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comparison mutational_patterns.xml @ 18:8d9f31389f33 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
author artbio
date Sun, 17 Oct 2021 15:51:05 +0000
parents 8c6ee1c2248f
children 69f09dff98f9
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17:8c6ee1c2248f 18:8d9f31389f33
1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy2"> 1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy3">
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="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</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>
5 <requirement type="package" version="1.6.6=r41hc72bb7e_1">r-optparse</requirement> 7 <requirement type="package" version="1.6.6=r41hc72bb7e_1">r-optparse</requirement>
6 <requirement type="package" version="0.2.20=r41h03ef668_1002">r-rjson</requirement> 8 <requirement type="package" version="0.2.20=r41h03ef668_1002">r-rjson</requirement>
7 <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>
8 <requirement type="package" version="2.3=r41hc72bb7e_1003">r-gridextra</requirement> 10 <requirement type="package" version="2.3=r41hc72bb7e_1003">r-gridextra</requirement>
9 <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement> 11 <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
10 <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement> 12 <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
11 <!--
12 <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement>
13 <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement>
14 -->
15 <!-- 13 <!--
16 install more bioconda genomes 14 install more bioconda genomes
17 bioconductor-bsgenome.mmusculus.ucsc.mm9 15 bioconductor-bsgenome.mmusculus.ucsc.mm9
18 bioconductor-bsgenome.mmusculus.ucsc.mm10 16 bioconductor-bsgenome.mmusculus.ucsc.mm10
19 --> 17 -->
48 --newsignum $set_denovo.newsignum 46 --newsignum $set_denovo.newsignum
49 --output_denovo $denovo 47 --output_denovo $denovo
50 --sigmatrix $sigmatrix 48 --sigmatrix $sigmatrix
51 #end if 49 #end if
52 50
53 #if $set_cosmic.choices == 'yes': 51 #if $set_preset.choices == 'yes':
54 --cosmic_version '$set_cosmic.cosmic_version' 52
55 --signum '$set_cosmic.signum' 53 #if $set_preset.set_signature_input.input_signature_choices == 'cosmic'
56 --output_cosmic $cosmic 54 --cosmic_version '$set_preset.set_signature_input.cosmic_version'
57 #if $set_cosmic.contrib_matrix_out == 'yes' 55 #end if
56
57 #if $set_preset.set_signature_input.input_signature_choices == 'user_signatures'
58 --own_signatures '$set_preset.set_signature_input.own_matrix'
59 #end if
60
61 --signum '$set_preset.signum'
62 --output_sigpattern $sig_contrib
63
64 #if $set_preset.contrib_matrix_out == 'yes'
58 --sig_contrib_matrix $sig_contrib_matrix 65 --sig_contrib_matrix $sig_contrib_matrix
59 #end if 66 #end if
67
60 #end if 68 #end if
61 69
62 #if $rdata_out 70 #if $rdata_out
63 --rdata '$rdata' 71 --rdata '$rdata'
64 #end if 72 #end if
67 75
68 ]]></command> 76 ]]></command>
69 <inputs> 77 <inputs>
70 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/> 78 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
71 <param name="genome" type="select" label="Reference Genome"> 79 <param name="genome" type="select" label="Reference Genome">
72 <!-- <option value="BSgenome.Hsapiens.1000genomes.hs37d5">BSgenome.Hsapiens.1000genomes.hs37d5</option> -->
73 <!-- <option value="BSgenome.Hsapiens.NCBI.GRCh38">BSgenome.Hsapiens.NCBI.GRCh38</option> -->
74 <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option> 80 <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option>
75 <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option> 81 <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option>
76 <!--<option value="BSgenome.Mmusculus.UCSC.mm10">BSgenome.Mmusculus.UCSC.mm10</option>
77 <option value="BSgenome.Mmusculus.UCSC.mm9">BSgenome.Mmusculus.UCSC.mm9</option>-->
78 </param> 82 </param>
79 <conditional name="set_levels"> 83 <conditional name="set_levels">
80 <param name="choices" type="select" label="samples have levels/labels for grouping them in the analysis" display="radio" 84 <param name="choices" type="select" label="samples have levels/labels for grouping them in the analysis" display="radio"
