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comparison snpEff.xml @ 22:bb0797deab78 draft

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author jjohnson
date Wed, 09 Dec 2015 10:20:13 -0500
parents c780e3f75b3d
children 924af057bbca
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21:c780e3f75b3d 22:bb0797deab78
1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.3"> 1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0">
2 <description>Variant effect and annotation</description> 2 <description>Variant effect and annotation</description>
3 <expand macro="requirements" />
4 <macros> 3 <macros>
5 <import>snpEff_macros.xml</import> 4 <import>snpEff_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <expand macro="version_command" />
7 <command> 9 <command>
8 <![CDATA[ 10 <![CDATA[
9 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff 11 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff
10 -c \$SNPEFF_JAR_PATH/snpEff.config 12 -c \$SNPEFF_JAR_PATH/snpEff.config
11 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength 13 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
12 #if $spliceSiteSize and $spliceSiteSize.__str__ != '': 14 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
13 -spliceSiteSize $spliceSiteSize 15 -spliceSiteSize $spliceSiteSize
14 #end if 16 #end if
15 #if $filterIn and $filterIn.__str__ != 'no_filter': 17 #if $spliceRegion.setSpliceRegions == 'yes':
16 $filterIn 18 #if $spliceRegion.spliceRegionExonSize and $spliceRegion.spliceRegionExonSize.__str__ != '':
19 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
20 #end if
21 #if $spliceRegion.spliceRegionIntronMin and $spliceRegion.spliceRegionIntronMin.__str__ != '':
22 -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
23 #end if
24 #if $spliceRegion.spliceRegionIntronMax and $spliceRegion.spliceRegionIntronMax.__str__ != '':
25 -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax
26 #end if
17 #end if 27 #end if
18 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': 28 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
19 $filterHomHet 29 $filterHomHet
20 #end if 30 #end if
21 #if $annotations and $annotations.__str__ != '': 31 #if $annotations and $annotations.__str__ != '':
22 #echo " " 32 #echo " "
23 #echo ' '.join($annotations.__str__.split(',')) 33 #echo ' '.join($annotations.__str__.split(','))
24 #end if 34 #end if
25 #if $filterOut and $filterOut.__str__ != '': 35 #if $filterOut and $filterOut.__str__ != '':
26 #echo " " 36 #echo " "
27 #echo ' '.join($filterOut.__str__.split(',')) 37 #echo ' '.join($filterOut.__str__.split(','))
28 #end if 38 #end if
39 #if $filter.specificEffects == 'yes' and $filter.effects:
40 #for $eff in str($filter.effects).split(','):
41 -no $eff
42 #end for
43 #end if
29 #if str( $transcripts ) != 'None': 44 #if str( $transcripts ) != 'None':
30 -onlyTr $transcripts 45 -onlyTr $transcripts
31 #end if 46 #end if
32 #if str( $intervals ) != 'None': ### fix this for multiple dataset input 47 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
33 -interval $intervals 48 -interval $intervals
34 #end if 49 #end if
35 #if $statsFile: 50 #if $statsFile:
36 -stats $statsFile 51 -stats $statsFile
37 #end if 52 #end if
38 #if $offset.__str__ != 'default': 53 #if $offset.__str__ != 'default':
39 ${offset} 54 ${offset}
40 #end if 55 #end if
41 #if $chr.__str__.strip() != '': 56 #if $chr.__str__.strip() != '':
42 -chr "$chr" 57 -chr "$chr"
43 #end if 58 #end if
44 $noLog 59 $noLog
45 #if $snpDb.genomeSrc == 'cached': 60 #if $snpDb.genomeSrc == 'cached':
46 -dataDir ${snpDb.genomeVersion.fields.path} 61 -dataDir ${snpDb.genomeVersion.fields.path}
47 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': 62 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
48 #echo " " 63 #echo " "
49 #echo ' '.join($snpDb.extra_annotations.__str__.split(',')) 64 #echo ' '.join($snpDb.extra_annotations.__str__.split(','))
61 #end if 76 #end if
62 #if $snpDb.regulation and $snpDb.regulation.__str__ != '': 77 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
63 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# 78 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
64 #end if 79 #end if
65 ${snpDb.snpeff_db.metadata.genome_version} 80 ${snpDb.snpeff_db.metadata.genome_version}
66 #else 81 #else
67 -download 82 -download
68 $snpDb.genome_version 83 $snpDb.genome_version
69 #end if 84 #end if
70 $input > $snpeff_output ; 85 $input > $snpeff_output ;
71 #if $statsFile: 86 #if $statsFile:
75 mkdir $statsFile.files_path; 90 mkdir $statsFile.files_path;
76 mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#; 91 mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#;
