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comparison mutational_patterns.xml @ 24:ca6c19ee7da0 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
author artbio
date Tue, 05 Jul 2022 21:41:43 +0000
parents 83f8c93c34b4
children b00fef2b1c2c
comparison
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23:83f8c93c34b4 24:ca6c19ee7da0
1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy8"> 1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.4.0+galaxy0">
2 <description>from genomic variations in vcf files</description> 2 <description>from genomic variations in vcf files</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement> 4 <requirement type="package" version="3.4.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
5 <requirement type="package" version="1.1.1l=h7f98852_0">openssl</requirement> 5 <!--requirement type="package" version="1.1.1l=h7f98852_0">openssl</requirement> -->
6 <requirement type="package" version="3.3.5=r41hc72bb7e_0">r-ggplot2</requirement> 6 <requirement type="package" version="3.3.6=r41hc72bb7e_0">r-ggplot2</requirement>
7 <requirement type="package" version="1.6.6=r41hc72bb7e_1">r-optparse</requirement> 7 <requirement type="package" version="1.7.1=r41hc72bb7e_0">r-optparse</requirement>
8 <requirement type="package" version="0.2.20=r41h03ef668_1002">r-rjson</requirement> 8 <requirement type="package" version="0.2.21=r41h7525677_1">r-rjson</requirement>
9 <requirement type="package" version="0.21.0=r41h03ef668_1004">r-nmf</requirement> 9 <requirement type="package" version="0.21.0=r41h03ef668_1004">r-nmf</requirement>
10 <requirement type="package" version="2.3=r41hc72bb7e_1003">r-gridextra</requirement> 10 <requirement type="package" version="2.3=r41hc72bb7e_1003">r-gridextra</requirement>
11 <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement> 11 <requirement type="package" version="1.4.3=r41hdfd78af_4">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
12 <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement> 12 <requirement type="package" version="1.4.4=r41hdfd78af_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
13 <!-- 13 <!--
14 install more bioconda genomes 14 install more bioconda genomes
15 bioconductor-bsgenome.mmusculus.ucsc.mm9 15 bioconductor-bsgenome.mmusculus.ucsc.mm9
16 bioconductor-bsgenome.mmusculus.ucsc.mm10 16 bioconductor-bsgenome.mmusculus.ucsc.mm10
17 --> 17 -->
198 <filter>rdata_out</filter> 198 <filter>rdata_out</filter>
199 </data> 199 </data>
200 200
201 </outputs> 201 </outputs>
202 <tests> 202 <tests>
203 <!-- user defined (v3.2 restricted 30 minus 27 renamed to test nomenclature effect) -->
204 <test>
205 <param name="vcfs">
206 <collection type="list">
207 <element name="6" value="F.vcf"/>
208 <element name="7" value="G.vcf"/>
209 <element name="8" value="H.vcf"/>
210 <element name="9" value="I.vcf"/>
211 </collection>
212 </param>
213 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
214 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
215 <conditional name="set_spectrum">
216 <param name="choices" value="no"/>
217 </conditional>
218 <conditional name="set_denovo">
219 <param name="choices" value="no"/>
220 </conditional>
221 <conditional name="set_preset">
222 <param name="choices" value="yes"/>
223 <conditional name="set_signature_input">
224 <param name="input_signature_choices" value="user_signatures" />
225 <param name="own_matrix" value="user_defined_signature.tsv" ftype="tabular"/>
226 </conditional>
227 <param name="contrib_matrix_out" value="yes" />
228 </conditional>
229 <param name="signum" value="4" />
230 <output name="sig_contrib" file="user_output.pdf" compare="sim_size"/>
231 <output name="sig_contrib_matrix" file="sig_contrib_table_user_defined.tsv" compare="sim_size"/>
232 </test>
233 <!-- cosmic v3.2 -->
234 <test>
235 <param name="vcfs">
236 <collection type="list">
237 <element name="6" value="F.vcf"/>
238 <element name="7" value="G.vcf"/>
239 <element name="8" value="H.vcf"/>
240 <element name="9" value="I.vcf"/>