81 help="for instance, female/male or genotype-1/genotype-2/genotype-3, etc."> 85 help="for instance, female/male or genotype-1/genotype-2/genotype-3, etc.">
82 <option value="no" selected="true">No</option> 86 <option value="no" selected="true">No</option>
106 <when value="no" /> 110 <when value="no" />
107 </conditional> 111 </conditional>
108 112
109 <conditional name="set_denovo"> 113 <conditional name="set_denovo">
110 <param name="choices" type="select" label="Extract de novo signatures with MutationalPatterns" display="radio"> 114 <param name="choices" type="select" label="Extract de novo signatures with MutationalPatterns" display="radio">
111 <option value="yes" selected="true">Yes</option> 115 <option value="yes">Yes</option>
112 <option value="no">No</option> 116 <option value="no" selected="true">No</option>
113 </param> 117 </param>
114 <when value="yes"> 118 <when value="yes">
115 <param name="nrun" type="integer" value="10" min="10" max="200" 119 <param name="nrun" type="integer" value="10" min="10" max="200"
116 label="Number of cycles to find best fitting of signatures" 120 label="Number of cycles to find best fitting of signatures"
117 help="High values extend the computational time"/> 121 help="High values extend the computational time"/>
123 help="High values extend the computational time. Note also that you cannot extract more signature than the number of available samples in the study"/> 127 help="High values extend the computational time. Note also that you cannot extract more signature than the number of available samples in the study"/>
124 </when> 128 </when>
125 <when value="no" /> 129 <when value="no" />
126 </conditional> 130 </conditional>
127 131
128 <conditional name="set_cosmic"> 132 <conditional name="set_preset">
129 <param name="choices" type="select" label="Decompose with Cosmic signatures" display="radio"> 133 <param name="choices" type="select" label="Decompose with preset signatures" display="radio">
130 <option value="yes" selected="true">Yes</option> 134 <option value="yes" selected="true">Yes</option>
131 <option value="no">No</option> 135 <option value="no">No</option>
132 </param> 136 </param>
133 <when value="yes"> 137 <when value="yes">
138 <conditional name="set_signature_input">
139 <param name="input_signature_choices" type="select" label="type of signatures" display="radio">
140 <option value="cosmic" selected="true">COSMIC signatures</option>
141 <option value="user_signatures">Use your own signature matrix</option>
142 </param>
143 <when value="cosmic">
144 <param name="cosmic_version" type="select" label="Version of the Cosmic signature set">
145 <option value="v2" selected="true">Cosmic v2, March 2015</option>
146 <option value="v3">Cosmic v3, May 2019</option>
147 <option value="v3.1">Cosmic v3.1, June 2020</option>
148 <option value="v3.2">Cosmic v3.2, March 2021</option>
149 </param>
150 </when>
151 <when value="user_signatures">
152 <param name="own_matrix" type="data" format="tabular"
153 label="A tab-separated matrix describing elementary signatures"
154 help="see https://cancer.sanger.ac.uk/signatures/documents/453/COSMIC_v3.2_SBS_GRCh38.txt for the required format" />
155 </when>
156 </conditional>
134 <param name="signum" type="integer" value="3" min="2" max="30" 157 <param name="signum" type="integer" value="3" min="2" max="30"
135 label="selects the N most significant signatures in samples to express mutational patterns" 158 label="selects the N most significant signatures in samples to express mutational patterns"
136 help="an integer between 2 and 30 signature types from cosmic"/> 159 help="an integer between 2 and the number of elementary signatures in your signature matrix"/>
137 <param name="cosmic_version" type="select" label="Version of the Cosmic signature set">
138 <option value="v2" selected="true">Cosmic v2, March 2015</option>
139 <option value="v3">Cosmic v3, May 2019</option>
140 <option value="v3.1">Cosmic v3.1, June 2020</option>
141 <option value="v3.2">Cosmic v3.2, March 2021</option>
142 </param>
143 <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?" 160 <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?"
