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comparison snpEff.xml @ 7:7adfd0589f49 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
author iuc
date Tue, 18 Apr 2017 09:33:56 -0400
parents 2950d5afa3fe
children ce135864629c
comparison
equal deleted inserted replaced
6:20f0429a4bfe 7:7adfd0589f49
4 <import>snpEff_macros.xml</import> 4 <import>snpEff_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command> 9 <command><![CDATA[
10 <![CDATA[ 10 snpEff -Xmx8g eff
11 @CONDA_SNPEFF_JAR_PATH@ &&
12 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff
13 -c "\$SNPEFF_JAR_PATH/snpEff.config"
14 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength 11 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
15 #if $spliceSiteSize and str($spliceSiteSize) != '': 12 #if $spliceSiteSize and str($spliceSiteSize) != '':
16 -spliceSiteSize "$spliceSiteSize" 13 -spliceSiteSize "$spliceSiteSize"
17 #end if 14 #end if
18 #if $spliceRegion.setSpliceRegions == 'yes': 15 #if $spliceRegion.setSpliceRegions == 'yes':
19 #if $spliceRegion.spliceRegionExonSize and str($spliceRegion.spliceRegionExonSize) != '': 16 #if str($spliceRegion.spliceRegionExonSize)
20 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize 17 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
21 #end if 18 #end if
22 #if $spliceRegion.spliceRegionIntronMin and str($spliceRegion.spliceRegionIntronMin) != '': 19 #if str($spliceRegion.spliceRegionIntronMin)
23 -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin 20 -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
24 #end if 21 #end if
25 #if $spliceRegion.spliceRegionIntronMax and str($spliceRegion.spliceRegionIntronMax) != '': 22 #if str($spliceRegion.spliceRegionIntronMax)
26 -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax 23 -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax
27 #end if 24 #end if
28 #end if 25 #end if
29 #if $annotations and str($annotations) != '': 26 #if $annotations and str($annotations) != '':
30 #echo " " 27 #echo " "
37 #if $filter.specificEffects == 'yes' and $filter.effects: 34 #if $filter.specificEffects == 'yes' and $filter.effects:
38 #for $eff in str($filter.effects).split(','): 35 #for $eff in str($filter.effects).split(','):
39 -no $eff 36 -no $eff
40 #end for 37 #end for
41 #end if 38 #end if
42 #if str( $transcripts ) != 'None': 39 #if $transcripts
43 -onlyTr $transcripts 40 -onlyTr '$transcripts'
44 #end if 41 #end if
45 #if str( $intervals ) != 'None': ### fix this for multiple dataset input 42 #if $intervals ### fix this for multiple dataset input
46 -interval $intervals 43 -interval '$intervals'
47 #end if 44 #end if
48 #if $statsFile: 45 #if $statsFile:
49 -stats $statsFile 46 -stats '$statsFile'
50 #end if 47 #end if
51 #if str($offset) != 'default': 48 #if str($offset) != 'default':
52 ${offset} 49 ${offset}
53 #end if 50 #end if
54 #if str($chr).strip() != '': 51 #if str($chr).strip() != '':
55 -chr "$chr" 52 -chr '$chr'
56 #end if 53 #end if
57 $noLog 54 $noLog
55 ## Regulation names can include parentheses: H3K4me3-MSC_(VB)_enriched_sites
56 ## Enclose them in in single and double quotes, as the conda snpEff bash script will remove outer quotes
58 #if $snpDb.genomeSrc == 'cached': 57 #if $snpDb.genomeSrc == 'cached':
59 -dataDir ${snpDb.genomeVersion.fields.path} 58 -dataDir ${snpDb.genomeVersion.fields.path}
60 #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '': 59 #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != '':
61 #echo " " 60 #set $regs = [x for x in str($snpDb.reg_section.regulation).split(',')]
62 #echo ' '.join(str($snpDb.extra_annotations).split(',')) 61 #for reg in $regs:
63 #end if 62 -reg '"${reg}"'
64 #if $snpDb.regulation and str($snpDb.regulation) != '': 63 #end for
65 -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))#
66 #end if 64 #end if
67 $snpDb.genomeVersion 65 $snpDb.genomeVersion
68 #elif $snpDb.genomeSrc == 'history': 66 #elif $snpDb.genomeSrc == 'history':
69 -dataDir ${snpDb.snpeff_db.extra_files_path} 67 -dataDir '${snpDb.snpeff_db.extra_files_path}'
70 #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '': 68 #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != '':
71 #set xannotations = [' '] + str($snpDb.extra_annotations).split(',') 69 #set $regs = [x for x in str($snpDb.reg_section.regulation).split(',')]
72 #echo " " 70 #for reg in $regs:
73 #echo ' -'.join($xannotations) 71 -reg '"${reg}"'
74 #end if 72 #end for
75 #if $snpDb.regulation and str($snpDb.regulation) != '': 73 #end if
76 -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))# 74 '${snpDb.snpeff_db.metadata.genome_version}'
77 #end if
78 ${snpDb.snpeff_db.metadata.genome_version}
79 #else 75 #else
80 -download 76 -download
81 $snpDb.genome_version 77 '$snpDb.genome_version'
82 #end if 78 #end if
83 "$input" > "$snpeff_output"; 79 '$input' > '$snpeff_output'
84 #if $statsFile: 80 #if $statsFile:
81 &&
85 #import os 82 #import os
86 #set $genes_file = str($statsFile) + '.genes.txt' 83 #set $genes_file = str($statsFile) + '.genes.txt'
87 #set $genes_file_name = os.path.split($genes_file)[-1] 84 #set $genes_file_name = os.path.split($genes_file)[-1]
88 mkdir $statsFile.files_path; 85 mkdir '$statsFile.files_path' &&
89 mv "$genes_file" #echo os.path.join($statsFile.files_path, $genes_file_name)#; 86 mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#'
