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comparison snpEff.xml @ 29:ca2b512e8d7c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
author iuc
date Mon, 21 Oct 2024 13:56:15 +0000
parents 6322be79bd8e
children
comparison
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28:6322be79bd8e 29:ca2b512e8d7c
1 <tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy2"> 1 <tool id="snpEff" name="SnpEff eff:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
2 <description> annotate variants</description> 2 <description> annotate variants</description>
3 <macros> 3 <macros>
4 <import>snpEff_macros.xml</import> 4 <import>snpEff_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
11 <command><![CDATA[ 11 <command><![CDATA[
12 #if $intervals 12 #if $intervals
13 ln -s '${intervals}' intervals.bed && 13 ln -s '${intervals}' intervals.bed &&
14 #end if 14 #end if
15 snpEff @JAVA_OPTIONS@ eff 15 snpEff @JAVA_OPTIONS@ eff
16 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength 16 -i $inputFormat -o ${outputFormat} -upDownStreamLen $udLength
17 #if $spliceSiteSize and str($spliceSiteSize) != '': 17 #if $spliceSiteSize and str($spliceSiteSize) != '':
18 -spliceSiteSize "$spliceSiteSize" 18 -spliceSiteSize "$spliceSiteSize"
19 #end if 19 #end if
20 #if $spliceRegion.setSpliceRegions == 'yes': 20 #if $spliceRegion.setSpliceRegions == 'yes':
21 #if str($spliceRegion.spliceRegionExonSize) 21 #if str($spliceRegion.spliceRegionExonSize)
50 #if $statsFile: 50 #if $statsFile:
51 -stats '$statsFile' 51 -stats '$statsFile'
52 #end if 52 #end if
53 #if $csvStats: 53 #if $csvStats:
54 -csvStats '$csvFile' 54 -csvStats '$csvFile'
55 #end if
56 #if str($offset) != 'default':
57 ${offset}
58 #end if 55 #end if
59 #if str($chr).strip() != '': 56 #if str($chr).strip() != '':
60 -chr '$chr' 57 -chr '$chr'
61 #end if 58 #end if
62 $noLog 59 $noLog
101 #end if 98 #end if
102 #set $genes_file_name = os.path.split($genes_file)[-1] 99 #set $genes_file_name = os.path.split($genes_file)[-1]
103 mkdir '$statsFile.files_path' && 100 mkdir '$statsFile.files_path' &&
104 mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#' 101 mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#'
105 #end if 102 #end if
106 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
107 &&
108 ## 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]"
109 sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' '$snpeff_output'
110 #end if
111 ]]></command> 103 ]]></command>
112 <inputs> 104 <inputs>
113 <param name="input" type="data" format="vcf,bed" label="Sequence changes (SNPs, MNPs, InDels)"/> 105 <param name="input" type="data" format="vcf,bed" label="Sequence changes (SNPs, MNPs, InDels)"/>
114 106 <param argument="-i" name="inputFormat" type="select" label="Input format" help="Specify the format of input dataset(s)">
115 <param name="inputFormat" type="select" label="Input format">
116 <option value="vcf" selected="true">VCF</option> 107 <option value="vcf" selected="true">VCF</option>
117 <option value="bed">BED (Deprecated)</option> 108 <option value="bed">BED</option>
118 </param> 109 </param>
119 110 <param argument="-o" name="outputFormat" type="select" label="Output format" help="Specify output format">
120 <conditional name="outputConditional"> 111 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
121 <param name="outputFormat" type="select" label="Output format"> 112 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
122 <option value="vcf" selected="true">VCF (only if input is VCF)</option> 113 <option value="bed">BED</option>
123 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option> 114 <option value="bedAnn">BED annotations</option>
124 <option value="bed">BED</option> 115 </param>
125 <option value="bedAnn">BED annotations</option> 116 <param argument="-csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report?" help="Useful for downstream analyses and report generation" />
126 </param> 117 <param argument="-noStats" name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats?" help="Generates an HTML summary of results"/>
127 <when value="vcf" />
128 <when value="gatk">
129 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
130 </when>
131 <when value="bed" />
132 <when value="bedAnn" />
133 </conditional>
134 <param name="csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report, useful for downstream analysis (-csvStats)" />
135 <conditional name="snpDb"> 118 <conditional name="snpDb">