144 help="Output the normalized signatures contributions for further visualization" > 161 help="Output the normalized signatures contributions for further visualization" >
145 <option value="no" selected="true">No</option> 162 <option value="no" selected="true">No</option>
146 <option value="yes">Yes</option> 163 <option value="yes">Yes</option>
147 </param> 164 </param>
148 </when> 165 </when>
149 <when value="no" /> 166 <when value="no" />
150 </conditional> 167 </conditional>
151 <param name="rdata_out" type="boolean" checked="false" label="Output RData file?" help="Output all the data used by R to construct the tables and plots, can be loaded into R" /> 168 <param name="rdata_out" type="boolean" checked="false" label="Output RData file?" help="Output all the data used by R to construct the tables and plots, can be loaded into R" />
152 </inputs> 169 </inputs>
153 <outputs> 170 <outputs>
154 <data name="spectrum" format="pdf" label="Mutational Spectrum"> 171 <data name="spectrum" format="pdf" label="Mutational Spectrum">
158 <filter>set_denovo['choices'] == "yes"</filter> 175 <filter>set_denovo['choices'] == "yes"</filter>
159 </data> 176 </data>
160 <data name="sigmatrix" format="tabular" label="De novo signatures probability matrix"> 177 <data name="sigmatrix" format="tabular" label="De novo signatures probability matrix">
161 <filter>set_denovo['choices'] == "yes"</filter> 178 <filter>set_denovo['choices'] == "yes"</filter>
162 </data> 179 </data>
163 <data name="cosmic" format="pdf" label="Cosmic signatures"> 180 <data name="sig_contrib" format="pdf" label="Signature contributions">
164 <filter>set_cosmic['choices'] == "yes"</filter> 181 <filter>set_preset['choices'] == "yes"</filter>
165 </data> 182 </data>
166 <data name="sig_contrib_matrix" format="tabular" label="${tool.name}: Signature contribution table"> 183 <data name="sig_contrib_matrix" format="tabular" label="${tool.name}: Signature contribution table">
167 <filter>set_cosmic['choices'] == "yes" and set_cosmic['contrib_matrix_out'] == "yes"</filter> 184 <filter>set_preset['choices'] == "yes" and set_preset['contrib_matrix_out'] == "yes"</filter>
168 </data> 185 </data>
169 186
170 <data name="rdata" format="rdata" label="${tool.name}: RData file"> 187 <data name="rdata" format="rdata" label="${tool.name}: RData file">
171 <filter>rdata_out</filter> 188 <filter>rdata_out</filter>
172 </data> 189 </data>
173 190
174 </outputs> 191 </outputs>
175 <tests> 192 <tests>
176 <!-- cosmic signatures with cosmic V3 --> 193 <!-- user defined (v3.2 restricted 30 minus 27) -->
177 <test> 194 <test>
178 <param name="vcfs"> 195 <param name="vcfs">
179 <collection type="list"> 196 <collection type="list">
180 <element name="6" value="F.vcf"/> 197 <element name="6" value="F.vcf"/>
181 <element name="7" value="G.vcf"/> 198 <element name="7" value="G.vcf"/>
189 <param name="choices" value="no"/> 206 <param name="choices" value="no"/>
190 </conditional> 207 </conditional>
191 <conditional name="set_denovo"> 208 <conditional name="set_denovo">
192 <param name="choices" value="no"/> 209 <param name="choices" value="no"/>
193 </conditional> 210 </conditional>
194 <conditional name="set_cosmic"> 211 <conditional name="set_preset">
195 <param name="choices" value="yes"/> 212 <param name="choices" value="yes"/>
213 <conditional name="set_signature_input">
214 <param name="input_signature_choices" value="user_signatures" />
215 <param name="own_matrix" value="user_defined_signature.tsv" ftype="tabular"/>
216 </conditional>
196 <param name="contrib_matrix_out" value="yes" /> 217 <param name="contrib_matrix_out" value="yes" />
197 <param name="cosmic_version" value="v3"/> 218 </conditional>
198 </conditional> 219 <param name="signum" value="4" />
199 <param name="signum" value="3" /> 220 <output name="sig_contrib" file="user_output.pdf" compare="sim_size"/>
200 <output name="cosmic" file="cosmic_output_v3.pdf" compare="sim_size"/> 221 <output name="sig_contrib_matrix" file="sig_contrib_table_user_defined.tsv" compare="sim_size"/>
201 <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/> 222 </test>
202 </test> 223 <!-- cosmic v3.2 -->
203
204 <!-- cosmic signatures -->
205 <test> 224 <test>
206 <param name="vcfs"> 225 <param name="vcfs">
207 <collection type="list"> 226 <collection type="list">
208 <element name="6" value="F.vcf"/> 227 <element name="6" value="F.vcf"/>
209 <element name="7" value="G.vcf"/> 228 <element name="7" value="G.vcf"/>
217 <param name="choices" value="no"/> 236 <param name="choices" value="no"/>
218 </conditional> 237 </conditional>
219 <conditional name="set_denovo"> 238 <conditional name="set_denovo">
