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comparison snpEff.xml @ 7:aaa749ea91a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
author iuc
date Tue, 07 Jun 2016 09:40:10 -0400
parents 9ec1cb6f760d
children 1501e66908de
comparison
equal deleted inserted replaced
6:9ec1cb6f760d 7:aaa749ea91a2
1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.1"> 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 <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" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" />
8 <command> 9 <command>
9 <![CDATA[ 10 <![CDATA[
10 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff 11 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff
11 -c \$SNPEFF_JAR_PATH/snpEff.config 12 -c "\$SNPEFF_JAR_PATH/snpEff.config"
12 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength 13 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
13 #if $spliceSiteSize and $spliceSiteSize.__str__ != '': 14 #if $spliceSiteSize and str($spliceSiteSize) != '':
14 -spliceSiteSize $spliceSiteSize 15 -spliceSiteSize "$spliceSiteSize"
15 #end if 16 #end if
16 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': 17 #if $spliceRegion.setSpliceRegions == 'yes':
17 $filterHomHet 18 #if $spliceRegion.spliceRegionExonSize and str($spliceRegion.spliceRegionExonSize) != '':
18 #end if 19 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
19 #if $annotations and $annotations.__str__ != '': 20 #end if
21 #if $spliceRegion.spliceRegionIntronMin and str($spliceRegion.spliceRegionIntronMin) != '':
22 -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
23 #end if
24 #if $spliceRegion.spliceRegionIntronMax and str($spliceRegion.spliceRegionIntronMax) != '':
25 -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax
26 #end if
27 #end if
28 #if $annotations and str($annotations) != '':
20 #echo " " 29 #echo " "
21 #echo ' '.join($annotations.__str__.split(',')) 30 #echo ' '.join(str($annotations).split(','))
22 #end if 31 #end if
23 #if $filterOut and $filterOut.__str__ != '': 32 #if $filterOut and str($filterOut) != '':
24 #echo " " 33 #echo " "
25 #echo ' '.join($filterOut.__str__.split(',')) 34 #echo ' '.join(str($filterOut).split(','))
26 #end if 35 #end if
27 #if $filter.specificEffects == 'yes' and $filter.effects: 36 #if $filter.specificEffects == 'yes' and $filter.effects:
28 #for $eff in str($filter.effects).split(','): 37 #for $eff in str($filter.effects).split(','):
29 -no $eff 38 -no $eff
30 #end for 39 #end for
36 -interval $intervals 45 -interval $intervals
37 #end if 46 #end if
38 #if $statsFile: 47 #if $statsFile:
39 -stats $statsFile 48 -stats $statsFile
40 #end if 49 #end if
41 #if $offset.__str__ != 'default': 50 #if str($offset) != 'default':
42 ${offset} 51 ${offset}
43 #end if 52 #end if
44 #if $chr.__str__.strip() != '': 53 #if str($chr).strip() != '':
45 -chr "$chr" 54 -chr "$chr"
46 #end if 55 #end if
47 $noLog 56 $noLog
48 #if $snpDb.genomeSrc == 'cached': 57 #if $snpDb.genomeSrc == 'cached':
49 -dataDir ${snpDb.genomeVersion.fields.path} 58 -dataDir ${snpDb.genomeVersion.fields.path}
50 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': 59 #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '':
51 #echo " " 60 #echo " "
52 #echo ' '.join($snpDb.extra_annotations.__str__.split(',')) 61 #echo ' '.join(str($snpDb.extra_annotations).split(','))
53 #end if 62 #end if
54 #if $snpDb.regulation and $snpDb.regulation.__str__ != '': 63 #if $snpDb.regulation and str($snpDb.regulation) != '':
55 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# 64 -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))#
56 #end if 65 #end if
57 $snpDb.genomeVersion 66 $snpDb.genomeVersion
58 #elif $snpDb.genomeSrc == 'history': 67 #elif $snpDb.genomeSrc == 'history':
59 -dataDir ${snpDb.snpeff_db.extra_files_path} 68 -dataDir ${snpDb.snpeff_db.extra_files_path}
60 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': 69 #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '':
61 #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',') 70 #set xannotations = [' '] + str($snpDb.extra_annotations).split(',')
62 #echo " " 71 #echo " "
63 #echo ' -'.join($xannotations) 72 #echo ' -'.join($xannotations)
64 #end if 73 #end if
65 #if $snpDb.regulation and $snpDb.regulation.__str__ != '': 74 #if $snpDb.regulation and str($snpDb.regulation) != '':
66 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# 75 -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))#
67 #end if 76 #end if
68 ${snpDb.snpeff_db.metadata.genome_version} 77 ${snpDb.snpeff_db.metadata.genome_version}
69 #else 78 #else
70 -download 79 -download
71 $snpDb.genome_version 80 $snpDb.genome_version
72 #end if 81 #end if
73 $input > $snpeff_output ; 82 "$input" > "$snpeff_output";
74 #if $statsFile: 83 #if $statsFile:
75 #import os 84 #import os
76 #set $genes_file = str($statsFile) + '.genes.txt' 85 #set $genes_file = str($statsFile) + '.genes.txt'
77 #set $genes_file_name = os.path.split($genes_file)[-1] 86 #set $genes_file_name = os.path.split($genes_file)[-1]
78 mkdir $statsFile.files_path; 87 mkdir $statsFile.files_path;
79 mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#; 88 mv "$genes_file" #echo os.path.join($statsFile.files_path, $genes_file_name)#;
80 #end if 89 #end if
81 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 90 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
82 ## 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]" 91 ## 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]"
83 sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output 92 sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output"
84 #end if 93 #end if
85 ]]> 94 ]]>
86 </command> 95 </command>
87 <inputs> 96 <inputs>
88 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> 97 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
89 98
90 <param name="inputFormat" type="select" label="Input format"> 99 <param name="inputFormat" type="select" label="Input format">