241 </collection>
242 </param>
243 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
244 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
245 <conditional name="set_spectrum">
246 <param name="choices" value="no"/>
247 </conditional>
248 <conditional name="set_denovo">
249 <param name="choices" value="no"/>
250 </conditional>
251 <conditional name="set_preset">
252 <param name="choices" value="yes"/>
253 <conditional name="set_signature_input">
254 <param name="input_signature_choices" value="cosmic" />
255 <param name="cosmic_version" value="v3.2"/>
256 </conditional>
257 <param name="display_signatures" value="no" />
258 <param name="contrib_matrix_out" value="yes" />
259 </conditional>
260 <param name="signum" value="3" />
261 <output name="sig_contrib" file="cosmic_output_v3.pdf" compare="sim_size"/>
262 <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/>
263 </test>
264 <!-- cosmic v2 -->
265 <test>
266 <param name="vcfs">
267 <collection type="list">
268 <element name="6" value="F.vcf"/>
269 <element name="7" value="G.vcf"/>
270 <element name="8" value="H.vcf"/>
271 <element name="9" value="I.vcf"/>
272 </collection>
273 </param>
274 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
275 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
276 <conditional name="set_spectrum">
277 <param name="choices" value="no"/>
278 </conditional>
279 <conditional name="set_denovo">
280 <param name="choices" value="no"/>
281 </conditional>
282 <conditional name="set_preset">
283 <param name="choices" value="yes"/>
284 <conditional name="set_signature_input">
285 <param name="input_signature_choices" value="cosmic" />
286 <param name="cosmic_version" value="v2"/>
287 </conditional>
288 <param name="contrib_matrix_out" value="yes" />
289 </conditional>
290 <param name="signum" value="3" />
291 <output name="sig_contrib" file="cosmic_output1.pdf" compare="sim_size"/>
292 <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/>
293 </test>
294 <!-- simple spectrum -->
295 <test>
296 <param name="vcfs">
297 <collection type="list">
298 <element name="1" ftype="vcf" value="G.vcf"/>
299 <element name="2" ftype="vcf" value="H.vcf"/>
300 </collection>
301 </param>
302 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
303 <conditional name="set_levels">
304 <param name="choices" value="yes"/>
305 </conditional>
306 <param name="levels" value="GH_levels.tab" ftype="tabular"/>
307 <conditional name="set_spectrum">
308 <param name="choices" value="yes"/>
309 </conditional>
310 <conditional name="set_denovo">
311 <param name="choices" value="no"/>
312 </conditional>
313 <conditional name="set_preset">
314 <param name="choices" value="no"/>
315 </conditional>
316 <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size"/>
317 </test>
318 <!-- de novo signatures --> 203 <!-- de novo signatures -->
319 <test> 204 <test>
320 <param name="vcfs"> 205 <param name="vcfs">
321 <collection type="list"> 206 <collection type="list">
322 <element name="6" value="F.vcf"/> 207 <element name="6" value="F.vcf"/>
340 <param name="newsignum" value="4" /> 225 <param name="newsignum" value="4" />
341 <param name="rdata_out" value="true" /> 226 <param name="rdata_out" value="true" />
342 <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/> 227 <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/>
343 <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/> 228 <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/>
344 <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!-- delta="170000" --> 229 <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!-- delta="170000" -->
230 </test>
231 <!-- user defined (v3.2 restricted 30 minus 27 renamed to test nomenclature effect) -->
232 <test>
233 <param name="vcfs">
234 <collection type="list">
235 <element name="6" value="F.vcf"/>
236 <element name="7" value="G.vcf"/>
237 <element name="8" value="H.vcf"/>
238 <element name="9" value="I.vcf"/>
239 </collection>
240 </param>
