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comparison snpEff.xml @ 3:b24873564cf6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
author iuc
date Tue, 07 Jun 2016 10:03:17 -0400
parents e09ce114d240
children 698ef30638a8
comparison
equal deleted inserted replaced
2:e09ce114d240 3:b24873564cf6
1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0"> 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>
7 <expand macro="requirements" /> 6 <expand macro="requirements" />
8 <expand macro="stdio" /> 7 <expand macro="stdio" />
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 $spliceSiteSize and str($spliceSiteSize) != '': 14 #if $spliceSiteSize and str($spliceSiteSize) != '':
15 -spliceSiteSize "$spliceSiteSize" 15 -spliceSiteSize "$spliceSiteSize"
16 #end if 16 #end if
17 #if $spliceRegion.setSpliceRegions == 'yes':
18 #if $spliceRegion.spliceRegionExonSize and str($spliceRegion.spliceRegionExonSize) != '':
19 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
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
17 #if $annotations and str($annotations) != '': 28 #if $annotations and str($annotations) != '':
18 #echo " " 29 #echo " "
19 #echo ' '.join(str($annotations).split(',')) 30 #echo ' '.join(str($annotations).split(','))
20 #end if 31 #end if
21 #if $filterOut and str($filterOut) != '': 32 #if $filterOut and str($filterOut) != '':
85 <inputs> 96 <inputs>
86 <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)"/>
87 98
88 <param name="inputFormat" type="select" label="Input format"> 99 <param name="inputFormat" type="select" label="Input format">
89 <option value="vcf" selected="true">VCF</option> 100 <option value="vcf" selected="true">VCF</option>
90 <option value="txt">Tabular (Deprecated)</option>
91 <option value="pileup">Pileup (Deprecated)</option>
92 <option value="bed">BED (Deprecated)</option> 101 <option value="bed">BED (Deprecated)</option>
93 </param> 102 </param>
94 103
95 <conditional name="outputConditional"> 104 <conditional name="outputConditional">
96 <param name="outputFormat" type="select" label="Output format"> 105 <param name="outputFormat" type="select" label="Output format">
97 <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>
98 <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>
99 <option value="txt">Tabular</option>
100 <option value="bed">BED</option> 108 <option value="bed">BED</option>
101 <option value="bedAnn">BED annotations</option> 109 <option value="bedAnn">BED annotations</option>
102 </param> 110 </param>
103 <when value="vcf" /> 111 <when value="vcf" />
104 <when value="gatk"> 112 <when value="gatk">
105 <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" />
106 </when> 114 </when>
107 <when value="txt" />
108 <when value="bed" /> 115 <when value="bed" />
109 <when value="bedAnn" /> 116 <when value="bedAnn" />
110 </conditional> 117 </conditional>
111 118
112 <conditional name="snpDb"> 119 <conditional name="snpDb">
188 <option value="7">7 bases</option> 195 <option value="7">7 bases</option>
189 <option value="8">8 bases</option> 196 <option value="8">8 bases</option>
190 <option value="9">9 bases</option> 197 <option value="9">9 bases</option>
191 </param> 198 </param>
192 199
200 <conditional name="spliceRegion">
201 <param name="setSpliceRegions" type="select" label="spliceRegion Settings">
202 <option value="no">Use Defaults</option>
203 <option value="yes">Set Splice Region Parameters</option>
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>
212
193 <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">
194 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> 214 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
195 <option value="-canon">Only use canonical transcripts</option> 215 <option value="-canon">Only use canonical transcripts</option>
196 <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>
197 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option> 217 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
198 <option value="-oicr">Add OICR tag in VCF file</option> 218 <option value="-oicr">Add OICR tag in VCF file</option>
199 <option value="-onlyReg">Only use regulation tracks</option> 219 <option value="-onlyReg">Only use regulation tracks</option>
200 <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>
201 <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>
202 <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>
203 </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. -->
204 <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"/>
205 <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."/>
206 <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">
207 <option value="-no-downstream">Do not show DOWNSTREAM changes</option> 233 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
208 <option value="-no-intergenic">Do not show INTERGENIC changes</option> 234 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
276 You can prepend any string you want to the chromosome name. 302 You can prepend any string you want to the chromosome name.
277 </help> 303 </help>
278 <validator type="regex" message="No whitespace allowed">^\S*$</validator> 304 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
279 </param> 305 </param>
280 <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"/>
281 <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"/>
282 </inputs> 308 </inputs>
283 <outputs> 309 <outputs>
284 <data format="vcf" name="snpeff_output" > 310 <data format="vcf" name="snpeff_output" >
285 <change_format> 311 <change_format>
286 <when input="outputConditional.outputFormat" value="txt" format="tabular" />
287 <when input="outputConditional.outputFormat" value="bed" format="bed" /> 312 <when input="outputConditional.outputFormat" value="bed" format="bed" />
288 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> 313 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
289 </change_format> 314 </change_format>
290 </data> 315 </data>
291 <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">
299 <output name="statsFile"> 324 <output name="statsFile">
300 <assert_contents> 325 <assert_contents>
301 <has_text text="SnpEff: Variant analysis" /> 326 <has_text text="SnpEff: Variant analysis" />
302 </assert_contents> 327 </assert_contents>
303 </output> 328 </output>
304 --> 329 -->
305 <!-- Setting filterOut throws exception in twilltestcase.py 330 <!-- Setting filterOut throws exception in twilltestcase.py
306 <test> 331 <test>
307 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> 332 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
308 <param name="inputFormat" value="vcf"/> 333 <param name="inputFormat" value="vcf"/>
309 <param name="outputFormat" value="vcf"/> 334 <param name="outputFormat" value="vcf"/>
316 <assert_contents> 341 <assert_contents>
317 <has_text text="EFF=" /> 342 <has_text text="EFF=" />
318 </assert_contents> 343 </assert_contents>
319 </output> 344 </output>
320 </test> 345 </test>
321 --> 346 -->
322 347
323 <test> 348 <test>
324 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> 349 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
325 <param name="inputFormat" value="vcf"/> 350 <param name="inputFormat" value="vcf"/>
326 <param name="outputFormat" value="vcf"/> 351 <param name="outputFormat" value="vcf"/>
359 </output> 384 </output>
360 </test> 385 </test>
361 --> 386 -->
362 387
363 </tests> 388 </tests>
364 <help> 389 <help><![CDATA[
365 390
366 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.
367 392
368 @EXTERNAL_DOCUMENTATION@ 393 @EXTERNAL_DOCUMENTATION@
369 394
370 @CITATION_SECTION@ 395 ]]>
371
372 </help> 396 </help>
373 <expand macro="citations" /> 397 <expand macro="citations" />
374 </tool> 398 </tool>
375 399