91 <option value="vcf" selected="true">VCF</option> 100 <option value="vcf" selected="true">VCF</option>
92 <option value="txt">Tabular (Deprecated)</option>
93 <option value="pileup">Pileup (Deprecated)</option>
94 <option value="bed">BED (Deprecated)</option> 101 <option value="bed">BED (Deprecated)</option>
95 </param> 102 </param>
96 103
97 <conditional name="outputConditional"> 104 <conditional name="outputConditional">
98 <param name="outputFormat" type="select" label="Output format"> 105 <param name="outputFormat" type="select" label="Output format">
99 <option value="vcf" selected="true">VCF (only if input is VCF)</option> 106 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
100 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option> 107 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
101 <option value="txt">Tabular</option>
102 <option value="bed">BED</option> 108 <option value="bed">BED</option>
103 <option value="bedAnn">BED annotations</option> 109 <option value="bedAnn">BED annotations</option>
104 </param> 110 </param>
105 <when value="vcf" /> 111 <when value="vcf" />
106 <when value="gatk"> 112 <when value="gatk">
107 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" /> 113 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
108 </when> 114 </when>
109 <when value="txt" />
110 <when value="bed" /> 115 <when value="bed" />
111 <when value="bedAnn" /> 116 <when value="bedAnn" />
112 </conditional> 117 </conditional>
113 118
114 <conditional name="snpDb"> 119 <conditional name="snpDb">
190 <option value="7">7 bases</option> 195 <option value="7">7 bases</option>
191 <option value="8">8 bases</option> 196 <option value="8">8 bases</option>
192 <option value="9">9 bases</option> 197 <option value="9">9 bases</option>
193 </param> 198 </param>
194 199
195 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes"> 200 <conditional name="spliceRegion">
196 <option value="no_filter" selected="true">No filter (analyze everything)</option> 201 <param name="setSpliceRegions" type="select" label="spliceRegion Settings">
197 <option value="-hom">Analyze homozygous sequence changes only</option> 202 <option value="no">Use Defaults</option>
198 <option value="-het">Analyze heterozygous sequence changes only</option> 203 <option value="yes">Set Splice Region Parameters</option>
199 </param> 204 </param>
205 <when value="no"/>
206 <when value="yes">
207 <param name="spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases"/>
208 <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"/>
209 <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"/>
210 </when>
211 </conditional>
200 212
201 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> 213 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
202 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> 214 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
203 <option value="-canon">Only use canonical transcripts</option> 215 <option value="-canon">Only use canonical transcripts</option>
204 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> 216 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
206 <option value="-oicr">Add OICR tag in VCF file</option> 218 <option value="-oicr">Add OICR tag in VCF file</option>
207 <option value="-onlyReg">Only use regulation tracks</option> 219 <option value="-onlyReg">Only use regulation tracks</option>
208 <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> 220 <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>
209 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option> 221 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
210 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option> 222 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
211 </param> 223 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN').</option>
224 <option value="-noHgvs">Do not add HGVS annotations.</option>
225 <option value="-noLof">Do not add LOF and NMD annotations.</option>
226 <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end).</option>
227 <option value="-oicr">Add OICR tag in VCF file. Default: false</option>
228 </param>
229 <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. -->
212 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/> 230 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
213 <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."/> 231 <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."/>
214 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output"> 232 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
215 <option value="-no-downstream">Do not show DOWNSTREAM changes</option> 233 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
216 <option value="-no-intergenic">Do not show INTERGENIC changes</option> 234 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
228 <param name="effects" type="select" display="checkboxes" multiple="true" label="Filter output: do not report these Effects"> 246 <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> 247 <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> 248 <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> 249 <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> 250 <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> 251 <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> 252 <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> 253 <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> 254 <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> 255 <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> 256 <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> 257 <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> 258 <option value="GENE">GENE (gene_variant) The variant hits a gene. MODIFIER</option>
284 You can prepend any string you want to the chromosome name. 302 You can prepend any string you want to the chromosome name.