90 #end if 87 #end if
91 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 88 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
89 &&
92 ## 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]" 90 ## 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]"
93 sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output" 91 sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' '$snpeff_output'
94 #end if 92 #end if
95 ]]> 93 ]]></command>
96 </command>
97 <inputs> 94 <inputs>
98 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> 95 <param name="input" type="data" format="vcf,tabular,pileup,bed" label="Sequence changes (SNPs, MNPs, InDels)"/>
99 96
100 <param name="inputFormat" type="select" label="Input format"> 97 <param name="inputFormat" type="select" label="Input format">
101 <option value="vcf" selected="true">VCF</option> 98 <option value="vcf" selected="true">VCF</option>
102 <option value="bed">BED (Deprecated)</option> 99 <option value="bed">BED (Deprecated)</option>
103 </param> 100 </param>
125 </param> 122 </param>
126 <when value="cached"> 123 <when value="cached">
127 <param name="genomeVersion" type="select" label="Genome"> 124 <param name="genomeVersion" type="select" label="Genome">
128 <!--GENOME DESCRIPTION--> 125 <!--GENOME DESCRIPTION-->
129 <options from_data_table="snpeffv_genomedb"> 126 <options from_data_table="snpeffv_genomedb">
130 <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/> 127 <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/>
131 <filter type="unique_value" column="2" /> 128 <filter type="unique_value" column="2" />
132 </options> 129 </options>
133 </param> 130 </param>
134 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> 131 <section name="reg_section" expanded="false" title="Regulation options">
135 <help>These are available for only a few genomes</help> 132 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes">
136 <options from_data_table="snpeffv_annotations"> 133 <options from_data_table="snpeffv_regulationdb">
137 <filter type="param_value" ref="genomeVersion" key="genome" column="2" /> 134 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
138 <filter type="unique_value" column="3" /> 135 <filter type="unique_value" column="3" />
139 </options> 136 </options>
140 </param> 137 </param>
141 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation"> 138 </section>
142 <help>These are available for only a few genomes</help>
143 <options from_data_table="snpeffv_regulationdb">
144 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
145 <filter type="unique_value" column="3" />
146 </options>
147 </param>
148 </when> 139 </when>
149 <when value="history"> 140 <when value="history">
150 <param format="snpeffdb" name="snpeff_db" type="data" label="@SNPEFF_VERSION@ Genome Data"> 141 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
151 <options options_filter_attribute="metadata.snpeff_version" > 142 <options options_filter_attribute="metadata.snpeff_version" >
152 <filter type="add_value" value="@SNPEFF_VERSION@" /> 143 <filter type="add_value" value="@SNPEFF_VERSION@" />
153 </options> 144 </options>
154 <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ Genome databases.">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator> 145 <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
155 </param> 146 </param>
156 <!-- From metadata --> 147 <section name="reg_section" expanded="false" title="Regulation options">
157 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> 148 <!-- From metadata -->
158 <help>These are available for only a few genomes</help> 149 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes">
159 <options> 150 <options>
160 <filter type="data_meta" ref="snpeff_db" key="annotation" /> 151 <filter type="data_meta" ref="snpeff_db" key="regulation" />
161 </options> 152 </options>
162 </param> 153 </param>
163 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation"> 154 </section>
164 <help>These are available for only a few genomes</help>
165 <options>
166 <filter type="data_meta" ref="snpeff_db" key="regulation" />
167 </options>
168 </param>
169 </when> 155 </when>
170 <when value="named"> 156 <when value="named">
171 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> 157 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
172 <help>@SNPEFF_DATABASE_URL@</help> 158 <help>@SNPEFF_DATABASE_URL@</help>
173 <validator type="regex" message="A genome version name is required">\S+</validator> 159 <validator type="regex" message="A genome version name is required">\S+</validator>
184 <option value="5000" selected="true">5000 bases</option> 170 <option value="5000" selected="true">5000 bases</option>
185 <option value="10000">10000 bases</option> 171 <option value="10000">10000 bases</option>
186 <option value="20000">20000 bases</option> 172 <option value="20000">20000 bases</option>
187 </param> 173 </param>
188 174
189 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2"> 175 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases">
190 <option value="1">1 base</option> 176 <option value="1">1 base</option>
191 <option value="2" selected="true">2 bases</option> 177 <option value="2" selected="true">2 bases</option>
192 <option value="3">3 bases</option> 178 <option value="3">3 bases</option>
193 <option value="4">4 bases</option> 179 <option value="4">4 bases</option>