241 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
242 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
243 <conditional name="set_spectrum">
244 <param name="choices" value="no"/>
245 </conditional>
246 <conditional name="set_denovo">
247 <param name="choices" value="no"/>
248 </conditional>
249 <conditional name="set_preset">
250 <param name="choices" value="yes"/>
251 <conditional name="set_signature_input">
252 <param name="input_signature_choices" value="user_signatures" />
253 <param name="own_matrix" value="user_defined_signature.tsv" ftype="tabular"/>
254 </conditional>
255 <param name="contrib_matrix_out" value="yes" />
256 </conditional>
257 <param name="signum" value="4" />
258 <output name="sig_contrib" file="user_output.pdf" compare="sim_size"/>
259 <output name="sig_contrib_matrix" file="sig_contrib_table_user_defined.tsv" compare="sim_size"/>
260 </test>
261 <!-- cosmic v3.2 -->
262 <test>
263 <param name="vcfs">
264 <collection type="list">
265 <element name="6" value="F.vcf"/>
266 <element name="7" value="G.vcf"/>
267 <element name="8" value="H.vcf"/>
268 <element name="9" value="I.vcf"/>
269 </collection>
270 </param>
271 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
272 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
273 <conditional name="set_spectrum">
274 <param name="choices" value="no"/>
275 </conditional>
276 <conditional name="set_denovo">
277 <param name="choices" value="no"/>
278 </conditional>
279 <conditional name="set_preset">
280 <param name="choices" value="yes"/>
281 <conditional name="set_signature_input">
282 <param name="input_signature_choices" value="cosmic" />
283 <param name="cosmic_version" value="v3.2"/>
284 </conditional>
285 <param name="display_signatures" value="no" />
286 <param name="contrib_matrix_out" value="yes" />
287 </conditional>
288 <param name="signum" value="3" />
289 <output name="sig_contrib" file="cosmic_output_v3.pdf" compare="sim_size"/>
290 <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/>
291 </test>
292 <!-- cosmic v2 -->
293 <test>
294 <param name="vcfs">
295 <collection type="list">
296 <element name="6" value="F.vcf"/>
297 <element name="7" value="G.vcf"/>
298 <element name="8" value="H.vcf"/>
299 <element name="9" value="I.vcf"/>
300 </collection>
301 </param>
302 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
303 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
304 <conditional name="set_spectrum">
305 <param name="choices" value="no"/>
306 </conditional>
307 <conditional name="set_denovo">
308 <param name="choices" value="no"/>
309 </conditional>
310 <conditional name="set_preset">
311 <param name="choices" value="yes"/>
312 <conditional name="set_signature_input">
313 <param name="input_signature_choices" value="cosmic" />
314 <param name="cosmic_version" value="v2"/>
315 </conditional>
316 <param name="contrib_matrix_out" value="yes" />
317 </conditional>
318 <param name="signum" value="3" />
319 <output name="sig_contrib" file="cosmic_output1.pdf" compare="sim_size"/>
320 <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/>
321 </test>
322 <!-- simple spectrum -->
323 <test>
324 <param name="vcfs">
325 <collection type="list">
326 <element name="1" ftype="vcf" value="G.vcf"/>
327 <element name="2" ftype="vcf" value="H.vcf"/>
328 </collection>
329 </param>
330 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
331 <conditional name="set_levels">
332 <param name="choices" value="yes"/>
333 </conditional>
334 <param name="levels" value="GH_levels.tab" ftype="tabular"/>
335 <conditional name="set_spectrum">
336 <param name="choices" value="yes"/>
337 </conditional>
338 <conditional name="set_denovo">
339 <param name="choices" value="no"/>
340 </conditional>
341 <conditional name="set_preset">
342 <param name="choices" value="no"/>
343 </conditional>
344 <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size"/>
345 </test> 345 </test>
346 </tests> 346 </tests>
347 <help> 347 <help>
348 348
349 **What it does** 349 **What it does**