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comparison epibuilder-1.1.xml @ 2:8fa9e663cca5 draft

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Uploaded corrected condition for use_hit
author bioinformatics_lab_ufsc
date Thu, 25 Nov 2021 03:59:45 +0000
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1:57555f63bbd3 2:8fa9e663cca5
1 <tool id="epibuilder_1.1" name="EpiBuilder" version="1.1">
2 <description>Predict B cell epitopes</description>
3 <requirements>
4 <requirement type="package" version=">=1.8">Java</requirement>
5 <requirement type="package" version=">=2.11.0+">Blastp</requirement>
6 <requirement type="package" version=">=2.11.0+">Makeblastdb</requirement>
7 </requirements>
8 <stdio>
9 <regex match="command not found"
10 source="both"
11 level="log"
12 description="WARNING: some methods could not be applied -> check inputs and outputs files" />
13 <regex match="makeblastdb "
14 source="both"
15 level="log"
16 description="makeblastdb and blastp must be in $PATH on your Galaxy server" />
17 <regex match="blastp "
18 source="both"
19 level="log"
20 description="makeblastdb and blastp must be in $PATH on your Galaxy server" />
21 </stdio>
22 <command><![CDATA[
23 #*<!--
24 Methods used will be saved in $param with each threshold
25 Threshold is separated from method by ":"
26 Each method is separated by ";"
27 example: emini:0.8;parker:d;
28
29 >> d means defalt threshold
30 -->*#
31
32 #*<!-- Set variables that concatenate methods -->*#
33 #set param = ''
34 #set nomethod = ''
35 #set proteomes = ''
36
37 #*<!-- Add Bepipred2.0 method -->*#
38 #if $bepi_type.bepipred_origin == 'y':
39 #set bepipred_origin = '-o'
40 #*<!-- jobid -->*#
41 #elif $bepi_type.bepipred_origin == 'id':
42 #set bepipred_origin = '-jobid ' + str($bepi_type.job_id)
43 #else:
44 #set bepipred_origin = ''
45 #end if
46
47 #*<!-- Add Emini method -->*#
48 #if $emini_method.emini_choice == 'eminiyes':
49 #if $emini_method.emini_t.t_emini == 't_emini_choice'
50 #set param += 'emini:' + str($emini_method.emini_t.thresh_em_value) + ';'
51 #else:
52 #set param += 'emini:d;'
53 #end if
54 #end if
55
56 #*<!-- Add Parker method -->*#
57 #if $parker_method.parker_choice == 'parkeryes':
58 #if $parker_method.parker_t.t_parker == 't_parker_choice'
59 #set param += 'parker:' + str($parker_method.parker_t.thresh_park_value) + ';'
60 #else:
61 #set param += 'parker:d;'
62 #end if
63 #end if
64
65 #*<!-- Add Chou method -->*#
66 #if $chou_method.chou_choice == 'chouyes':
67 #if $chou_method.chou_t.t_chou == 't_chou_choice'
68 #set param += 'chou_fosman:' + str($chou_method.chou_t.thresh_chou_value) + ';'
69 #else:
70 #set param += 'chou_fosman:d;'
71 #end if
72 #end if
73
74 #*<!-- Add Karplus method -->*#
75 #if $karplus_method.karplus_choice == 'karplusyes':
76 #if $karplus_method.karplus_t.t_karplus == 't_karplus_choice'
77 #set param += 'karplus_schulz:' + str($karplus_method.karplus_t.thresh_karplus_value) + ';'
78 #else:
79 #set param += 'karplus_schulz:d;'
80 #end if
81 #end if
82
83 #*<!-- Add Kolaskar method -->*#
84 #if $kolaskar_method.kolaskar_choice == 'kolaskaryes':
85 #if $kolaskar_method.kolaskar_t.t_kolaskar == 't_kolaskar_choice'
86 #set param += 'kolaskar:' + str($kolaskar_method.kolaskar_t.thresh_kolaskar_value) + ';'
87 #else:
88 #set param += 'kolaskar:d;'
89 #end if
90 #end if
91
92
93
94 #*<!-- Clean $proteome if there's no protome -->*#
95 #if proteomes == '-proteomes ':
96 #set proteomes = ''
97 #end if
98
99
100 #*<!-- Parse blast command -->*#
101
102 #if $use_search.search_use_bool == "use":
103 #*<!-- Add proteomes, as many as given -->*#
104 #if $use_search.prot_input:
105 #for $file in $use_search.prot_input:
106 #set proteomes += str($file.prot_name) + '=' + str($file.prot_file) + ';'
107 #end for
108 #end if
109 #if $use_search.prot_input:
110 #if $use_search.blast.blast_search == 'blastyes':