220 <param name="choices" value="no"/> 239 <param name="choices" value="no"/>
221 </conditional> 240 </conditional>
222 <conditional name="set_cosmic"> 241 <conditional name="set_preset">
223 <param name="choices" value="yes"/> 242 <param name="choices" value="yes"/>
243 <conditional name="set_signature_input">
244 <param name="input_signature_choices" value="cosmic" />
245 <param name="cosmic_version" value="v3.2"/>
246 </conditional>
224 <param name="contrib_matrix_out" value="yes" /> 247 <param name="contrib_matrix_out" value="yes" />
225 </conditional> 248 </conditional>
226 <param name="signum" value="3" /> 249 <param name="signum" value="3" />
227 <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size"/> 250 <output name="sig_contrib" file="cosmic_output_v3.pdf" compare="sim_size"/>
228 <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/> 251 <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/>
229 </test> 252 </test>
230 253 <!-- cosmic v2 -->
231 <!-- cosmic signature on single sample -->
232 <test>
233 <param name="vcfs">
234 <collection type="list">
235 <element name="1" value="G.vcf"/>
236 </collection>
237 </param>
238 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
239 <conditional name="set_spectrum">
240 <param name="choices" value="no"/>
241 </conditional>
242 <conditional name="set_denovo">
243 <param name="choices" value="no"/>
244 </conditional>
245 <conditional name="set_cosmic">
246 <param name="choices" value="yes"/>
247 </conditional>
248 <param name="signum" value="5" />
249 <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000"/>
250 </test>
251
252 <!-- simple profile -->
253 <test>
254 <param name="vcfs">
255 <collection type="list">
256 <element name="1" ftype="vcf" value="G.vcf"/>
257 <element name="2" ftype="vcf" value="H.vcf"/>
258 </collection>
259 </param>
260 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
261 <conditional name="set_levels">
262 <param name="choices" value="yes"/>
263 </conditional>
264 <param name="levels" value="GH_levels.tab" ftype="tabular"/>
265 <conditional name="set_spectrum">
266 <param name="choices" value="yes"/>
267 </conditional>
268 <conditional name="set_denovo">
269 <param name="choices" value="no"/>
270 </conditional>
271 <conditional name="set_cosmic">
272 <param name="choices" value="no"/>
273 </conditional>
274 <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size"/>
275 </test>
276
277 <!-- de novo signatures -->
278 <test> 254 <test>
279 <param name="vcfs"> 255 <param name="vcfs">
280 <collection type="list"> 256 <collection type="list">
281 <element name="6" value="F.vcf"/> 257 <element name="6" value="F.vcf"/>
282 <element name="7" value="G.vcf"/> 258 <element name="7" value="G.vcf"/>
283 <element name="8" value="H.vcf"/> 259 <element name="8" value="H.vcf"/>
284 <element name="9" value="I.vcf"/> 260 <element name="9" value="I.vcf"/>
285 </collection> 261 </collection>
286 </param> 262 </param>
287 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> 263 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
288 <conditional name="set_spectrum"> 264 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
289 <param name="choices" value="no"/> 265 <conditional name="set_spectrum">
290 </conditional> 266 <param name="choices" value="no"/>
291 <conditional name="set_denovo"> 267 </conditional>
292 <param name="choices" value="yes"/> 268 <conditional name="set_denovo">
293 </conditional> 269 <param name="choices" value="no"/>
294 <conditional name="set_cosmic"> 270 </conditional>
271 <conditional name="set_preset">
272 <param name="choices" value="yes"/>
273 <conditional name="set_signature_input">
274 <param name="input_signature_choices" value="cosmic" />
275 <param name="cosmic_version" value="v2"/>
276 </conditional>
277 <param name="contrib_matrix_out" value="yes" />
278 </conditional>
279 <param name="signum" value="3" />
280 <output name="sig_contrib" file="cosmic_output1.pdf" compare="sim_size"/>
281 <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/>
282 </test>
283 <!-- simple spectrum -->
284 <test>
285 <param name="vcfs">
286 <collection type="list">
287 <element name="1" ftype="vcf" value="G.vcf"/>
288 <element name="2" ftype="vcf" value="H.vcf"/>
289 </collection>
290 </param>
291 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
292 <conditional name="set_levels">
293 <param name="choices" value="yes"/>
294 </conditional>
295 <param name="levels" value="GH_levels.tab" ftype="tabular"/>
296 <conditional name="set_spectrum">
297 <param name="choices" value="yes"/>
298 </conditional>
299 <conditional name="set_denovo">
300 <param name="choices" value="no"/>
