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date Mon, 29 Mar 2021 23:44:21 +0000
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1 <tool id="epifinder_0.2" name="EpiFinder" version="1.0">
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_blast.blast_use_bool == "use":
103 #*<!-- Add proteomes, as many as given -->*#
104 #if $use_blast.prot_input:
105 #for $file in $use_blast.prot_input:
106 #set proteomes += str($file.prot_name) + '=' + str($file.prot_file) + ';'
107 #end for
108 #end if
109 #if $use_blast.prot_input:
110 #if $use_blast.blast.blast_search == 'blastyes':
111 #set blast_command = 'task=' + str($use_blast.blast.blast_task)
112 #set blast_command += ';identity=' + str($use_blast.blast.blast_id) + ';cover=' + str($use_blast.blast.blast_cover) + ';word-size=' + str($use_blast.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__/epifinder-1.0.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 $use_blast.blast.blast_search == 'blastyes':
139 -blast "${blast_command}"
140 #end if
141 #end if
142 #*<!-- DONT REMOVE THIS ; -->*#
143 >log.log 2>log.log;
144
145 mv $basename-epifinder.xlsx epifinder_report.xlsx;
146
147 #*<!-- Rename output files -->*#
148 mv ${basename}-epifinder.txt epifinder;
149
150
151 ]]>
152 </command>
153 <inputs>
154 <!-- Bepipred 2.0 -->
155 <conditional name="bepi_type">
156 <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" >
157 <option value="y" selected="true">csv file from Bepipred 2.0</option>
158 <option value="n" >text file from IEDB Bcell Software standalone</option>
159 <option value="id">JobID from Bepipred 2.0 Server</option>
160 </param>
161 <when value="y" >
162 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
163 </when>
164 <when value="n" >
165 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
166 </when>
167 <when value="id" >
168 <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" >
169 <!-- Check if its an empty value-->
170 <validator type="empty_field" message="ID required"/>
171 </param>
172 </when>
173 </conditional>
174 <param name="tresh_bepi2" min="0.0" value="0.6" type="float" label="Threshold for Bepipred 2.0" help="Default = 0.6" />
175 <!-- Epitope Length -->
176 <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" />
177 <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" />
178 <!-- EMINI -->
179 <conditional name="emini_method">
180 <param name="emini_choice" type="boolean" checked="true" truevalue="eminiyes" falsevalue="eminino" label="Use Emini Surface Accessibility Prediction method?" />
181 <when value="eminino">
182 </when>
183 <when value="eminiyes">
184 <conditional name="emini_t">
185 <param name="t_emini" display="radio" type="select" label="Threshold" help="Define threshold for Emini" >
186 <option value="d_emini_choice" selected="true">Default (calculated by method)</option>
187 <option value="t_emini_choice">Set Threshold</option>
188 </param>
189 <when value="t_emini_choice">
190 <param name="thresh_em_value" value="0" type="float" label="Value" />
191 </when>
192 <when value="d_emini_choice">
193 </when>
194 </conditional>
195 </when>
196 </conditional>
197 <!-- PARKER -->
198 <conditional name="parker_method">
199 <param name="parker_choice" type="boolean" checked="true" truevalue="parkeryes" falsevalue="parkerno" label="Use Parker Hydrophilicity Prediction method?" />
200 <when value="parkerno">
201 </when>
202 <when value="parkeryes">
203 <conditional name="parker_t">
204 <param name="t_parker" display="radio" type="select" label="Threshold" help="Define threshold for Parker" >
205 <option value="d_parker_choice" selected="true">Default (calculated by method)</option>
206 <option value="t_parker_choice">Set Threshold</option>
207 </param>
208 <when value="t_parker_choice">
209 <param name="thresh_park_value" value="0" type="float" label="Value" />
210 </when>
211 <when value="d_parker_choice">
212 </when>
213 </conditional>
214 </when>
215 </conditional>
216 <!-- Chou -->
217 <conditional name="chou_method">
218 <param name="chou_choice" type="boolean" checked="true" truevalue="chouyes" falsevalue="chouno" label="Use Chou &amp; Fasman Beta-Turn Prediction method?" />
219 <when value="chouno">
220 </when>
221 <when value="chouyes">
222 <conditional name="chou_t">
223 <param name="t_chou" display="radio" type="select" label="Threshold" help="Define threshold for Chou &amp; Fasman" >
224 <option value="d_chou_choice" selected="true">Default (calculated by method)</option>