77 #end if 92 #end if
78 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 93 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
79 ## 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]" 94 ## 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]"
80 sed -i 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output 95 sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output
81 #end if 96 #end if
82 ]]> 97 ]]>
83 </command> 98 </command>
84 <inputs> 99 <inputs>
85 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> 100 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
86 101
87 <param name="inputFormat" type="select" label="Input format"> 102 <param name="inputFormat" type="select" label="Input format">
88 <option value="vcf" selected="true">VCF</option> 103 <option value="vcf" selected="true">VCF</option>
89 <option value="txt">Tabular (Deprecated)</option>
90 <option value="pileup">Pileup (Deprecated)</option>
91 <option value="bed">BED (Deprecated)</option> 104 <option value="bed">BED (Deprecated)</option>
92 </param> 105 </param>
93 106
94 <conditional name="outputConditional"> 107 <conditional name="outputConditional">
95 <param name="outputFormat" type="select" label="Output format"> 108 <param name="outputFormat" type="select" label="Output format">
96 <option value="vcf" selected="true">VCF (only if input is VCF)</option> 109 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
97 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option> 110 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
98 <option value="txt">Tabular</option>
99 <option value="bed">BED</option> 111 <option value="bed">BED</option>
100 <option value="bedAnn">BED annotations</option> 112 <option value="bedAnn">BED annotations</option>
101 </param> 113 </param>
102 <when value="vcf" /> 114 <when value="vcf" />
103 <when value="gatk"> 115 <when value="gatk">
104 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" /> 116 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
105 </when> 117 </when>
106 <when value="txt" />
107 <when value="bed" /> 118 <when value="bed" />
108 <when value="bedAnn" /> 119 <when value="bedAnn" />
109 </conditional> 120 </conditional>
110 121
111 <conditional name="snpDb"> 122 <conditional name="snpDb">
157 <filter type="data_meta" ref="snpeff_db" key="regulation" /> 168 <filter type="data_meta" ref="snpeff_db" key="regulation" />
158 </options> 169 </options>
159 </param> 170 </param>
160 </when> 171 </when>
161 <when value="named"> 172 <when value="named">
162 <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> 173 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
163 <help>@SNPEFF_DATABASE_URL@</help> 174 <help>@SNPEFF_DATABASE_URL@</help>
164 <validator type="regex" message="A genome version name is required">\S+</validator> 175 <validator type="regex" message="A genome version name is required">\S+</validator>
165 </param> 176 </param>
166 </when> 177 </when>
167 </conditional> 178 </conditional>
187 <option value="7">7 bases</option> 198 <option value="7">7 bases</option>
188 <option value="8">8 bases</option> 199 <option value="8">8 bases</option>
189 <option value="9">9 bases</option> 200 <option value="9">9 bases</option>
190 </param> 201 </param>
191 202
203 <conditional name="spliceRegion">
204 <param name="setSpliceRegions" type="select" label="spliceRegion Settings">
205 <option value="no">Use Defaults</option>
206 <option value="yes">Set Splice Region Parameters</option>
207 </param>
208 <when value="no"/>
209 <when value="yes">
210 <param name="spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases"/>
211 <param name="spliceRegionIntronMin" type="integer" value="" min="1" max="10" optional="true" label="Set minimum number of bases for splice site region within intron. Default: 3 bases"/>
212 <param name="spliceRegionIntronMax" type="integer" value="" min="1" max="10" optional="true" label="Set maximum number of bases for splice site region within intron. Default: 8 bases"/>
213 </when>
214 </conditional>
215
192 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes"> 216 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
193 <option value="no_filter" selected="true">No filter (analyze everything)</option> 217 <option value="no_filter" selected="true">No filter (analyze everything)</option>
194 <option value="-hom">Analyze homozygous sequence changes only</option> 218 <option value="-hom">Analyze homozygous sequence changes only</option>
195 <option value="-het">Analyze heterozygous sequence changes only</option> 219 <option value="-het">Analyze heterozygous sequence changes only</option>
196 </param>