136 <param name="genomeSrc" type="select" label="Genome source"> 119 <param name="genomeSrc" type="select" label="Genome source">
137 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well --> 120 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well -->
138 <option value="cached">Locally installed snpEff database</option> 121 <option value="cached">Locally installed snpEff database</option>
139 <option value="history">Downloaded snpEff database in your history</option> 122 <option value="history">Downloaded snpEff database in your history</option>
169 </options> 152 </options>
170 </param> 153 </param>
171 </section> 154 </section>
172 </when> 155 </when>
173 <when value="named"> 156 <when value="named">
174 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)"> 157 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)" help="A list of databases can be obtained with 'snpEff download' tool">
175 <help>@SNPEFF_DATABASE_URL@</help>
176 <validator type="empty_field" message="A genome version name is required" /> 158 <validator type="empty_field" message="A genome version name is required" />
177 </param> 159 </param>
178 </when> 160 </when>
179 <when value="custom"> 161 <when value="custom">
180 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> 162 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
207 <option value="Scenedesmus_obliquus_Mitochondrial">Scenedesmus_obliquus_Mitochondrial</option> 189 <option value="Scenedesmus_obliquus_Mitochondrial">Scenedesmus_obliquus_Mitochondrial</option>
208 <option value="Thraustochytrium_Mitochondrial">Thraustochytrium_Mitochondrial</option> 190 <option value="Thraustochytrium_Mitochondrial">Thraustochytrium_Mitochondrial</option>
209 </param> 191 </param>
210 </when> 192 </when>
211 </conditional> 193 </conditional>
212
213 <param name="udLength" argument="-ud" type="select" label="Upstream / Downstream length"> 194 <param name="udLength" argument="-ud" type="select" label="Upstream / Downstream length">
214 <option value="0">No upstream / downstream intervals (0 bases)</option> 195 <option value="0" selected="true">No upstream / downstream intervals (0 bases)</option>
215 <option value="200">200 bases</option> 196 <option value="200">200 bases</option>
216 <option value="500">500 bases</option> 197 <option value="500">500 bases</option>
217 <option value="1000">1000 bases</option> 198 <option value="1000">1000 bases</option>
218 <option value="2000">2000 bases</option> 199 <option value="2000">2000 bases</option>
219 <option value="5000" selected="true">5000 bases</option> 200 <option value="5000">5000 bases</option>
220 <option value="10000">10000 bases</option> 201 <option value="10000">10000 bases</option>
221 <option value="20000">20000 bases</option> 202 <option value="20000">20000 bases</option>
222 </param> 203 </param>
223
224 <param name="spliceSiteSize" argument="-ss" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases"> 204 <param name="spliceSiteSize" argument="-ss" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases">
225 <option value="1">1 base</option> 205 <option value="1">1 base</option>
226 <option value="2" selected="true">2 bases</option> 206 <option value="2" selected="true">2 bases</option>
227 <option value="3">3 bases</option> 207 <option value="3">3 bases</option>
228 <option value="4">4 bases</option> 208 <option value="4">4 bases</option>
230 <option value="6">6 bases</option> 210 <option value="6">6 bases</option>
231 <option value="7">7 bases</option> 211 <option value="7">7 bases</option>
232 <option value="8">8 bases</option> 212 <option value="8">8 bases</option>
233 <option value="9">9 bases</option> 213 <option value="9">9 bases</option>
234 </param> 214 </param>
235
236 <conditional name="spliceRegion"> 215 <conditional name="spliceRegion">
237 <param name="setSpliceRegions" type="select" label="spliceRegion Settings"> 216 <param name="setSpliceRegions" type="select" label="spliceRegion Settings">
238 <option value="no">Use Defaults</option> 217 <option value="no">Use Defaults</option>
239 <option value="yes">Set Splice Region Parameters</option> 218 <option value="yes">Set Splice Region Parameters</option>
240 </param> 219 </param>
243 <param argument="-spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases" /> 222 <param argument="-spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases" />
244 <param argument="-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" /> 223 <param argument="-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" />