225 <option value="t_chou_choice">Set Threshold</option>
226 </param>
227 <when value="t_chou_choice">
228 <param name="thresh_chou_value" value="0" type="float" label="Value" />
229 </when>
230 <when value="d_chou_choice">
231 </when>
232 </conditional>
233 </when>
234 </conditional>
235 <!-- Karplus -->
236 <conditional name="karplus_method">
237 <param name="karplus_choice" type="boolean" checked="true" truevalue="karplusyes" falsevalue="karplusno" label="Use Karplus &amp; Schulz Flexibility Prediction method?" />
238 <when value="karplusno">
239 </when>
240 <when value="karplusyes">
241 <conditional name="karplus_t">
242 <param name="t_karplus" display="radio" type="select" label="Threshold" help="Define threshold for Karplus &amp; Schulz" >
243 <option value="d_karplus_choice" selected="true">Default (calculated by method)</option>
244 <option value="t_karplus_choice">Set Threshold</option>
245 </param>
246 <when value="t_karplus_choice">
247 <param name="thresh_karplus_value" type="float" value="0" label="Value" />
248 </when>
249 <when value="d_karplus_choice">
250 </when>
251 </conditional>
252 </when>
253 </conditional>
254 <!-- Kolaskar -->
255 <conditional name="kolaskar_method">
256 <param name="kolaskar_choice" type="boolean" checked="true" truevalue="kolaskaryes" falsevalue="kolaskarno" label="Use Kolaskar &amp; Tongaonkar Antigenicity method?" />
257 <when value="kolaskarno">
258 </when>
259 <when value="kolaskaryes">
260 <conditional name="kolaskar_t">
261 <param name="t_kolaskar" display="radio" type="select" label="Threshold" help="Define threshold for Kolaskar &amp; Tongaonkar" >
262 <option value="d_kolaskar_choice" selected="true">Default (calculated by method)</option>
263 <option value="t_kolaskar_choice">Set Threshold</option>
264 </param>
265 <when value="t_kolaskar_choice">
266 <param name="thresh_kolaskar_value" type="float" value="0" label="Value" />
267 </when>
268 <when value="d_kolaskar_choice">
269 </when>
270 </conditional>
271 </when>
272 </conditional>
273 <!-- Insert Proteome -->
274 <conditional name="use_blast">
275 <param name="blast_use_bool" type="boolean" checked="false" truevalue="use" falsevalue="dont" label="Do you want to search the predicted epitopes in a proteome file?" />
276 <when value="dont">
277 </when>
278 <when value="use">
279 <repeat name="prot_input" title="Proteome" min="1">
280 <param type="data" name="prot_file" format="fasta" label="Proteome file" help="Protein sequences in fasta format" />
281 <param type="text" name="prot_name" label="Proteome name" help="Give a name to this dataset" >
282 <!-- Change spaces for '_' -->
283 <sanitizer>
284 <valid initial="string.printable">
285 <remove value=" "/>
286 </valid>
287 <mapping initial="none">
288 <add source=" " target="_"/>
289 </mapping>
290 </sanitizer>
291 <!-- Check if its an empty value-->
292 <validator type="empty_field" message="Basename required"/>
293 </param>
294 </repeat>
295 <conditional name="blast">
296 <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" />
297 <when value="blastno">
298 </when>
299 <when value="blastyes">
300 <param name="blast_id" value="90" min="1" type="integer" label="Identity" help="[0-100] Minimal identity accepted to parse blast results" />
301 <param name="blast_cover" value="90" min="2" type="integer" label="Coverage" help="[0-100] Minimal coverage accepted to parse blast results" />
302 <param name="blast_wordsize" value="4" min="1" type="integer" label="Word-Size" help="Blast argument word-size" />
303 <param name="blast_task" type="select" label="Task" help="How blastp should run">
304 <option value="blastp-short" selected="True">Blastp-short</option>
305 <option value="blastp-fast">Blastp-fast</option>
306 <option value="blastp">Blastp</option>
307 </param>
308 </when>
309 </conditional>
310 </when>
311 </conditional>
312 <param name="basename" type="text" value="" label="Basename" help="Provide a name for this run (string text without special characters)" >
313 <!-- Change spaces for '_' -->
314 <sanitizer>
315 <valid initial="string.printable">
316 <remove value=" "/>
317 </valid>
318 <mapping initial="none">
319 <add source=" " target="_"/>
320 </mapping>
321 </sanitizer>
322 <!-- Check if its an empty value-->
323 <validator type="empty_field" message="Basename required"/>
324 </param>
325 </inputs>
326 <outputs>
327 <data name="epif_out" format="txt" from_work_dir="epifinder" label="EpiFinder Output Summary - ${basename}" />