194 <option value="5">5 bases</option> 180 <option value="5">5 bases</option>
210 <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"/> 196 <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"/>
211 </when> 197 </when>
212 </conditional> 198 </conditional>
213 199
214 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> 200 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
201 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN')</option>
202 <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>
203 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
204 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
205 <option value="-hgvsOld">Old notation style notation: E.g. 'c.G123T' instead of 'c.123G>T' and 'X' instead of '*'</option>
206 <option value="-hgvs1LetterAa">Use one letter Amino acid codes in HGVS notation. E.g. p.R47G instead of p.Arg47Gly</option>
207 <option value="-hgvsTrId">Use transcript ID in HGVS notation. E.g. ENST00000252100:c.914C>G instead of c.914C>G</option>
208 <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end)</option>
209 <option value="-noHgvs">Do not add HGVS annotations</option>
210 <option value="-canon">Only use canonical transcripts</option>
211 <option value="-onlyProtein">Only use protein coding transcripts</option>
212 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
213 <option value="-noExpandIUB">Disable IUB code expansion in input variants</option>
214 <option value="-oicr">Add OICR tag in VCF file</option>
215 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
216 <option value="-noLof">Do not add LOF and NMD annotations</option>
217 <option value="-noMotif">Disable motif annotations</option>
218 <option value="-noNextProt">Disable NextProt annotations</option>
219 <option value="-noInteraction">Disable interaction annotations</option>
215 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> 220 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
216 <option value="-canon">Only use canonical transcripts</option> 221 <!-- onlyReg option results in ifrequent exceptions with version 4.3k
217 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
218 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
219 <option value="-oicr">Add OICR tag in VCF file</option>
220 <option value="-onlyReg">Only use regulation tracks</option> 222 <option value="-onlyReg">Only use regulation tracks</option>
221 <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> 223 -->
222 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
223 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
224 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN').</option>
225 <option value="-noHgvs">Do not add HGVS annotations.</option>
226 <option value="-noLof">Do not add LOF and NMD annotations.</option>
227 <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end).</option>
228 <option value="-oicr">Add OICR tag in VCF file. Default: false</option>
229 </param> 224 </param>
230 <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. --> 225 <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. -->
231 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/> 226 <param name="intervals" type="data" format="bed" optional="true" label="Use custom interval file for annotation"/>
232 <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."/> 227 <param name="transcripts" type="data" format="tabular" optional="true" label="Only use the transcripts in this file" help="Format is one transcript ID per line"/>
233 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output"> 228 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
234 <option value="-no-downstream">Do not show DOWNSTREAM changes</option> 229 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
235 <option value="-no-intergenic">Do not show INTERGENIC changes</option> 230 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
236 <option value="-no-intron">Do not show INTRON changes</option> 231 <option value="-no-intron">Do not show INTRON changes</option>
237 <option value="-no-upstream">Do not show UPSTREAM changes</option> 232 <option value="-no-upstream">Do not show UPSTREAM changes</option>
285 <option value="UTR_3_PRIME">UTR_3_PRIME (3_prime_UTR_variant) Variant hits 3'UTR region MODIFIER</option> 280 <option value="UTR_3_PRIME">UTR_3_PRIME (3_prime_UTR_variant) Variant hits 3'UTR region MODIFIER</option>
286 <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> 281 <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>
287 <option value="UTR_5_PRIME">UTR_5_PRIME (5_prime_UTR_variant) Variant hits 5'UTR region MODIFIER</option> 282 <option value="UTR_5_PRIME">UTR_5_PRIME (5_prime_UTR_variant) Variant hits 5'UTR region MODIFIER</option>
288 <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> 283 <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>
289 <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> 284 <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>
290
291 </param> 285 </param>
292 </when> 286 </when>
293 </conditional> 287 </conditional>
294 288
295 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> 289 <param name="offset" type="select" display="radio" label="Chromosomal position">
296 <option value="default" selected="true">Use default (based on input type)</option> 290 <option value="default" selected="true">Use default (based on input type)</option>