197
198 <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation -->
199 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
200 <option value="no_filter" selected="true">No filter (analyze everything)</option>
201 <option value="-del">Analyze deletions only</option>
202 <option value="-ins">Analyze insertions only</option>
203 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms)</option>
204 <option value="-snp">Only SNPs (single nucleotide polymorphisms)</option>
205 </param> 220 </param>
206 221
207 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> 222 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
208 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> 223 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
209 <option value="-canon">Only use canonical transcripts</option> 224 <option value="-canon">Only use canonical transcripts</option>
212 <option value="-oicr">Add OICR tag in VCF file</option> 227 <option value="-oicr">Add OICR tag in VCF file</option>
213 <option value="-onlyReg">Only use regulation tracks</option> 228 <option value="-onlyReg">Only use regulation tracks</option>
214 <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> 229 <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>
215 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option> 230 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
216 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option> 231 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
217 </param> 232 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN').</option>
233 <option value="-noHgvs">Do not add HGVS annotations.</option>
234 <option value="-noLof">Do not add LOF and NMD annotations.</option>
235 <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end).</option>
236 <option value="-oicr">Add OICR tag in VCF file. Default: false</option>
237 </param>
238 <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. -->
218 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/> 239 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
219 <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."/> 240 <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."/>
220 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output"> 241 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
221 <option value="-no-downstream">Do not show DOWNSTREAM changes</option> 242 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
222 <option value="-no-intergenic">Do not show INTERGENIC changes</option> 243 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
223 <option value="-no-intron">Do not show INTRON changes</option> 244 <option value="-no-intron">Do not show INTRON changes</option>
224 <option value="-no-upstream">Do not show UPSTREAM changes</option> 245 <option value="-no-upstream">Do not show UPSTREAM changes</option>
225 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option> 246 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
226 </param> 247 </param>
248 <conditional name="filter">
249 <param name="specificEffects" type="select" label="Filter out specific Effects">
250 <option value="no">No</option>
251 <option value="yes">Yes</option>
252 </param>
253 <when value="no"/>
254 <when value="yes">
255 <param name="effects" type="select" display="checkboxes" multiple="true" label="Filter output: do not report these Effects">
256 <option value="CDS">CDS (coding_sequence_variant) The variant hits a CDS. MODIFIER</option>
257 <option value="CHROMOSOME_LARGE_DELETION">CHROMOSOME_LARGE_DELETION (chromosome) A large parte (over 1%) of the chromosome was deleted. HIGH</option>
258 <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>
259 <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>
260 <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>
261 <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>
262 <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>
263 <option value="DOWNSTREAM">DOWNSTREAM (downstream_gene_variant) Downstream of a gene (default length: 5K bases) MODIFIER</option>
264 <option value="EXON">EXON (exon_variant) The variant hits an exon (from a non-coding transcript) or a retained intron. MODIFIER</option>
265 <option value="EXON_DELETED">EXON_DELETED (exon_loss_variant) A deletion removes the whole exon. HIGH</option>
266 <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>
267 <option value="GENE">GENE (gene_variant) The variant hits a gene. MODIFIER</option>
268 <option value="INTERGENIC">INTERGENIC (intergenic_region) The variant is in an intergenic region MODIFIER</option>
269 <option value="INTERGENIC_CONSERVED">INTERGENIC_CONSERVED (conserved_intergenic_variant) The variant is in a highly conserved intergenic region MODIFIER</option>