328 <data name="ep_xls" format="xlsx" from_work_dir="epifinder_report.xlsx" label="EpiFinder Report - ${basename}" />
329 <collection type="list" label="EpiFinder Files - ${basename}" name="epif_collection" >
330 <discover_datasets format="fasta" pattern="(?P&lt;designation&gt;.*)\.fasta" visible="false" />
331 <discover_datasets format="txt" pattern="(?P&lt;designation&gt;.*)\.tsv" visible="false" />
332 <discover_datasets format="txt" pattern="(?P&lt;designation&gt;.*)\.txt" visible="false" />
333 </collection>
334 <collection type="list" label="EpiFinder Blast Run - ${basename}" name="blast_collection" >
335 <filter>use_blast['blast_use_bool'] is True and use_blast['blast']['blast_search'] is True</filter>
336 <discover_datasets pattern="(?P&lt;designation&gt;.*)blast\.csv" visible="false" />
337 </collection>
338 </outputs>
339 <tests>
340 <test>
341 <!-- Test all methods threshold selected, command line version of input with proteome-->
342 <conditional name="bepi_type">
343 <param name="bepipred_origin" value="y"/>
344 <param name="bepi_out" value="input_bepi_online.csv"/>
345 </conditional>
346 <param name="tresh_bepi2" value="0.6"/>
347
348 <param name="min_length" value="10" />
349 <param name="max_length" value="30" />
350
351 <conditional name="emini_method">
352 <param name="emini_choice" value="eminiyes"/>
353 <conditional name="emini_t">
354 <param name="t_emini" value="t_emini_choice"/>
355 <param name="thresh_em_value" value="0.8" />
356 </conditional>
357 </conditional>
358
359 <conditional name="parker_method">
360 <param name="parker_choice" value="parkeryes"/>
361 <conditional name="parker_t">
362 <param name="t_parker" value="t_parker_choice"/>
363 <param name="thresh_park_value" value="0.8" />
364 </conditional>
365 </conditional>
366
367 <conditional name="chou_method">
368 <param name="chou_choice" value="chouyes"/>
369 <conditional name="chou_t">
370 <param name="t_chou" value="t_chou_choice"/>
371 <param name="thresh_chou_value" value="0.8" />
372 </conditional>
373 </conditional>
374
375 <conditional name="karplus_method">
376 <param name="karplus_choice" value="karplusyes"/>
377 <conditional name="karplus_t">
378 <param name="t_karplus" value="t_karplus_choice"/>
379 <param name="thresh_karplus_value" value="0.8" />
380 </conditional>
381 </conditional>
382
383
384 <conditional name="kolaskar_method">
385 <param name="kolaskar_choice" value="kolaskaryes"/>
386 <conditional name="kolaskar_t">
387 <param name="t_kolaskar" value="t_kolaskar_choice"/>
388 <param name="thresh_kolaskar_value" value="0.8" />
389 </conditional>
390 </conditional>
391 <!-- This first part test all methods-->
392
393 <conditional name="use_blast" >
394 <param name="blast_use_bool" value="use" />
395 <repeat name="prot_input">
396 <param name="prot_name" value="test_proteom" />
397 <param name="prot_file" value="proteom.fasta" />
398 </repeat>
399 <conditional name="blast">
400 <param name="blast_search" value="blastyes" />
401 <param name="blast_id" value="90" />
402 <param name="blast_cover" value="90" />
403 <param name="blast_wordsize" value="4" />
404 <param name="blast_task" value="blastp-short" />
405 </conditional>
406 </conditional>
407
408 <param name="basename" value="online" />
409
410 <output name="epif_out" file="online-epifinder.txt" />
411 <output name="ep_xls" file="online-epifinder.xlsx" />
412 <output_collection name= "epif_collection">
413 <element name="ep_prot_sum" file="online-epifinder-protein-summary.tsv" />
414 <element name="ep_top" file="online-epifinder-topology.tsv" />
415 <element name="ep_score" file="online-epifinder-socre.tsv" />
416 <element name="ep_detail" file="online-epifinder-epitope-detail.tsv" />
417 <element name="ep_parameters" file="online-epifinder-parameters.tsv" />
418 <element name="ep_fasta" file="online-epifinder-fasta.fasta" />
419 </output_collection>
420 <output_collection name="blast_collection" >
421 <element name="test_proteom" file="online-test_proteom_blast.csv" ftype="csv" />
422 </output_collection >
423 </test>
424
425 <test>
426 <!-- Test all methods threshold selected, online version of input with proteome-->
427 <conditional name="bepi_type">
428 <param name="bepipred_origin" value="y"/>
429 <param name="bepi_out" value="input_bcell_command_line.txt"/>
430 </conditional>
431
432 <param name="bepipred_origin" value="n"/>
433 <param name="tresh_bepi2" value="0.6"/>
434
435 <param name="min_length" value="10" />
436 <param name="max_length" value="30" />
437
438 <conditional name="emini_method">
