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comparison sigmut.xml @ 0:9f48c5d97be8 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
author artbio
date Mon, 16 Mar 2020 06:15:02 -0400
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children 02861b32a62f
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-1:000000000000 0:9f48c5d97be8
1 <tool id="SigProfiler" name="SigProfiler" version="@VERSION@">
2 <description>SigProfiler performs the mutational signature characterization from VCF files.</description>
3
4 <macros>
5 <import>sigmut_macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command detect_errors="exit_code"><![CDATA[
10 @VERSION@
11 @pipefail@
12 #import os
13 #import random
14 #import datetime
15 #set job_dir=os.getcwd()
16 #set run_dir = job_dir + (' ' + str(random.randint(1,100000))).strip() + '/'
17 #set job_num = "Job_" + (' ' + str(random.randint(1,500))).strip()
18
19 mkdir $run_dir &&
20
21 #if str( $set_analysis.choices ) == "install_genome":
22 ln -s -f '$__tool_directory__/install.log' '${logref}' &&
23 #else if str( $set_analysis.choices ) == "get_sigmut":
24 #set err_file = $run_dir + "logs/SigProfilerMatrixGenerator_" + $job_num + "_" + str($set_analysis.refgendat) + str(datetime.date.today()) + ".err"
25 #set log_file = $run_dir + "logs/SigProfilerMatrixGenerator_" + $job_num + "_" + str($set_analysis.refgendat) + str(datetime.date.today()) + ".out"
26
27 #set plot1 = $run_dir + "output/plots/SBS_6_plots_" + $job_num + ".pdf"
28 #set plot2 = $run_dir + "output/plots/SBS_24_plots_" + $job_num + ".pdf"
29 #set plot3 = $run_dir + "output/plots/SBS_78_plots_" + $job_num + ".pdf"
30 #set plot4 = $run_dir + "output/plots/SBS_96_plots_" + $job_num + ".pdf"
31 #set plot5 = $run_dir + "output/plots/SBS_384_plots_" + $job_num + ".pdf"
32 #set plot6 = $run_dir + "output/plots/SBS_1536_plots_" + $job_num + ".pdf"
33 #set plot7 = $run_dir + "output/plots/DBS_78_plots_" + $job_num + ".pdf"
34 #set plot8 = $run_dir + "output/plots/DBS_186_plots_" + $job_num + ".pdf"
35
36 #set plot9 = $run_dir + "output/plots/ID_simple_plots_" + $job_num + ".pdf"
37 #set plot10 = $run_dir + "output/plots/ID_TSB_plots_" + $job_num + ".pdf"
38 #set plot11 = $run_dir + "output/plots/ID_83_plots_" + $job_num + ".pdf"
39 #set plot12 = $run_dir + "output/plots/ID_94_plots_" + $job_num + ".pdf"
40 #set plot13 = $run_dir + "output/plots/ID_96_plots_" + $job_num + ".pdf"
41
42 #set exo1 = $run_dir + "output/DBS/" + $job_num + ".DBS78" + ".exome"
43 #set exo2 = $run_dir + "output/DBS/" + $job_num + ".DBS186" + ".exome"
44 #set exo3 = $run_dir + "output/DBS/" + $job_num + ".DBS1248" + ".exome"
45 #set exo4 = $run_dir + "output/DBS/" + $job_num + ".DBS2976" + ".exome"
46
47 #set exo5 = $run_dir + "output/SBS/" + $job_num + ".SBS6" + ".exome"
48 #set exo6 = $run_dir + "output/SBS/" + $job_num + ".SBS24" + ".exome"
49 #set exo7 = $run_dir + "output/SBS/" + $job_num + ".SBS96" + ".exome"
50 #set exo8 = $run_dir + "output/SBS/" + $job_num + ".SBS384" + ".exome"
51 #set exo9 = $run_dir + "output/SBS/" + $job_num + ".SBS1536" + ".exome"
52 #set exo10 = $run_dir + "output/SBS/" + $job_num + ".SBS6144" + ".exome"
53
54 #set exo11 = $run_dir + "output/vcf_files/DBS/" + $job_num + "_" + "DBS_exome.vcf"
55 #set exo12 = $run_dir + "output/vcf_files/SNV/" + $job_num + "_" + "SNV_exome.vcf"
56
57 #set tsb1 = $run_dir + "output/TSB/strandBiasTest_24.txt"
58 #set tsb2 = $run_dir + "output/TSB/strandBiasTest_384.txt"
59 #set tsb3 = $run_dir + "output/TSB/strandBiasTest_6144.txt"
60 #set tsb4 = $run_dir + "output/TSB/significantResults_strandBiasTest.txt"