111 #set blast_command = 'task=' + str($use_search.blast.blast_task)
112 #set blast_command += ';identity=' + str($use_search.blast.blast_id) + ';cover=' + str($use_search.blast.blast_cover) + ';word-size=' + str($use_search.blast.blast_wordsize)
113 #set blast_command += ';makeblastdb_path=makeblastdb;blastp_path=blastp'
114 #end if
115 #end if
116 #end if
117
118 #*<!-- Paste Command-line and run -->*#
119
120 java -jar $__tool_directory__/epibuilder-1.1.jar
121
122 #*<!-- bepipred_origin give -o if online, nothing if command and -jobid if jobID -->*#
123 #*<!-- if origin is not jobid, there is a file, and -b must be passed -->*#
124 #if $bepi_type.bepipred_origin != 'id':
125 -b ${bepi_type.bepi_out}
126 #end if
127 -t ${tresh_bepi2}
128 ${bepipred_origin}
129 #if $param:
130 -p "${param}"
131 #end if
132 -f "${basename}"
133 -min_len ${min_length}
134 -max_len ${max_length}
135 #if $proteomes:
136 -proteomes
137 "${proteomes}"
138 #if $use_search.blast.blast_search == 'blastyes':
139 -blast "${blast_command}"
140 #end if
141 #end if
142
143 #if $use_search.check_use_hit == 'nousehit':
144 -nohitacc
145 #end if
146 #*<!-- DONT REMOVE THIS ; -->*#
147 >log.log 2>log.log;
148
149 mv $basename-epibuilder.xlsx EpiBuilder_report.xlsx;
150
151 #*<!-- Rename output files -->*#
152 mv ${basename}-epibuilder.txt EpiBuilder;
153
154
155 ]]>
156 </command>
157 <inputs>
158 <!-- Bepipred 2.0 -->
159 <conditional name="bepi_type">
160 <param name="bepipred_origin" type="select" display="radio" label="Input files" help="Online prediction returns a csv file, command-line based returns a tsv file" >
161 <option value="y" selected="true">csv file from Bepipred 2.0</option>
162 <option value="n" >text file from IEDB Bcell Software standalone</option>
163 <option value="id">JobID from Bepipred 2.0 Server</option>
164 </param>
165 <when value="y" >
166 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
167 </when>
168 <when value="n" >
169 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
170 </when>
171 <when value="id" >
172 <param name="job_id" type="text" value="" label="JobID" help="Prediction must be complete - check it in: http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi?jobid=YOUR_JOB_ID" >
173 <!-- Check if its an empty value-->
174 <validator type="empty_field" message="ID required"/>
175 </param>
176 </when>
177 </conditional>
178 <param name="tresh_bepi2" min="0.0" value="0.6" type="float" label="Threshold for Bepipred 2.0" help="Default = 0.6" />
179 <!-- Epitope Length -->
180 <param name="min_length" value="10" min="1" type="integer" label="Min epitope length" help="[1-X] Minimal length must be smaller than maximal length" />
181 <param name="max_length" value="30" min="2" type="integer" label="Max epitope length" help="[2-X] Maximal length must be greather than minimal length" />
182 <!-- EMINI -->
183 <conditional name="emini_method">
184 <param name="emini_choice" type="boolean" checked="true" truevalue="eminiyes" falsevalue="eminino" label="Use Emini Surface Accessibility Prediction method?" />
185 <when value="eminino">
186 </when>
187 <when value="eminiyes">
188 <conditional name="emini_t">
189 <param name="t_emini" display="radio" type="select" label="Threshold" help="Define threshold for Emini" >
190 <option value="d_emini_choice" selected="true">Default (calculated by method)</option>
191 <option value="t_emini_choice">Set Threshold</option>
192 </param>
193 <when value="t_emini_choice">
194 <param name="thresh_em_value" value="0" type="float" label="Value" />
195 </when>
196 <when value="d_emini_choice">
197 </when>
198 </conditional>
199 </when>
200 </conditional>
201 <!-- PARKER -->
202 <conditional name="parker_method">
203 <param name="parker_choice" type="boolean" checked="true" truevalue="parkeryes" falsevalue="parkerno" label="Use Parker Hydrophilicity Prediction method?" />
204 <when value="parkerno">