301 </conditional>
302 <conditional name="set_preset">
303 <param name="choices" value="no"/>
304 </conditional>
305 <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size"/>
306 </test>
307 <!-- de novo signatures -->
308 <test>
309 <param name="vcfs">
310 <collection type="list">
311 <element name="6" value="F.vcf"/>
312 <element name="7" value="G.vcf"/>
313 <element name="8" value="H.vcf"/>
314 <element name="9" value="I.vcf"/>
315 </collection>
316 </param>
317 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
318 <conditional name="set_spectrum">
319 <param name="choices" value="no"/>
320 </conditional>
321 <conditional name="set_denovo">
322 <param name="choices" value="yes"/>
323 </conditional>
324 <conditional name="set_preset">
295 <param name="choices" value="no"/> 325 <param name="choices" value="no"/>
296 </conditional> 326 </conditional>
297 <param name="nrun" value="10" /> 327 <param name="nrun" value="10" />
298 <param name="rank" value="4" /> 328 <param name="rank" value="4" />
299 <param name="newsignum" value="4" /> 329 <param name="newsignum" value="4" />
305 </tests> 335 </tests>
306 <help> 336 <help>
307 337
308 **What it does** 338 **What it does**
309 339
310 Takes as inputs 340 This tool implement the R package MutationalPatterns to decompose mutations found in cancers
311 341 in a linear combination of elementary mutational signatures, as first described by
312 * a collection of n vcf files corresponding to n samples. 342 Alexandrov_ et al (2013) and recently improved in an update_ published in 2020.
313 * a tabular table describing the correspondance of sample names to levels (tissues, ages, sexes, etc.) 343
314 * the number of cosmic signatures to decompose mutational patterns of samples 344 .. _Alexandrov: https://www.nature.com/articles/nature12477
315 345 .. _update: https://www.nature.com/articles/s41586-020-1943-3
316 346
317 This tool returns a pdf file with the visualisation : 347 Sets of elementary signatures found by analyzing large cohortes of patients are published
318 348 in the COSMIC databases v2_ to v3.2_. You can choose among these COSMIC signature sets to
319 * the Cosine similarity of samples when decomposed over the 30 signatures of cosmic_ 349 analyse your own VCFs.
320 * the absolute contribution of the n most contributing cosmic_ signatures in the samples mutational patterns (to be set by the user, between 2 and 30) 350
321 * the relative contribution of the n most contributing cosmic_ signatures in the samples mutational patterns (to be set by the user, between 2 and 30) 351 In addition, you can use your own signature sets (or filtered COSMIC signature sets)
322 * a clustering of the samples with respect to the relative contribution of their cosmic_ signatures 352 since MutationalPatterns implements a method to extract elementary signatures from
323 * pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic_ signatures to their mutational pattern 353 user-provided VCFs.
324 354
325 .. _cosmic: https://cancer.sanger.ac.uk/cosmic/signatures_v2.tt 355 **Inputs**
356
357 * a collection of VCF files with somatic mutations calls from analysis of samples.
358 * a tabular table describing the correspondance of sample names to levels of a factor
359 (tissues, ages, sexes, etc.)
360
361 **Outputs**
362
363 This tool returns pdf files with various visualisations of :
364
365 * the spectrum of single nucleotide mutation types
366 * the absolute contribution of the elementary signatures in the samples
367 * the relative contribution of the elementary signatures in the samples
368 * an unrooted hierarchical clustering of the reconstructed samples with respect to the relative contribution of elementary signatures
369 * the Cosine similarity between true samples and samples reconstructed with elementary signatures
370 * pie charts displaying the relative contribution of the n most contributing elementary signatures in the reconstructed sample profiles
371
372 .. _v2: https://cancer.sanger.ac.uk/signatures/signatures_v2/
373 .. _v3.2: https://cancer.sanger.ac.uk/signatures/sbs/
326 374
327 </help> 375 </help>
328 <citations> 376 <citations>
329 <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation> 377 <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation>
330 <citation type="doi">10.1186/s13073-018-0539-0</citation> 378 <citation type="doi">10.1186/s13073-018-0539-0</citation>
331 <citation type="doi">10.1038/nature12477</citation> 379 <citation type="doi">10.1038/nature12477</citation>
380 <citation type="doi">10.1038/s41586-020-1943-3</citation>
332 </citations> 381 </citations>
333 </tool> 382 </tool>