61
62 #set seqinf1 = $run_dir + "output/DBS/" + $job_num + ".DBS78" + ".all"
63 #set seqinf2 = $run_dir + "output/DBS/" + $job_num + ".DBS186" + ".all"
64 #set seqinf3 = $run_dir + "output/DBS/" + $job_num + ".DBS1248" + ".all"
65 #set seqinf4 = $run_dir + "output/DBS/" + $job_num + ".DBS2976" + ".all"
66
67 #set seqinf5 = $run_dir + "output/SBS/" + $job_num + ".SBS6" + ".all"
68 #set seqinf6 = $run_dir + "output/SBS/" + $job_num + ".SBS24" + ".all"
69 #set seqinf7 = $run_dir + "output/SBS/" + $job_num + ".SBS96" + ".all"
70 #set seqinf8 = $run_dir + "output/SBS/" + $job_num + ".SBS384" + ".all"
71 #set seqinf9 = $run_dir + "output/SBS/" + $job_num + ".SBS1536" + ".all"
72 #set seqinf10 = $run_dir + "output/SBS/" + $job_num + ".SBS6144" + ".all"
73
74 #set seqinf11 = $run_dir + "output/ID/" + $job_num + ".ID28" + ".all"
75 #set seqinf12 = $run_dir + "output/ID/" + $job_num + ".ID83" + ".all"
76 #set seqinf13 = $run_dir + "output/ID/" + $job_num + ".ID94" + ".all"
77 #set seqinf14 = $run_dir + "output/ID/" + $job_num + ".ID96" + ".all"
78 #set seqinf15 = $run_dir + "output/ID/" + $job_num + ".ID415" + ".all"
79 #set seqinf16 = $run_dir + "output/ID/" + $job_num + ".ID8628" + ".all"
80
81 ln -s -f '$log_file' '${logsmt}' &&
82
83 #if str($set_analysis.plot) == "true":
84 ln -s -f '$plot1' '${SBS6}' &&
85 ln -s -f '$plot2' '${SBS24}' &&
86 ln -s -f '$plot3' '${SBS78}' &&
87 ln -s -f '$plot4' '${SBS96}' &&
88 ln -s -f '$plot5' '${SBS384}' &&
89 ln -s -f '$plot6' '${SBS1536}' &&
90 ln -s -f '$plot7' '${DBS78}' &&
91 ln -s -f '$plot8' '${DBS186}' &&
92 ln -s -f '$plot9' '${ID_simple}' &&
93 ln -s -f '$plot10' '${ID_TSB}' &&
94 ln -s -f '$plot11' '${ID_83}' &&
95 ln -s -f '$plot12' '${ID_94}' &&
96 ln -s -f '$plot13' '${ID_96}' &&
97
98 ln -s -f '$seqinf1' '${SeqInf1}' &&
99 ln -s -f '$seqinf2' '${SeqInf2}' &&
100 ln -s -f '$seqinf3' '${SeqInf3}' &&
101 ln -s -f '$seqinf4' '${SeqInf4}' &&
102 ln -s -f '$seqinf5' '${SeqInf5}' &&
103 ln -s -f '$seqinf6' '${SeqInf6}' &&
104 ln -s -f '$seqinf7' '${SeqInf7}' &&
105 ln -s -f '$seqinf8' '${SeqInf8}' &&
106 ln -s -f '$seqinf9' '${SeqInf9}' &&
107 ln -s -f '$seqinf10' '${SeqInf10}' &&
108
109 ln -s -f '$seqinf11' '${SeqInf11}' &&
110 ln -s -f '$seqinf12' '${SeqInf12}' &&
111 ln -s -f '$seqinf13' '${SeqInf13}' &&
112 ln -s -f '$seqinf14' '${SeqInf14}' &&
113 ln -s -f '$seqinf15' '${SeqInf15}' &&
114 ln -s -f '$seqinf16' '${SeqInf16}' &&
115
116 #end if
117
118 #if str($set_analysis.exome) == "true":
119 ln -s -f '$exo1' '${Exo1}' &&
120 ln -s -f '$exo2' '${Exo2}' &&
121 ln -s -f '$exo3' '${Exo3}' &&
122 ln -s -f '$exo4' '${Exo4}' &&
123 ln -s -f '$exo5' '${Exo5}' &&
124 ln -s -f '$exo6' '${Exo6}' &&
125 ln -s -f '$exo7' '${Exo7}' &&
126 ln -s -f '$exo8' '${Exo8}' &&
127 ln -s -f '$exo9' '${Exo9}' &&
128 ln -s -f '$exo10' '${Exo10}' &&
129 ln -s -f '$exo11' '${Exo11}' &&
130 ln -s -f '$exo12' '${Exo12}' &&
131 #end if
132
133 #if str($set_analysis.tsb_stat) == "true":
134 ln -s -f '$tsb1' '${TSB24}' &&
135 ln -s -f '$tsb2' '${TSB384}' &&
136 ln -s -f '$tsb3' '${TSB6144}' &&
137 ln -s -f '$tsb4' '${sigRes}' &&
138 #end if
139
140
141 #if str($set_analysis.seqInfo) == "true":
142 ln -s -f '$seqinf1' '${SeqInf1}' &&
143 ln -s -f '$seqinf2' '${SeqInf2}' &&
144 ln -s -f '$seqinf3' '${SeqInf3}' &&
145 ln -s -f '$seqinf4' '${SeqInf4}' &&
146 ln -s -f '$seqinf5' '${SeqInf5}' &&
147 ln -s -f '$seqinf6' '${SeqInf6}' &&
148 ln -s -f '$seqinf7' '${SeqInf7}' &&
149 ln -s -f '$seqinf8' '${SeqInf8}' &&
150 ln -s -f '$seqinf9' '${SeqInf9}' &&
151 ln -s -f '$seqinf10' '${SeqInf10}' &&