270 <option value="INTRAGENIC">INTRAGENIC (intragenic_variant) The variant hits a gene, but no transcripts within the gene MODIFIER</option>
271 <option value="INTRON">INTRON (intron_variant) Variant hits and intron. Technically, hits no exon in the transcript. MODIFIER</option>
272 <option value="INTRON_CONSERVED">INTRON_CONSERVED (conserved_intron_variant) The variant is in a highly conserved intronic region MODIFIER</option>
273 <option value="MICRO_RNA">MICRO_RNA (miRNA) Variant affects an miRNA MODIFIER</option>
274 <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>
275 <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>
276 <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>
277 <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>
278 <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>
279 <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>
280 <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>
281 <option value="SPLICE_SITE_BRANCH">SPLICE_SITE_BRANCH (splice_region_variant) A varaint affective putative (Lariat) branch point, located in the intron. LOW</option>
282 <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>
283 <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>
284 <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>
285 <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>
286 <option value="STOP_GAINED">STOP_GAINED (stop_gained) Variant causes a STOP codon e.g.: Cag/Tag, Q/* HIGH</option>
287 <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>
288 <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>
289 <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>
290 <option value="TRANSCRIPT">TRANSCRIPT (transcript_variant) The variant hits a transcript. MODIFIER</option>
291 <option value="REGULATION">REGULATION (regulatory_region_variant) The variant hits a known regulatory feature (non-coding). MODIFIER</option>
292 <option value="UPSTREAM">UPSTREAM (upstream_gene_variant) Upstream of a gene (default length: 5K bases) MODIFIER</option>
293 <option value="UTR_3_PRIME">UTR_3_PRIME (3_prime_UTR_variant) Variant hits 3'UTR region MODIFIER</option>
294 <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>
295 <option value="UTR_5_PRIME">UTR_5_PRIME (5_prime_UTR_variant) Variant hits 5'UTR region MODIFIER</option>
296 <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>
297 <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>
298
299 </param>
300 </when>
301 </conditional>
227 302
228 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> 303 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
229 <option value="default" selected="true">Use default (based on input type)</option> 304 <option value="default" selected="true">Use default (based on input type)</option>
230 <option value="-0">Force zero-based positions (both input and output)</option> 305 <option value="-0">Force zero-based positions (both input and output)</option>
231 <option value="-1">Force one-based positions (both input and output)</option> 306 <option value="-1">Force one-based positions (both input and output)</option>
241 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/> 316 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
242 </inputs> 317 </inputs>
243 <outputs> 318 <outputs>
244 <data format="vcf" name="snpeff_output" > 319 <data format="vcf" name="snpeff_output" >
245 <change_format> 320 <change_format>
246 <when input="outputConditional.outputFormat" value="txt" format="tabular" />
247 <when input="outputConditional.outputFormat" value="bed" format="bed" /> 321 <when input="outputConditional.outputFormat" value="bed" format="bed" />
248 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> 322 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
249 </change_format> 323 </change_format>
250 </data> 324 </data>
251 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats"> 325 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">
252 <filter>generate_stats == True</filter> 326 <filter>generate_stats == True</filter>
253 </data> 327 </data>
254 </outputs> 328 </outputs>
255 <expand macro="stdio" />
256 <tests> 329 <tests>
257 <!-- Check that an effect was added in out VCF --> 330 <!-- Check that an effect was added in out VCF -->
258 <!-- Check for a HTML header indicating that this was successful --> 331 <!-- Check for a HTML header indicating that this was successful -->
259 <!-- 332 <!--
260 <output name="statsFile"> 333 <output name="statsFile">
261 <assert_contents> 334 <assert_contents>
262 <has_text text="SnpEff: Variant analysis" /> 335 <has_text text="SnpEff: Variant analysis" />