205 </when>
206 <when value="parkeryes">
207 <conditional name="parker_t">
208 <param name="t_parker" display="radio" type="select" label="Threshold" help="Define threshold for Parker" >
209 <option value="d_parker_choice" selected="true">Default (calculated by method)</option>
210 <option value="t_parker_choice">Set Threshold</option>
211 </param>
212 <when value="t_parker_choice">
213 <param name="thresh_park_value" value="0" type="float" label="Value" />
214 </when>
215 <when value="d_parker_choice">
216 </when>
217 </conditional>
218 </when>
219 </conditional>
220 <!-- Chou -->
221 <conditional name="chou_method">
222 <param name="chou_choice" type="boolean" checked="true" truevalue="chouyes" falsevalue="chouno" label="Use Chou &amp; Fasman Beta-Turn Prediction method?" />
223 <when value="chouno">
224 </when>
225 <when value="chouyes">
226 <conditional name="chou_t">
227 <param name="t_chou" display="radio" type="select" label="Threshold" help="Define threshold for Chou &amp; Fasman" >
228 <option value="d_chou_choice" selected="true">Default (calculated by method)</option>
229 <option value="t_chou_choice">Set Threshold</option>
230 </param>
231 <when value="t_chou_choice">
232 <param name="thresh_chou_value" value="0" type="float" label="Value" />
233 </when>
234 <when value="d_chou_choice">
235 </when>
236 </conditional>
237 </when>
238 </conditional>
239 <!-- Karplus -->
240 <conditional name="karplus_method">
241 <param name="karplus_choice" type="boolean" checked="true" truevalue="karplusyes" falsevalue="karplusno" label="Use Karplus &amp; Schulz Flexibility Prediction method?" />
242 <when value="karplusno">
243 </when>
244 <when value="karplusyes">
245 <conditional name="karplus_t">
246 <param name="t_karplus" display="radio" type="select" label="Threshold" help="Define threshold for Karplus &amp; Schulz" >
247 <option value="d_karplus_choice" selected="true">Default (calculated by method)</option>
248 <option value="t_karplus_choice">Set Threshold</option>
249 </param>
250 <when value="t_karplus_choice">
251 <param name="thresh_karplus_value" type="float" value="0" label="Value" />
252 </when>
253 <when value="d_karplus_choice">
254 </when>
255 </conditional>
256 </when>
257 </conditional>
258 <!-- Kolaskar -->
259 <conditional name="kolaskar_method">
260 <param name="kolaskar_choice" type="boolean" checked="true" truevalue="kolaskaryes" falsevalue="kolaskarno" label="Use Kolaskar &amp; Tongaonkar Antigenicity method?" />
261 <when value="kolaskarno">
262 </when>
263 <when value="kolaskaryes">
264 <conditional name="kolaskar_t">
265 <param name="t_kolaskar" display="radio" type="select" label="Threshold" help="Define threshold for Kolaskar &amp; Tongaonkar" >
266 <option value="d_kolaskar_choice" selected="true">Default (calculated by method)</option>
267 <option value="t_kolaskar_choice">Set Threshold</option>
268 </param>
269 <when value="t_kolaskar_choice">
270 <param name="thresh_kolaskar_value" type="float" value="0" label="Value" />
271 </when>
272 <when value="d_kolaskar_choice">
273 </when>
274 </conditional>
275 </when>
276 </conditional>
277 <!-- Insert Proteome -->
278 <conditional name="use_search">
279 <param name="search_use_bool" type="boolean" checked="false" truevalue="use" falsevalue="dont" label="Do you want to search the predicted epitopes in a proteome file?" />
280 <when value="dont">
281 </when>
282 <when value="use">
283 <repeat name="prot_input" title="Proteome" min="1">
284 <param type="data" name="prot_file" format="fasta" label="Proteome file" help="Protein sequences in fasta format" />
285 <param type="text" name="prot_name" label="Proteome name" help="Give a name to this dataset" >
286 <!-- Change spaces for '_' -->
287 <sanitizer>
288 <valid initial="string.printable">
289 <remove value=" "/>
290 </valid>
291 <mapping initial="none">
292 <add source=" " target="_"/>
293 </mapping>