285 </help> 303 </help>
286 <validator type="regex" message="No whitespace allowed">^\S*$</validator> 304 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
287 </param> 305 </param>
288 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/> 306 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
289 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/> 307 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server"/>
290 </inputs> 308 </inputs>
291 <outputs> 309 <outputs>
292 <data format="vcf" name="snpeff_output" > 310 <data format="vcf" name="snpeff_output" >
293 <change_format> 311 <change_format>
294 <when input="outputConditional.outputFormat" value="txt" format="tabular" />
295 <when input="outputConditional.outputFormat" value="bed" format="bed" /> 312 <when input="outputConditional.outputFormat" value="bed" format="bed" />
296 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> 313 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
297 </change_format> 314 </change_format>
298 </data> 315 </data>
299 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats"> 316 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">
316 <param name="inputFormat" value="vcf"/> 333 <param name="inputFormat" value="vcf"/>
317 <param name="outputFormat" value="vcf"/> 334 <param name="outputFormat" value="vcf"/>
318 <param name="genomeSrc" value="named"/> 335 <param name="genomeSrc" value="named"/>
319 <param name="genome_version" value="testCase"/> 336 <param name="genome_version" value="testCase"/>
320 <param name="udLength" value="0"/> 337 <param name="udLength" value="0"/>
321 <param name="filterHomHet" value="no_filter"/>
322 <param name="generate_stats" value="False"/> 338 <param name="generate_stats" value="False"/>
323 <param name="filterOut" value="+-no-upstream"/> 339 <param name="filterOut" value="+-no-upstream"/>
324 <output name="snpeff_output"> 340 <output name="snpeff_output">
325 <assert_contents> 341 <assert_contents>
326 <has_text text="EFF=" /> 342 <has_text text="EFF=" />
334 <param name="inputFormat" value="vcf"/> 350 <param name="inputFormat" value="vcf"/>
335 <param name="outputFormat" value="vcf"/> 351 <param name="outputFormat" value="vcf"/>
336 <param name="genomeSrc" value="named"/> 352 <param name="genomeSrc" value="named"/>
337 <param name="genome_version" value="testCase"/> 353 <param name="genome_version" value="testCase"/>
338 <param name="udLength" value="0"/> 354 <param name="udLength" value="0"/>
339 <param name="filterHomHet" value="+-het"/>
340 <!--
341 <param name="filterOut" value=""/>
342 -->
343 <param name="generate_stats" value="False"/>
344 <output name="snpeff_output">
345 <assert_contents>
346 <!-- Check that NO effects were added since -het is set -->
347 <not_has_text text="EFF=NON_SYNONYMOUS_CODING" />
348 </assert_contents>
349 </output>
350 </test>
351
352 <test>
353 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
354 <param name="inputFormat" value="vcf"/>
355 <param name="outputFormat" value="vcf"/>
356 <param name="genomeSrc" value="named"/>
357 <param name="genome_version" value="testCase"/>
358 <param name="udLength" value="0"/>
359 <param name="filterHomHet" value="no_filter"/>
360 <!-- 355 <!--
361 <param name="filterOut" value=""/> 356 <param name="filterOut" value=""/>
362 --> 357 -->
363 <param name="generate_stats" value="False"/> 358 <param name="generate_stats" value="False"/>
364 <output name="snpeff_output"> 359 <output name="snpeff_output">
378 <param name="inputFormat" value="vcf"/> 373 <param name="inputFormat" value="vcf"/>
379 <param name="outputFormat" value="vcf"/> 374 <param name="outputFormat" value="vcf"/>
380 <param name="genomeSrc" value="named"/> 375 <param name="genomeSrc" value="named"/>
381 <param name="genome_version" value="testCase"/> 376 <param name="genome_version" value="testCase"/>
382 <param name="udLength" value="0"/> 377 <param name="udLength" value="0"/>
383 <param name="filterHomHet" value="no_filter"/>
384 <param name="filterOut" value="+-no-upstream"/> 378 <param name="filterOut" value="+-no-upstream"/>
385 <param name="generate_stats" value="False"/> 379 <param name="generate_stats" value="False"/>
386 <output name="snpeff_output"> 380 <output name="snpeff_output">
387 <assert_contents> 381 <assert_contents>
388 <not_has_text text="UPSTREAM" /> 382 <not_has_text text="UPSTREAM" />
390 </output> 384 </output>
391 </test> 385 </test>
392 --> 386 -->
393 387
394 </tests> 388 </tests>
395 <help> 389 <help><![CDATA[
396 390
397 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. 391 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
398 392
399 @EXTERNAL_DOCUMENTATION@ 393 @EXTERNAL_DOCUMENTATION@
400 394
401 @CITATION_SECTION@ 395 ]]>
402
403 </help> 396 </help>
404 <expand macro="citations" /> 397 <expand macro="citations" />
405 </tool> 398 </tool>
406 399