152 ln -s -f '$seqinf11' '${SeqInf11}' &&
153 ln -s -f '$seqinf12' '${SeqInf12}' &&
154 ln -s -f '$seqinf13' '${SeqInf13}' &&
155 ln -s -f '$seqinf14' '${SeqInf14}' &&
156 ln -s -f '$seqinf15' '${SeqInf15}' &&
157 ln -s -f '$seqinf16' '${SeqInf16}' &&
158 #end if
159
160
161 #if str( $set_analysis.vcfile_input.vcfile ) == "maf":
162 #set $infile = $run_dir + 'snps.maf'
163 ln -s -f '$set_analysis.vcfile_input.maf_file' '$infile' &&
164 #else if str( $set_analysis.vcfile_input.vcfile ) == "icgc":
165 #set $infile = $run_dir + 'snps.txt'
166 ln -s -f '$set_analysis.vcfile_input.icgc_file' '$infile' &&
167 #else if str( $set_analysis.vcfile_input.vcfile ) == "vcf":
168 #set $infile = $run_dir + 'snps.vcf'
169 ln -s -f '$set_analysis.vcfile_input.vcf_file' '$infile' &&
170 #end if
171
172 #end if
173
174 sigprofiler
175 #if str( $set_analysis.choices ) == "install_genome":
176 -ig $set_analysis.refgendwn
177 #else if str( $set_analysis.choices ) == "get_sigmut":
178 -n $job_num
179 -g $set_analysis.refgendat
180 -f $run_dir
181
182 #if str( $set_analysis.exome ) == "true":
183 -e
184 #end if
185 #if str( $set_analysis.chrom_based ) == "true":
186 -c
187 #end if
188 #if str( $set_analysis.plot ) == "true":
189 -p
190 #end if
191 #if str( $set_analysis.tsb_stat ) == "true":
192 -t
193 #end if
194 #if str( $set_analysis.gs ) == "true":
195 -s
196 #end if
197 ##-b $set_analysis.bed
198 #end if
199 ]]></command>
200
201 <inputs>
202 <conditional name="set_analysis">
203 <param name="choices" type="select" label="Which of the following jobs do you want perform?">
204 <option value="install_genome">Install 'de novo' a reference genome </option>
205 <option value="get_sigmut">Obtain the mutational signatures from VCF files</option>
206 </param>
207 <when value="install_genome">
208 <param name="refgendwn" type="select" label="Reference genome" help="Get data from any of the following reference genomes:">
209 <option value="GRCh37">Homo sapiens, GRCh37.p13 [GCA_000001405.14] </option>
210 <option value="GRCh38">Homo sapiens, GRCh38.p12 [GCA_000001405.27] </option>
211 <option value="mm9">Mus musculus, GRCm37 [GCA_000001635.18]</option>
212 <option value="mm10">Mus musculus, GRCm38.p6 [GCA_000001635.8]</option>
213 <option value="rn6">Rattus norvegicus, Rnor_6.0 [GCA_000001895.4]</option>
214 <option value="c_elegans">Caenorhabditis elegans</option>
215 <option value="dog">Dog</option>
216 </param>
217 </when>
218
219 <when value="get_sigmut">
220 <conditional name="vcfile_input">
221 <param name="vcfile" type="select" label="VC file" help="Select the format of your input data">
222 <option value="maf">Mutation Annotation Format</option>
223 <option value="icgc">Tab-separated file</option>
224 <option value="vcf">Variant Call Format</option>
225 </param>
226 <when value='maf'>
227 <param name="maf_file" type="data" format="maf" label="select VC file" help="Select the input file in MAF format." />
228 </when>
229 <when value='icgc'>
230 <param name="icgc_file" type="data" format="txt" label="select VC file" help="Select the input file in ICGC format." />
231 </when>
232 <when value='vcf'>
233 <param name="vcf_file" type="data" format="vcf" label="select VC file" help="Select the input file in VCF format." />
234 </when>
235 </conditional>
236
237 <param name="refgendat" type="select" label="Reference genome to be analyzed" help="Use the following reference genome:">
238 <option value="GRCh37">Homo sapiens, GRCh37.p13 [GCA_000001405.14] </option>
239 <option value="GRCh38">Homo sapiens, GRCh38.p12 [GCA_000001405.27] </option>
