletes an exon which is in the 5'UTR of the transcript MODERATE</option>
270 <option value="NEXT_PROT">NEXT_PROT (sequence_feature + exon_loss_variant) A 'NextProt' based annotation. Details are provided in the 'feature type' sub-field (ANN), or in the effect details (EFF). MODERATE </option>
271
272 </param>
273 </when>
274 </conditional>
228 275
229 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> 276 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
230 <option value="default" selected="true">Use default (based on input type)</option> 277 <option value="default" selected="true">Use default (based on input type)</option>
231 <option value="-0">Force zero-based positions (both input and output)</option> 278 <option value="-0">Force zero-based positions (both input and output)</option>
232 <option value="-1">Force one-based positions (both input and output)</option> 279 <option value="-1">Force one-based positions (both input and output)</option>
270 <param name="outputFormat" value="vcf"/> 317 <param name="outputFormat" value="vcf"/>
271 <param name="genomeSrc" value="named"/> 318 <param name="genomeSrc" value="named"/>
272 <param name="genome_version" value="testCase"/> 319 <param name="genome_version" value="testCase"/>
273 <param name="udLength" value="0"/> 320 <param name="udLength" value="0"/>
274 <param name="filterHomHet" value="no_filter"/> 321 <param name="filterHomHet" value="no_filter"/>
275 <param name="filterIn" value="no_filter"/>
276 <param name="generate_stats" value="False"/> 322 <param name="generate_stats" value="False"/>
277 <param name="filterOut" value="+-no-upstream"/> 323 <param name="filterOut" value="+-no-upstream"/>
278 <output name="snpeff_output"> 324 <output name="snpeff_output">
279 <assert_contents> 325 <assert_contents>
280 <has_text text="EFF=" /> 326 <has_text text="EFF=" />
289 <param name="outputFormat" value="vcf"/> 335 <param name="outputFormat" value="vcf"/>
290 <param name="genomeSrc" value="named"/> 336 <param name="genomeSrc" value="named"/>
291 <param name="genome_version" value="testCase"/> 337 <param name="genome_version" value="testCase"/>
292 <param name="udLength" value="0"/> 338 <param name="udLength" value="0"/>
293 <param name="filterHomHet" value="+-het"/> 339 <param name="filterHomHet" value="+-het"/>
294 <param name="filterIn" value="no_filter"/>
295 <!-- 340 <!--
296 <param name="filterOut" value=""/> 341 <param name="filterOut" value=""/>
297 --> 342 -->
298 <param name="generate_stats" value="False"/> 343 <param name="generate_stats" value="False"/>
299 <output name="snpeff_output"> 344 <output name="snpeff_output">
310 <param name="outputFormat" value="vcf"/> 355 <param name="outputFormat" value="vcf"/>
311 <param name="genomeSrc" value="named"/> 356 <param name="genomeSrc" value="named"/>
312 <param name="genome_version" value="testCase"/> 357 <param name="genome_version" value="testCase"/>
313 <param name="udLength" value="0"/> 358 <param name="udLength" value="0"/>
314 <param name="filterHomHet" value="no_filter"/> 359 <param name="filterHomHet" value="no_filter"/>
315 <param name="filterIn" value="+-del"/>
316 <!-- 360 <!--
317 <param name="filterOut" value=""/> 361 <param name="filterOut" value=""/>
318 --> 362 -->
319 <param name="generate_stats" value="False"/> 363 <param name="generate_stats" value="False"/>
320 <output name="snpeff_output"> 364 <output name="snpeff_output">
335 <param name="outputFormat" value="vcf"/> 379 <param name="outputFormat" value="vcf"/>
336 <param name="genomeSrc" value="named"/> 380 <param name="genomeSrc" value="named"/>
337 <param name="genome_version" value="testCase"/> 381 <param name="genome_version" value="testCase"/>
338 <param name="udLength" value="0"/> 382 <param name="udLength" value="0"/>
339 <param name="filterHomHet" value="no_filter"/> 383 <param name="filterHomHet" value="no_filter"/>
340 <param name="filterIn" value="no_filter"/>
341 <param name="filterOut" value="+-no-upstream"/> 384 <param name="filterOut" value="+-no-upstream"/>
342 <param name="generate_stats" value="False"/> 385 <param name="generate_stats" value="False"/>
343 <output name="snpeff_output"> 386 <output name="snpeff_output">
344 <assert_contents> 387 <assert_contents>
345 <not_has_text text="UPSTREAM" /> 388 <not_has_text text="UPSTREAM" />