294 </sanitizer>
295 <!-- Check if its an empty value-->
296 <validator type="empty_field" message="Basename required"/>
297 </param>
298 </repeat>
299 <param name="check_use_hit" type="boolean" checked="true" truevalue="usehit" falsevalue="nousehit" label="Show accession ID on result files?" help="Choose this option if you want to add accession ID numbers" />
300 <conditional name="blast">
301 <param name="blast_search" type="boolean" checked="false" truevalue="blastyes" falsevalue="blastno" label="Blastp" help="Choose this option if you want to add a blast search for epitopes in proteomes" />
302 <when value="blastno">
303 </when>
304 <when value="blastyes">
305 <param name="blast_id" value="90" min="1" type="integer" label="Identity" help="[0-100] Minimal identity accepted to parse blast results" />
306 <param name="blast_cover" value="90" min="2" type="integer" label="Coverage" help="[0-100] Minimal coverage accepted to parse blast results" />
307 <param name="blast_wordsize" value="4" min="1" type="integer" label="Word-Size" help="Blast argument word-size" />
308 <param name="blast_task" type="select" label="Task" help="How blastp should run">
309 <option value="blastp-short" selected="True">Blastp-short</option>
310 <option value="blastp-fast">Blastp-fast</option>
311 <option value="blastp">Blastp</option>
312 </param>
313 </when>
314 </conditional>
315 </when>
316 </conditional>
317 <param name="basename" type="text" value="" label="Basename" help="Provide a name for this run (string text without special characters)" >
318 <!-- Change spaces for '_' -->
319 <sanitizer>
320 <valid initial="string.printable">
321 <remove value=" "/>
322 </valid>
323 <mapping initial="none">
324 <add source=" " target="_"/>
325 </mapping>
326 </sanitizer>
327 <!-- Check if its an empty value-->
328 <validator type="empty_field" message="Basename required"/>
329 </param>
330 </inputs>
331 <outputs>
332 <data name="epif_out" format="txt" from_work_dir="EpiBuilder" label="EpiBuilder Output Summary - ${basename}" />
333 <data name="ep_xls" format="xlsx" from_work_dir="EpiBuilder_report.xlsx" label="EpiBuilder Report - ${basename}" />
334 <collection type="list" label="EpiBuilder Files - ${basename}" name="epif_collection" >
335 <discover_datasets format="fasta" pattern="(?P&lt;designation&gt;.*)\.fasta" visible="false" />
336 <discover_datasets format="txt" pattern="(?P&lt;designation&gt;.*)\.tsv" visible="false" />
337 <discover_datasets format="txt" pattern="(?P&lt;designation&gt;.*)\.txt" visible="false" />
338 </collection>
339 <collection type="list" label="EpiBuilder Blast Run - ${basename}" name="blast_collection" >
340 <filter>use_search['search_use_bool'] is True and use_search['blast']['blast_search'] is True</filter>
341 <discover_datasets pattern="(?P&lt;designation&gt;.*)blast\.csv" visible="false" />
342 </collection>
343 </outputs>
344 <tests>
345 <test>
346 <!-- Test all methods threshold selected, command line version of input with proteome-->
347 <conditional name="bepi_type">
348 <param name="bepipred_origin" value="y"/>
349 <param name="bepi_out" value="input_bepi_online.csv"/>
350 </conditional>
351 <param name="tresh_bepi2" value="0.6"/>
352
353 <param name="min_length" value="10" />
354 <param name="max_length" value="30" />
355
356 <conditional name="emini_method">
357 <param name="emini_choice" value="eminiyes"/>
358 <conditional name="emini_t">
359 <param name="t_emini" value="t_emini_choice"/>
360 <param name="thresh_em_value" value="0.8" />
361 </conditional>
362 </conditional>
363
364 <conditional name="parker_method">
365 <param name="parker_choice" value="parkeryes"/>
366 <conditional name="parker_t">
367 <param name="t_parker" value="t_parker_choice"/>
368 <param name="thresh_park_value" value="0.8" />
369 </conditional>
370 </conditional>
371
372 <conditional name="chou_method">