240 <option value="mm9">Mus musculus, GRCm37 [GCA_000001635.18]</option>
241 <option value="mm10">Mus musculus, GRCm38.p6 [GCA_000001635.8]</option>
242 <option value="rn6">Rattus norvegicus, Rnor_6.0 [GCA_000001895.4]</option>
243 <option value="c_elegans">Caenorhabditis elegans</option>
244 <option value="dog">Dog</option>
245 </param>
246
247 <conditional name="bed_input">
248 <param name="bedfile" type="select" label="BED file" help="Input a BED file">
249 <option value="yes">Yes</option>
250 <option value="no" selected="true">No</option>
251 </param>
252 <when value='yes'>
253 <param name="bed_file" format="bed" type="data" label="Use a BED file containing the set of regions" help="Provide a BED file"/>
254 </when>
255 <when value='no'>
256 </when>
257 </conditional>
258 <param name="plot" type="boolean" truevalue="true" label="Produce plot results?" checked="False" help="Show plots"/>
259 <param name="exome" type="boolean" label="Use only the exome?" checked="False" help="Use exome"/>
260 <param name="chrom_based" type="boolean" label="Create the matrices on a per chromosome basis?" checked="False" help="Show snvs"/>
261 <param name="tsb_stat" type="boolean" truevalue="true" label="Performs a transcriptional strand bias test?" checked="False" help="Show snvs"/>
262 <param name="seqInfo" type="boolean" truevalue="true" label="Export sequence information?" checked="False" help="Show sequence information"/>
263 <param name="gs" type="boolean" label="Performs gene strand bias test?" checked="False" help="Show snvs"/>
264 </when>
265 </conditional>
266 </inputs>
267
268 <outputs>
269 <data format="txt" name="logref" label="Log file: Install a Reference Genome">
270 <filter>set_analysis['choices'] == 'install_genome'</filter>
271 </data>
272
273 <data format="txt" name="logsmt" label="Log file: Calculate Mutational Signatures">
274 <filter>set_analysis['choices'] == 'get_sigmut'</filter>
275 </data>
276
277 <data format="pdf" name="SBS6" label="--> Plot SBS 6 Sig. Mut.">
278 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
279 </data>
280
281 <data format="pdf" name="SBS24" label="--> Plot SBS 24 Sig. Mut.">
282 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
283 </data>
284
285 <data format="pdf" name="SBS78" label="--> Plot SBS 78 Sig. Mut.">
286 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
287 </data>
288
289 <data format="pdf" name="SBS96" label="--> Plot SBS 96 Sig. Mut.">
290 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
291 </data>
292
293 <data format="pdf" name="SBS384" label="--> Plot SBS 384 Sig. Mut.">
294 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
295 </data>
296
297 <data format="pdf" name="SBS1536" label="--> Plot SBS 1536 Sig. Mut.">
298 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
299 </data>
300
301 <data format="pdf" name="DBS78" label="--> Plot DBS 78 Sig. Mut.">
302 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
303 </data>
304
305 <data format="pdf" name="DBS186" label="--> Plot DBS 186 Sig. Mut.">
306 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
307 </data>
308
309 <data format="pdf" name="ID_simple" label="--> Plot ID simple Sig. Mut.">
310 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
311 </data>
312
313 <data format="pdf" name="ID_TSB" label="--> Plot ID TSB Sig. Mut.">
314 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
315 </data>
316
317 <data format="pdf" name="ID_83" label="--> Plot ID 83 Sig. Mut.">
318 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
319 </data>
320
321 <data format="pdf" name="ID_94" label="--> Plot ID 94 Sig. Mut.">