439 <param name="emini_choice" value="eminiyes"/>
440 <conditional name="emini_t">
441 <param name="t_emini" value="t_emini_choice"/>
442 <param name="thresh_em_value" value="0.8" />
443 </conditional>
444 </conditional>
445
446 <conditional name="parker_method">
447 <param name="parker_choice" value="parkeryes"/>
448 <conditional name="parker_t">
449 <param name="t_parker" value="t_parker_choice"/>
450 <param name="thresh_park_value" value="0.8" />
451 </conditional>
452 </conditional>
453
454 <conditional name="chou_method">
455 <param name="chou_choice" value="chouyes"/>
456 <conditional name="chou_t">
457 <param name="t_chou" value="t_chou_choice"/>
458 <param name="thresh_chou_value" value="0.8" />
459 </conditional>
460 </conditional>
461
462 <conditional name="karplus_method">
463 <param name="karplus_choice" value="karplusyes"/>
464 <conditional name="karplus_t">
465 <param name="t_karplus" value="t_karplus_choice"/>
466 <param name="thresh_karplus_value" value="0.8" />
467 </conditional>
468 </conditional>
469
470
471 <conditional name="kolaskar_method">
472 <param name="kolaskar_choice" value="kolaskaryes"/>
473 <conditional name="kolaskar_t">
474 <param name="t_kolaskar" value="t_kolaskar_choice"/>
475 <param name="thresh_kolaskar_value" value="0.8" />
476 </conditional>
477 </conditional>
478 <!-- This first part test all methods-->
479
480 <conditional name="use_blast">
481 <param name="blast_use_bool" value="use"/>
482 <repeat name="prot_input">
483 <param name="prot_name" value="test_proteom" />
484 <param name="prot_file" value="proteom.fasta" />
485 </repeat>
486 <conditional name="blast">
487 <param name="blast_search" value="blastyes" />
488 <param name="blast_id" value="90" />
489 <param name="blast_cover" value="90"/>
490 <param name="blast_wordsize" value="4" />
491 <param name="blast_task" value="blastp-short" />
492 </conditional>
493 </conditional>
494
495 <param name="basename" value="command" />
496
497 <output name="epif_out" file="command-epifinder.txt" />
498 <output name="ep_xls" file="command-epifinder.xlsx" />
499 <output_collection name= "epif_collection">
500 <element name="ep_prot_sum" file="command-epifinder-protein-summary.tsv" />
501 <element name="ep_top" file="command-epifinder-topology.tsv" />
502 <element name="ep_score" file="command-epifinder-socre.tsv" />
503 <element name="ep_detail" file="command-epifinder-epitope-detail.tsv" />
504 <element name="ep_parameters" file="command-epifinder-parameters.tsv" />
505 <element name="ep_fasta" file="command-epifinder-fasta.fasta" />
506 </output_collection>
507 <output_collection name="blast_collection" >
508 <element name="test_proteom" file="command-test_proteom_blast.csv" ftype="csv" />
509 </output_collection >
510 </test>
511 </tests>
512 <help>
513 **How to Run**
514
515 First, you must have a file with epitopes predicted by Bepipred 2.0 or have one job submmited into bepipred's server.
516
517 .. class:: warningmark
518
519 Input this file (or jobID) and specify if Bepipred 2.0 was ran online or command-line based through bcell standalone suite.
520
521 Select methods that you want to check your epitopes for validation.
522
523 Give a threshold for each method (or use default threshold).
524
525 Optionaly, you can search validated epitopes in proteomes datasets, as many as you wish.
526
527 .. class:: warningmark
528
529 If you want to search using Blastp, this software and Makeblastdb must be avaliable on your server's $PATH.
530
531 -----
532
533 **Outputs**
534
535
536 **Summary** : Prediction overview
537
538 **Protein Summary** : Show proteins that have epitopes predicted
539
540 **Fasta** : Epitopes' sequences
541
542 **Topology** : Show epitope match in each method, aminoacid per aminoacid
543
544 **Score** : Detailed score for aminoacids
545
546 **Epitope Detail** : Properties of each predicted epitope
547
548 **Parameters** : Softwares, thresholds and parameters used for prediction
549
550 **Xls Report** : Table with epitope detail, protein summary, topology and scores
551
552 **Collection with blast files** : All blast results for each proteome
553
554
555 -----
556
557 .. class:: infomark
558
559 **For more information, checkout our GitHub page**: https://github.com/bioinfo-ufsc/epifinder
560
561 -----
562
563 Please cite methods used in your analysis, available bellow
564
565 | Bioinformatics Lab - UFSC - 2021
566
567 </help>
568 <citations>
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