245 <param argument="-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" /> 224 <param argument="-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" />
246 </when> 225 </when>
247 </conditional> 226 </conditional>
248
249 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> 227 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
250 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN')</option> 228 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN')</option>
251 <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>
252 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option> 230 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
253 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option> 231 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
332 <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> 310 <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>
333 <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> 311 <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>
334 </param> 312 </param>
335 </when> 313 </when>
336 </conditional> 314 </conditional>
337
338 <param name="offset" type="select" display="radio" label="Chromosomal position">
339 <option value="default" selected="true">Use default (based on input type)</option>
340 <option value="-0">Force zero-based positions (both input and output)</option>
341 <option value="-1">Force one-based positions (both input and output)</option>
342 </param>
343 <param argument="-chr" type="text" label="Text to prepend to chromosome name"> 315 <param argument="-chr" type="text" label="Text to prepend to chromosome name">
344 <help> 316 <help>
345 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. 317 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
346 You can prepend any string you want to the chromosome name 318 You can prepend any string you want to the chromosome name
347 </help> 319 </help>
348 <validator type="regex" message="No whitespace allowed">^\S*$</validator> 320 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
349 </param> 321 </param>
350 <param name="generate_stats" argument="-noStats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats" />
351 <param argument="-noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server" /> 322 <param argument="-noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server" />
352 </inputs> 323 </inputs>
353 <outputs> 324 <outputs>
354 <data name="snpeff_output" format="vcf"> 325 <data name="snpeff_output" format="vcf">
355 <change_format> 326 <change_format>
373 <param name="genome_version" value="ebola_zaire"/> 344 <param name="genome_version" value="ebola_zaire"/>
374 <param name="udLength" value="0"/> 345 <param name="udLength" value="0"/>
375 <param name="generate_stats" value="true"/> 346 <param name="generate_stats" value="true"/>
376 <output name="snpeff_output"> 347 <output name="snpeff_output">
377 <assert_contents> 348 <assert_contents>
378 <has_text_matching expression="KJ660346\t572\t.*missense_variant" /> 349 <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
379 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" /> 350 <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
380 </assert_contents> 351 </assert_contents>
381 </output> 352 </output>
382 <output name="statsFile"> 353 <output name="statsFile">
383 <assert_contents> 354 <assert_contents>
384 <has_text text="&lt;b&gt;"/> 355 <has_text text="&lt;b&gt;"/>
396 <param name="udLength" value="0"/> 367 <param name="udLength" value="0"/>
397 <param name="generate_stats" value="false"/> 368 <param name="generate_stats" value="false"/>
398 <param name="csvStats" value="true"/> 369 <param name="csvStats" value="true"/>
399 <output name="snpeff_output"> 370 <output name="snpeff_output">
400 <assert_contents> 371 <assert_contents>
401 <has_text_matching expression="KJ660346\t572\t.*missense_variant" /> 372 <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
402 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" /> 373 <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
403 </assert_contents> 374 </assert_contents>
404 </output> 375 </output>
405 <output name="csvFile"> 376 <output name="csvFile">
406 <assert_contents> 377 <assert_contents>
407 <has_n_lines n="185"/> 378 <has_n_lines n="134"/>
408 <has_n_columns n="1" sep=","/> 379 <has_n_columns n="1" sep=","/>
409 </assert_contents> 380 </assert_contents>
410 </output> 381 </output>
411 </test> 382 </test>
412 </tests> 383 </tests>