322 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
323 </data>
324
325 <data format="pdf" name="ID_96" label="--> Plot ID 96 Sig. Mut.">
326 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
327 </data>
328
329 <data format="txt" name="Exo11" label="--> DBS_exome.vcf">
330 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
331 </data>
332
333 <data format="txt" name="Exo12" label="--> SNV_exome.vcf">
334 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
335 </data>
336
337 <data format="txt" name="Exo1" label="--> DBS 78 Sig. Mut. EXOME">
338 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
339 </data>
340
341 <data format="txt" name="Exo2" label="--> DBS 186 Sig. Mut. EXOME">
342 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
343 </data>
344
345 <data format="txt" name="Exo3" label="--> DBS 1248 Sig. Mut. EXOME">
346 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
347 </data>
348
349 <data format="txt" name="Exo4" label="--> DBS 2976 Sig. Mut. EXOME">
350 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
351 </data>
352
353 <data format="txt" name="Exo5" label="--> SBS 6 Sig. Mut. EXOME">
354 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
355 </data>
356
357 <data format="txt" name="Exo6" label="--> SBS 24 Sig. Mut. EXOME">
358 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
359 </data>
360
361 <data format="txt" name="Exo7" label="--> SBS 96 Sig. Mut. EXOME">
362 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
363 </data>
364
365 <data format="txt" name="Exo8" label="--> SBS 384 Sig. Mut. EXOME">
366 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
367 </data>
368
369 <data format="txt" name="Exo9" label="--> SBS 1536 Sig. Mut. EXOME">
370 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
371 </data>
372
373 <data format="txt" name="Exo10" label="--> SBS 6144 Sig. Mut. EXOME">
374 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
375 </data>
376
377 <data format="txt" name="sigRes" label="--> TSB: Significant Results">
378 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] is True</filter>
379 </data>
380
381 <data format="txt" name="TSB24" label="--> TSB: 24 Sig. Mut.">
382 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] is True</filter>
383 </data>
384
385 <data format="txt" name="TSB384" label="--> TSB: 96 Sig. Mut.">
386 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] is True</filter>
387 </data>
388
389 <data format="txt" name="TSB6144" label="--> TSB: 1536 Sig. Mut.">
390 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] is True</filter>
391 </data>
392
393
394 <data format="txt" name="SeqInf1" label="--> DBS 78 Sig. Mut. ALL">
395 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
396 </data>
397
398 <data format="txt" name="SeqInf2" label="--> DBS 186 Sig. Mut. ALL">
399 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
400 </data>
401
402 <data format="txt" name="SeqInf3" label="--> DBS 1248 Sig. Mut. ALL">
403 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
404 </data>
405
406 <data format="txt" name="SeqInf4" label="--> DBS 2976 Sig. Mut. ALL">
407 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
408 </data>
409
410 <data format="txt" name="SeqInf5" label="--> SBS 6 Sig. Mut. ALL">
411 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
412 </data>
413
414 <data format="txt" name="SeqInf6" label="--> SBS 24 Sig. Mut. ALL">
415 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
416 </data>
417
418 <data format="txt" name="SeqInf7" label="--> SBS 96 Sig. Mut. ALL">
419 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
