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comparison snpEff.xml @ 23:924af057bbca draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
author jjohnson
date Sat, 09 Apr 2016 11:51:40 -0400
parents bb0797deab78
children
comparison
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22:bb0797deab78 23:924af057bbca
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>
10 <![CDATA[ 10 <![CDATA[
11 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff 11 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff
12 -c \$SNPEFF_JAR_PATH/snpEff.config 12 -c "\$SNPEFF_JAR_PATH/snpEff.config"
13 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength 13 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
14 #if $spliceSiteSize and $spliceSiteSize.__str__ != '': 14 #if $spliceSiteSize and str($spliceSiteSize) != '':
15 -spliceSiteSize $spliceSiteSize 15 -spliceSiteSize "$spliceSiteSize"
16 #end if 16 #end if
17 #if $spliceRegion.setSpliceRegions == 'yes': 17 #if $spliceRegion.setSpliceRegions == 'yes':
18 #if $spliceRegion.spliceRegionExonSize and $spliceRegion.spliceRegionExonSize.__str__ != '': 18 #if $spliceRegion.spliceRegionExonSize and str($spliceRegion.spliceRegionExonSize) != '':
19 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize 19 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
20 #end if 20 #end if
21 #if $spliceRegion.spliceRegionIntronMin and $spliceRegion.spliceRegionIntronMin.__str__ != '': 21 #if $spliceRegion.spliceRegionIntronMin and str($spliceRegion.spliceRegionIntronMin) != '':
22 -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin 22 -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
23 #end if 23 #end if
24 #if $spliceRegion.spliceRegionIntronMax and $spliceRegion.spliceRegionIntronMax.__str__ != '': 24 #if $spliceRegion.spliceRegionIntronMax and str($spliceRegion.spliceRegionIntronMax) != '':
25 -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax 25 -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax
26 #end if 26 #end if
27 #end if 27 #end if
28 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': 28 #if $annotations and str($annotations) != '':
29 $filterHomHet
30 #end if
31 #if $annotations and $annotations.__str__ != '':
32 #echo " " 29 #echo " "
33 #echo ' '.join($annotations.__str__.split(',')) 30 #echo ' '.join(str($annotations).split(','))
34 #end if 31 #end if
35 #if $filterOut and $filterOut.__str__ != '': 32 #if $filterOut and str($filterOut) != '':
36 #echo " " 33 #echo " "
37 #echo ' '.join($filterOut.__str__.split(',')) 34 #echo ' '.join(str($filterOut).split(','))
38 #end if 35 #end if
39 #if $filter.specificEffects == 'yes' and $filter.effects: 36 #if $filter.specificEffects == 'yes' and $filter.effects:
40 #for $eff in str($filter.effects).split(','): 37 #for $eff in str($filter.effects).split(','):
41 -no $eff 38 -no $eff
42 #end for 39 #end for
48 -interval $intervals 45 -interval $intervals
49 #end if 46 #end if
50 #if $statsFile: 47 #if $statsFile:
51 -stats $statsFile 48 -stats $statsFile
52 #end if 49 #end if
53 #if $offset.__str__ != 'default': 50 #if str($offset) != 'default':
54 ${offset} 51 ${offset}
55 #end if 52 #end if
56 #if $chr.__str__.strip() != '': 53 #if str($chr).strip() != '':
57 -chr "$chr" 54 -chr "$chr"
58 #end if 55 #end if
59 $noLog 56 $noLog
60 #if $snpDb.genomeSrc == 'cached': 57 #if $snpDb.genomeSrc == 'cached':
61 -dataDir ${snpDb.genomeVersion.fields.path} 58 -dataDir ${snpDb.genomeVersion.fields.path}
62 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': 59 #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '':
63 #echo " " 60 #echo " "
64 #echo ' '.join($snpDb.extra_annotations.__str__.split(',')) 61 #echo ' '.join(str($snpDb.extra_annotations).split(','))
65 #end if 62 #end if
66 #if $snpDb.regulation and $snpDb.regulation.__str__ != '': 63 #if $snpDb.regulation and str($snpDb.regulation) != '':
67 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# 64 -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))#
68 #end if 65 #end if
69 $snpDb.genomeVersion 66 $snpDb.genomeVersion
70 #elif $snpDb.genomeSrc == 'history': 67 #elif $snpDb.genomeSrc == 'history':
71 -dataDir ${snpDb.snpeff_db.extra_files_path} 68 -dataDir ${snpDb.snpeff_db.extra_files_path}
72 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': 69 #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '':
73 #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',') 70 #set xannotations = [' '] + str($snpDb.extra_annotations).split(',')
74 #echo " " 71 #echo " "
75 #echo ' -'.join($xannotations) 72 #echo ' -'.join($xannotations)
76 #end if 73 #end if
77 #if $snpDb.regulation and $snpDb.regulation.__str__ != '': 74 #if $snpDb.regulation and str($snpDb.regulation) != '':
78 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# 75 -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))#
79 #end if 76 #end if
80 ${snpDb.snpeff_db.metadata.genome_version} 77 ${snpDb.snpeff_db.metadata.genome_version}
81 #else 78 #else
82 -download 79 -download
83 $snpDb.genome_version 80 $snpDb.genome_version
84 #end if 81 #end if
85 $input > $snpeff_output ; 82 "$input" > "$snpeff_output";
86 #if $statsFile: 83 #if $statsFile:
87 #import os 84 #import os
88 #set $genes_file = str($statsFile) + '.genes.txt' 85 #set $genes_file = str($statsFile) + '.genes.txt'
89 #set $genes_file_name = os.path.split($genes_file)[-1] 86 #set $genes_file_name = os.path.split($genes_file)[-1]
90 mkdir $statsFile.files_path; 87 mkdir $statsFile.files_path;
91 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)#;
92 #end if 89 #end if
93 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 90 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
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]" 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]"
95 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"
96 #end if 93 #end if
97 ]]> 94 ]]>
98 </command> 95 </command>
99 <inputs> 96 <inputs>
100 <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)"/>
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"/> 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"/>
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"/> 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"/>
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"/> 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"/>
213 </when> 210 </when>
214 </conditional> 211 </conditional>
215
216 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
217 <option value="no_filter" selected="true">No filter (analyze everything)</option>
218 <option value="-hom">Analyze homozygous sequence changes only</option>
219 <option value="-het">Analyze heterozygous sequence changes only</option>
220 </param>
221 212
222 <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">
223 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> 214 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
224 <option value="-canon">Only use canonical transcripts</option> 215 <option value="-canon">Only use canonical transcripts</option>
225 <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>
255 <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">
256 <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>
257 <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>
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> 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>
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> 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>
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> 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>
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> 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>
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> 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>
263 <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>
264 <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>
265 <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>
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> 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>
267 <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>
311 You can prepend any string you want to the chromosome name. 302 You can prepend any string you want to the chromosome name.