373 <param name="chou_choice" value="chouyes"/>
374 <conditional name="chou_t">
375 <param name="t_chou" value="t_chou_choice"/>
376 <param name="thresh_chou_value" value="0.8" />
377 </conditional>
378 </conditional>
379
380 <conditional name="karplus_method">
381 <param name="karplus_choice" value="karplusyes"/>
382 <conditional name="karplus_t">
383 <param name="t_karplus" value="t_karplus_choice"/>
384 <param name="thresh_karplus_value" value="0.8" />
385 </conditional>
386 </conditional>
387
388
389 <conditional name="kolaskar_method">
390 <param name="kolaskar_choice" value="kolaskaryes"/>
391 <conditional name="kolaskar_t">
392 <param name="t_kolaskar" value="t_kolaskar_choice"/>
393 <param name="thresh_kolaskar_value" value="0.8" />
394 </conditional>
395 </conditional>
396 <!-- This first part test all methods-->
397
398 <conditional name="use_search">
399 <param name="search_use_bool" value="use" />
400 <repeat name="prot_input">
401 <param name="prot_name" value="test_proteom" />
402 <param name="prot_file" value="proteom.fasta" />
403 </repeat>
404 <param name="check_use_hit" value="usehit"/>
405 <conditional name="blast">
406 <param name="blast_search" value="blastyes" />
407 <param name="blast_id" value="90" />
408 <param name="blast_cover" value="90" />
409 <param name="blast_wordsize" value="4" />
410 <param name="blast_task" value="blastp-short" />
411 </conditional>
412 </conditional>
413
414 <param name="basename" value="online" />
415
416 <output name="epif_out" file="online-EpiBuilder.txt" />
417 <output name="ep_xls" file="online-EpiBuilder.xlsx" />
418 <output_collection name= "epif_collection">
419 <element name="ep_prot_sum" file="online-EpiBuilder-protein-summary.tsv" />
420 <element name="ep_top" file="online-EpiBuilder-topology.tsv" />
421 <element name="ep_score" file="online-EpiBuilder-socre.tsv" />
422 <element name="ep_detail" file="online-EpiBuilder-epitope-detail.tsv" />
423 <element name="ep_parameters" file="online-EpiBuilder-parameters.tsv" />
424 <element name="ep_fasta" file="online-EpiBuilder-fasta.fasta" />
425 </output_collection>
426 <output_collection name="blast_collection" >
427 <element name="test_proteom" file="online-test_proteom_blast.csv" ftype="csv" />
428 </output_collection >
429 </test>
430
431 <test>
432 <!-- Test all methods threshold selected, online version of input with proteome-->
433 <conditional name="bepi_type">
434 <param name="bepipred_origin" value="y"/>
435 <param name="bepi_out" value="input_bcell_command_line.txt"/>
436 </conditional>
437
438 <param name="bepipred_origin" value="n"/>
439 <param name="tresh_bepi2" value="0.6"/>
440
441 <param name="min_length" value="10" />
442 <param name="max_length" value="30" />
443
444 <conditional name="emini_method">
445 <param name="emini_choice" value="eminiyes"/>
446 <conditional name="emini_t">
447 <param name="t_emini" value="t_emini_choice"/>
448 <param name="thresh_em_value" value="0.8" />
449 </conditional>
450 </conditional>
451
452 <conditional name="parker_method">
453 <param name="parker_choice" value="parkeryes"/>
454 <conditional name="parker_t">
455 <param name="t_parker" value="t_parker_choice"/>
456 <param name="thresh_park_value" value="0.8" />
457 </conditional>
458 </conditional>
459
460 <conditional name="chou_method">
461 <param name="chou_choice" value="chouyes"/>
462 <conditional name="chou_t">
463 <param name="t_chou" value="t_chou_choice"/>
464 <param name="thresh_chou_value" value="0.8" />
465 </conditional>
466 </conditional>
467
468 <conditional name="karplus_method">
469 <param name="karplus_choice" value="karplusyes"/>
470 <conditional name="karplus_t">
471 <param name="t_karplus" value="t_karplus_choice"/>
472 <param name="thresh_karplus_value" value="0.8" />
473 </conditional>
474 </conditional>
475
476
477 <conditional name="kolaskar_method">
478 <param name="kolaskar_choice" value="kolaskaryes"/>