420 </data>
421
422 <data format="txt" name="SeqInf8" label="--> SBS 384 Sig. Mut. ALL">
423 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
424 </data>
425
426 <data format="txt" name="SeqInf9" label="--> SBS 1536 Sig. Mut. ALL">
427 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
428 </data>
429
430 <data format="txt" name="SeqInf10" label="--> SBS 6144 Sig. Mut. ALL">
431 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
432 </data>
433
434
435 <data format="txt" name="SeqInf11" label="--> ID 28 Sig. Mut. ALL">
436 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
437 </data>
438
439 <data format="txt" name="SeqInf12" label="--> ID 83 Sig. Mut. ALL">
440 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
441 </data>
442
443 <data format="txt" name="SeqInf13" label="--> ID 94 Sig. Mut. ALL">
444 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
445 </data>
446
447 <data format="txt" name="SeqInf14" label="--> ID 96 Sig. Mut. ALL">
448 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
449 </data>
450
451 <data format="txt" name="SeqInf15" label="--> ID 415 Sig. Mut. ALL">
452 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
453 </data>
454
455 <data format="txt" name="SeqInf16" label="--> ID 8628 Sig. Mut. ALL">
456 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
457 </data>
458
459 </outputs>
460
461 <tests>
462 <test>
463 <conditional name="set_analysis">
464 <param name="choices" value="install_genome"/>
465 <param name="refgendwn" ftype="fasta" value="c_elegans"/>
466 </conditional>
467 <output name="logref" file="c_elegans.log" lines_diff="5"/>
468 </test>
469
470
471 <test>
472 <conditional name="set_analysis">
473 <param name="choices" value="get_sigmut"/>
474 <param name="refgendat" ftype="fasta" value="c_elegans"/>
475 <conditional name="vcfile_input">
476 <param name="vcfile" value="icgc"/>
477 <param name="icgc_file" ftype="txt" value="test_matrix.txt"/>
478 </conditional>
479 <conditional name="bed_input">
480 <param name="bedfile" value="no"/>
481 </conditional>
482 <param name="plot" value="True"/>
483 </conditional>
484
485 <output name="ID_simple" file="ID_simple.pdf" lines_diff="5"/>
486 <output name="ID_TSB" file="ID_TSB.pdf" lines_diff="5"/>
487 <output name="ID_83" file="ID_83.pdf" lines_diff="5"/>
488
489 </test>
490
491 </tests>
492
493 <help><![CDATA[
494
495 **SigProfiler**
496
497 This script configures the SigProfiler analysis pipeline.
498 You must specify a VCF file for at least one sample.
499
500
501 **Options**
502 --version show program's version number and exit
503
504 -h, --help show this help message and exit
505
506 --install_genome Install de novo any of the following reference
507 genomes: 'GRCh37', 'GRCh38', 'mm9' or 'mm10'.
508
509 --name=APPENDIX Provide a project name
510
511 --genome=NAME Provide a reference genome (ex: GRCh37, GRCh38,
512 mm9 or mm10).
513
514 --files=Abs_path Path where the input vcf files are located
515
516 --exome Use only the exome or not
517
518 --bed=FILE BED file containing the set of regions to be used
519 in generating the matrices
520
521 --chrom Create the matrices on a per chromosome basis
522
523 --plot Generate the plots for each context
524
525 --tsb Performs a transcriptional strand bias test for the
526 24, 384, and 6144 contexts
527
528 --gs Performs a gene strand bias test
529
530 For further info see: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator
531
532 ]]></help>
533
534 <citations>
535 <citation type="doi">10.1186/s12864-019-6041-2</citation>
536 </citations>
537
538 </tool>