297 <option value="-0">Force zero-based positions (both input and output)</option> 291 <option value="-0">Force zero-based positions (both input and output)</option>
298 <option value="-1">Force one-based positions (both input and output)</option> 292 <option value="-1">Force one-based positions (both input and output)</option>
299 </param> 293 </param>
300 <param name="chr" type="text" label="Text to prepend to chromosome name"> 294 <param name="chr" type="text" label="Text to prepend to chromosome name">
301 <help> 295 <help>
302 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. 296 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
303 You can prepend any string you want to the chromosome name. 297 You can prepend any string you want to the chromosome name
304 </help> 298 </help>
305 <validator type="regex" message="No whitespace allowed">^\S*$</validator> 299 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
306 </param> 300 </param>
307 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/> 301 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
308 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server"/> 302 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server"/>
309 </inputs> 303 </inputs>
310 <outputs> 304 <outputs>
311 <data format="vcf" name="snpeff_output" > 305 <data name="snpeff_output" format="vcf">
312 <change_format> 306 <change_format>
313 <when input="outputConditional.outputFormat" value="bed" format="bed" /> 307 <when input="outputConditional.outputFormat" value="bed" format="bed" />
314 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> 308 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
315 </change_format> 309 </change_format>
316 </data> 310 </data>
317 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats"> 311 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - stats">
318 <filter>generate_stats == True</filter> 312 <filter>generate_stats == True</filter>
319 </data> 313 </data>
320 </outputs> 314 </outputs>
321 <tests> 315 <tests>
322 <!-- Check that an effect was added in out VCF -->
323 <!-- Check for a HTML header indicating that this was successful -->
324 <!--
325 <output name="statsFile">
326 <assert_contents>
327 <has_text text="SnpEff: Variant analysis" />
328 </assert_contents>
329 </output>
330 -->
331 <!-- Setting filterOut throws exception in twilltestcase.py
332 <test> 316 <test>
333 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> 317 <param name="input" ftype="vcf" value="input.vcf"/>
334 <param name="inputFormat" value="vcf"/> 318 <param name="inputFormat" value="vcf"/>
335 <param name="outputFormat" value="vcf"/> 319 <param name="outputFormat" value="vcf"/>
336 <param name="genomeSrc" value="named"/> 320 <param name="genomeSrc" value="named"/>
337 <param name="genome_version" value="testCase"/> 321 <param name="genome_version" value="ebola_zaire"/>
338 <param name="udLength" value="0"/> 322 <param name="udLength" value="0"/>
339 <param name="generate_stats" value="False"/> 323 <param name="generate_stats" value="False"/>
340 <param name="filterOut" value="+-no-upstream"/> 324 <output name="snpeff_output">
341 <output name="snpeff_output"> 325 <assert_contents>
342 <assert_contents> 326 <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
343 <has_text text="EFF=" /> 327 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
344 </assert_contents> 328 </assert_contents>
345 </output> 329 </output>
346 </test> 330 </test>
347 -->
348
349 <test>
350 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
351 <param name="inputFormat" value="vcf"/>
352 <param name="outputFormat" value="vcf"/>
353 <param name="genomeSrc" value="named"/>
354 <param name="genome_version" value="testCase"/>
355 <param name="udLength" value="0"/>
356 <!--
357 <param name="filterOut" value=""/>
358 -->
359 <param name="generate_stats" value="False"/>
360 <output name="snpeff_output">
361 <assert_contents>
362 <!-- Check that deleletions were evaluated -->
363 <has_text_matching expression="Y\t59030478\t.*intergenic_region" />
364 <!-- Check that insertion on last line was NOT evaluated -->
365 <has_text_matching expression="Y\t59032947\t.*\tGT" />
366 </assert_contents>
367 </output>
368 </test>
369
370 <!-- Check that NO UPSTREAM effect was added -->
371 <!-- Setting filterOut throws exception in twilltestcase.py
372 <test>
373 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
374 <param name="inputFormat" value="vcf"/>
375 <param name="outputFormat" value="vcf"/>
376 <param name="genomeSrc" value="named"/>
377 <param name="genome_version" value="testCase"/>
378 <param name="udLength" value="0"/>
379 <param name="filterOut" value="+-no-upstream"/>
380 <param name="generate_stats" value="False"/>
381 <output name="snpeff_output">
382 <assert_contents>
383 <not_has_text text="UPSTREAM" />
384 </assert_contents>
385 </output>
386 </test>
387 -->
388
389 </tests> 331 </tests>
390 <help><![CDATA[ 332 <help><![CDATA[
391
392 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. 333 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
393 334
394 @EXTERNAL_DOCUMENTATION@ 335 @EXTERNAL_DOCUMENTATION@
395
396 ]]> 336 ]]>
397 </help> 337 </help>
398 <expand macro="citations" /> 338 <expand macro="citations" />
399 </tool> 339 </tool>
400