312 </help> 303 </help>
313 <validator type="regex" message="No whitespace allowed">^\S*$</validator> 304 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
314 </param> 305 </param>
315 <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"/>
316 <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"/>
317 </inputs> 308 </inputs>
318 <outputs> 309 <outputs>
319 <data format="vcf" name="snpeff_output" > 310 <data format="vcf" name="snpeff_output" >
320 <change_format> 311 <change_format>
321 <when input="outputConditional.outputFormat" value="bed" format="bed" /> 312 <when input="outputConditional.outputFormat" value="bed" format="bed" />
342 <param name="inputFormat" value="vcf"/> 333 <param name="inputFormat" value="vcf"/>
343 <param name="outputFormat" value="vcf"/> 334 <param name="outputFormat" value="vcf"/>
344 <param name="genomeSrc" value="named"/> 335 <param name="genomeSrc" value="named"/>
345 <param name="genome_version" value="testCase"/> 336 <param name="genome_version" value="testCase"/>
346 <param name="udLength" value="0"/> 337 <param name="udLength" value="0"/>
347 <param name="filterHomHet" value="no_filter"/>
348 <param name="generate_stats" value="False"/> 338 <param name="generate_stats" value="False"/>
349 <param name="filterOut" value="+-no-upstream"/> 339 <param name="filterOut" value="+-no-upstream"/>
350 <output name="snpeff_output"> 340 <output name="snpeff_output">
351 <assert_contents> 341 <assert_contents>
352 <has_text text="EFF=" /> 342 <has_text text="EFF=" />
360 <param name="inputFormat" value="vcf"/> 350 <param name="inputFormat" value="vcf"/>
361 <param name="outputFormat" value="vcf"/> 351 <param name="outputFormat" value="vcf"/>
362 <param name="genomeSrc" value="named"/> 352 <param name="genomeSrc" value="named"/>
363 <param name="genome_version" value="testCase"/> 353 <param name="genome_version" value="testCase"/>
364 <param name="udLength" value="0"/> 354 <param name="udLength" value="0"/>
365 <param name="filterHomHet" value="+-het"/>
366 <!--
367 <param name="filterOut" value=""/>
368 -->
369 <param name="generate_stats" value="False"/>
370 <output name="snpeff_output">
371 <assert_contents>
372 <!-- Check that NO effects were added since -het is set -->
373 <not_has_text text="EFF=NON_SYNONYMOUS_CODING" />
374 </assert_contents>
375 </output>
376 </test>
377
378 <test>
379 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
380 <param name="inputFormat" value="vcf"/>
381 <param name="outputFormat" value="vcf"/>
382 <param name="genomeSrc" value="named"/>
383 <param name="genome_version" value="testCase"/>
384 <param name="udLength" value="0"/>
385 <param name="filterHomHet" value="no_filter"/>
386 <!-- 355 <!--
387 <param name="filterOut" value=""/> 356 <param name="filterOut" value=""/>
388 --> 357 -->
389 <param name="generate_stats" value="False"/> 358 <param name="generate_stats" value="False"/>
390 <output name="snpeff_output"> 359 <output name="snpeff_output">
404 <param name="inputFormat" value="vcf"/> 373 <param name="inputFormat" value="vcf"/>
405 <param name="outputFormat" value="vcf"/> 374 <param name="outputFormat" value="vcf"/>
406 <param name="genomeSrc" value="named"/> 375 <param name="genomeSrc" value="named"/>
407 <param name="genome_version" value="testCase"/> 376 <param name="genome_version" value="testCase"/>
408 <param name="udLength" value="0"/> 377 <param name="udLength" value="0"/>
409 <param name="filterHomHet" value="no_filter"/>
410 <param name="filterOut" value="+-no-upstream"/> 378 <param name="filterOut" value="+-no-upstream"/>
411 <param name="generate_stats" value="False"/> 379 <param name="generate_stats" value="False"/>
412 <output name="snpeff_output"> 380 <output name="snpeff_output">
413 <assert_contents> 381 <assert_contents>
414 <not_has_text text="UPSTREAM" /> 382 <not_has_text text="UPSTREAM" />
422 390
423 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.
424 392
425 @EXTERNAL_DOCUMENTATION@ 393 @EXTERNAL_DOCUMENTATION@
426 394
427 @CITATION_SECTION@
428
429 ]]> 395 ]]>
430 </help> 396 </help>
431 <expand macro="citations" /> 397 <expand macro="citations" />
432 </tool> 398 </tool>
433 399