479 <conditional name="kolaskar_t">
480 <param name="t_kolaskar" value="t_kolaskar_choice"/>
481 <param name="thresh_kolaskar_value" value="0.8" />
482 </conditional>
483 </conditional>
484 <!-- This first part test all methods-->
485
486 <conditional name="use_search">
487 <param name="search_use_bool" value="use"/>
488 <repeat name="prot_input">
489 <param name="prot_name" value="test_proteom" />
490 <param name="prot_file" value="proteom.fasta" />
491 </repeat>
492 <param name="check_use_hit" value="usehit"/>
493 <conditional name="blast">
494 <param name="blast_search" value="blastyes" />
495 <param name="blast_id" value="90" />
496 <param name="blast_cover" value="90"/>
497 <param name="blast_wordsize" value="4" />
498 <param name="blast_task" value="blastp-short" />
499 </conditional>
500 </conditional>
501
502 <param name="basename" value="command" />
503
504 <output name="epif_out" file="command-EpiBuilder.txt" />
505 <output name="ep_xls" file="command-EpiBuilder.xlsx" />
506 <output_collection name= "epif_collection">
507 <element name="ep_prot_sum" file="command-EpiBuilder-protein-summary.tsv" />
508 <element name="ep_top" file="command-EpiBuilder-topology.tsv" />
509 <element name="ep_score" file="command-EpiBuilder-socre.tsv" />
510 <element name="ep_detail" file="command-EpiBuilder-epitope-detail.tsv" />
511 <element name="ep_parameters" file="command-EpiBuilder-parameters.tsv" />
512 <element name="ep_fasta" file="command-EpiBuilder-fasta.fasta" />
513 </output_collection>
514 <output_collection name="blast_collection" >
515 <element name="test_proteom" file="command-test_proteom_blast.csv" ftype="csv" />
516 </output_collection >
517 </test>
518 </tests>
519 <help>
520 **How to Run**
521
522 First, you must have a file with epitopes predicted by Bepipred 2.0 or have one job submmited into bepipred's server.
523
524 .. class:: warningmark
525
526 Input this file (or jobID) and specify if Bepipred 2.0 was ran online or command-line based through bcell standalone suite.
527
528 Select methods that you want to check your epitopes for validation.
529
530 Give a threshold for each method (or use default threshold).
531
532 Optionaly, you can search validated epitopes in proteomes datasets, as many as you wish.
533
534 .. class:: warningmark
535
536 If you want to search using Blastp, this software and Makeblastdb must be avaliable on your server's $PATH.
537
538 -----
539
540 **Outputs**
541
542
543 **Summary** : Prediction overview
544
545 **Protein Summary** : Show proteins that have epitopes predicted
546
547 **Fasta** : Epitopes' sequences
548
549 **Topology** : Show epitope match in each method, aminoacid per aminoacid
550
551 **Score** : Detailed score for aminoacids
552
553 **Epitope Detail** : Properties of each predicted epitope
554
555 **Parameters** : Softwares, thresholds and parameters used for prediction
556
557 **Xls Report** : Table with epitope detail, protein summary, topology and scores
558
559 **Collection with blast files** : All blast results for each proteome
560
561
562 -----
563
564 .. class:: infomark
565
566 **For more information, checkout our GitHub page**: https://github.com/bioinfo-ufsc/EpiBuilder
567
568 -----
569
570 Please cite methods used in your analysis, available bellow
571
572 | Bioinformatics Lab - UFSC - 2021
573
574 </help>
575 <citations>
576 <citation type="doi">10.1093/nar/gkx346</citation>
577 <citation type="doi">10.1016/0014-5793(90)80535-q</citation>
578 <citation type="doi">10.1002/9780470122921.ch2</citation>
579 <citation type="doi">10.1021/bi00367a013</citation>
580 <citation type="doi">https://doi.org/10.1007/BF01195768</citation>
581 <citation type="doi">doi:10.1128/jvi.55.3.836-839.1985</citation>
582 <citation type="doi">10.1371/journal.pcbi.1006791</citation>
583 <citation type="doi">https://doi.org/10.1093/nar/gky379</citation>
584 </citations>
585 </tool>