263 </assert_contents> 336 </assert_contents>
264 </output> 337 </output>
265 --> 338 -->
266 <!-- Setting filterOut throws exception in twilltestcase.py 339 <!-- Setting filterOut throws exception in twilltestcase.py
267 <test> 340 <test>
268 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> 341 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
269 <param name="inputFormat" value="vcf"/> 342 <param name="inputFormat" value="vcf"/>
270 <param name="outputFormat" value="vcf"/> 343 <param name="outputFormat" value="vcf"/>
271 <param name="genomeSrc" value="named"/> 344 <param name="genomeSrc" value="named"/>
272 <param name="genome_version" value="testCase"/> 345 <param name="genome_version" value="testCase"/>
273 <param name="udLength" value="0"/> 346 <param name="udLength" value="0"/>
274 <param name="filterHomHet" value="no_filter"/> 347 <param name="filterHomHet" value="no_filter"/>
275 <param name="filterIn" value="no_filter"/>
276 <param name="generate_stats" value="False"/> 348 <param name="generate_stats" value="False"/>
277 <param name="filterOut" value="+-no-upstream"/> 349 <param name="filterOut" value="+-no-upstream"/>
278 <output name="snpeff_output"> 350 <output name="snpeff_output">
279 <assert_contents> 351 <assert_contents>
280 <has_text text="EFF=" /> 352 <has_text text="EFF=" />
281 </assert_contents> 353 </assert_contents>
282 </output> 354 </output>
283 </test> 355 </test>
284 --> 356 -->
285 357
286 <test> 358 <test>
287 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> 359 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
288 <param name="inputFormat" value="vcf"/> 360 <param name="inputFormat" value="vcf"/>
289 <param name="outputFormat" value="vcf"/> 361 <param name="outputFormat" value="vcf"/>
290 <param name="genomeSrc" value="named"/> 362 <param name="genomeSrc" value="named"/>
291 <param name="genome_version" value="testCase"/> 363 <param name="genome_version" value="testCase"/>
292 <param name="udLength" value="0"/> 364 <param name="udLength" value="0"/>
293 <param name="filterHomHet" value="+-het"/> 365 <param name="filterHomHet" value="+-het"/>
294 <param name="filterIn" value="no_filter"/>
295 <!-- 366 <!--
296 <param name="filterOut" value=""/> 367 <param name="filterOut" value=""/>
297 --> 368 -->
298 <param name="generate_stats" value="False"/> 369 <param name="generate_stats" value="False"/>
299 <output name="snpeff_output"> 370 <output name="snpeff_output">
310 <param name="outputFormat" value="vcf"/> 381 <param name="outputFormat" value="vcf"/>
311 <param name="genomeSrc" value="named"/> 382 <param name="genomeSrc" value="named"/>
312 <param name="genome_version" value="testCase"/> 383 <param name="genome_version" value="testCase"/>
313 <param name="udLength" value="0"/> 384 <param name="udLength" value="0"/>
314 <param name="filterHomHet" value="no_filter"/> 385 <param name="filterHomHet" value="no_filter"/>
315 <param name="filterIn" value="+-del"/>
316 <!-- 386 <!--
317 <param name="filterOut" value=""/> 387 <param name="filterOut" value=""/>
318 --> 388 -->
319 <param name="generate_stats" value="False"/> 389 <param name="generate_stats" value="False"/>
320 <output name="snpeff_output"> 390 <output name="snpeff_output">
335 <param name="outputFormat" value="vcf"/> 405 <param name="outputFormat" value="vcf"/>
336 <param name="genomeSrc" value="named"/> 406 <param name="genomeSrc" value="named"/>
337 <param name="genome_version" value="testCase"/> 407 <param name="genome_version" value="testCase"/>
338 <param name="udLength" value="0"/> 408 <param name="udLength" value="0"/>
339 <param name="filterHomHet" value="no_filter"/> 409 <param name="filterHomHet" value="no_filter"/>
340 <param name="filterIn" value="no_filter"/>
341 <param name="filterOut" value="+-no-upstream"/> 410 <param name="filterOut" value="+-no-upstream"/>
342 <param name="generate_stats" value="False"/> 411 <param name="generate_stats" value="False"/>
343 <output name="snpeff_output"> 412 <output name="snpeff_output">
344 <assert_contents> 413 <assert_contents>
345 <not_has_text text="UPSTREAM" /> 414 <not_has_text text="UPSTREAM" />
347 </output> 416 </output>
348 </test> 417 </test>
349 --> 418 -->
350 419
351 </tests> 420 </tests>
352 <help> 421 <help><![CDATA[
353 422
354 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. 423 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
355 424
356 @EXTERNAL_DOCUMENTATION@ 425 @EXTERNAL_DOCUMENTATION@
357 426
358 @CITATION_SECTION@ 427 @CITATION_SECTION@
359 428
429 ]]>
360 </help> 430 </help>
361 <expand macro="citations" /> 431 <expand macro="citations" />
362 </tool> 432 </tool>
363 433