|
6
|
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.search_use_bool == "use":
|
|
|
144 #if $use_search.check_use_hit == 'nousehit':
|
|
|
145 -nohitacc
|
|
|
146 #end if
|
|
|
147 #end if
|
|
|
148 #*<!-- DONT REMOVE THIS ; -->*#
|
|
|
149 >log.log 2>log.log;
|
|
|
150
|
|
|
151 mv $basename-epibuilder.xlsx EpiBuilder_report.xlsx;
|
|
|
152
|
|
|
153 #*<!-- Rename output files -->*#
|
|
|
154 mv ${basename}-epibuilder.txt EpiBuilder;
|
|
|
155
|
|
|
156
|
|
|
157 ]]>
|
|
|
158 </command>
|
|
|
159 <inputs>
|
|
|
160 <!-- Bepipred 2.0 -->
|
|
|
161 <conditional name="bepi_type">
|
|
|
162 <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" >
|
|
|
163 <option value="y" selected="true">csv file from Bepipred 2.0</option>
|
|
|
164 <option value="n" >text file from IEDB Bcell Software standalone</option>
|
|
|
165 <option value="id">JobID from Bepipred 2.0 Server</option>
|
|
|
166 </param>
|
|
|
167 <when value="y" >
|
|
|
168 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
|
|
|
169 </when>
|
|
|
170 <when value="n" >
|
|
|
171 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
|
|
|
172 </when>
|
|
|
173 <when value="id" >
|
|
|
174 <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" >
|
|
|
175 <!-- Check if its an empty value-->
|
|
|
176 <validator type="empty_field" message="ID required"/>
|
|
|
177 </param>
|
|
|
178 </when>
|
|
|
179 </conditional>
|
|
|
180 <param name="tresh_bepi2" min="0.0" value="0.6" type="float" label="Threshold for Bepipred 2.0" help="Default = 0.6" />
|
|
|
181 <!-- Epitope Length -->
|
|
|
182 <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" />
|
|
|
183 <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" />
|
|
|
184 <!-- EMINI -->
|
|
|
185 <conditional name="emini_method">
|
|
|
186 <param name="emini_choice" type="boolean" checked="true" truevalue="eminiyes" falsevalue="eminino" label="Use Emini Surface Accessibility Prediction method?" />
|
|
|
187 <when value="eminino">
|
|
|
188 </when>
|
|
|
189 <when value="eminiyes">
|
|
|
190 <conditional name="emini_t">
|
|
|
191 <param name="t_emini" display="radio" type="select" label="Threshold" help="Define threshold for Emini" >
|
|
|
192 <option value="d_emini_choice" selected="true">Default (calculated by method)</option>
|
|
|
193 <option value="t_emini_choice">Set Threshold</option>
|
|
|
194 </param>
|
|
|
195 <when value="t_emini_choice">
|
|
|
196 <param name="thresh_em_value" value="0" type="float" label="Value" />
|
|
|
197 </when>
|
|
|
198 <when value="d_emini_choice">
|
|
|
199 </when>
|
|
|
200 </conditional>
|
|
|
201 </when>
|
|
|
202 </conditional>
|
|
|
203 <!-- PARKER -->
|
|
|
204 <conditional name="parker_method">
|
|
|
205 <param name="parker_choice" type="boolean" checked="true" truevalue="parkeryes" falsevalue="parkerno" label="Use Parker Hydrophilicity Prediction method?" />
|
|
|
206 <when value="parkerno">
|
|
|
207 </when>
|
|
|
208 <when value="parkeryes">
|
|
|
209 <conditional name="parker_t">
|
|
|
210 <param name="t_parker" display="radio" type="select" label="Threshold" help="Define threshold for Parker" >
|
|
|
211 <option value="d_parker_choice" selected="true">Default (calculated by method)</option>
|
|
|
212 <option value="t_parker_choice">Set Threshold</option>
|
|
|
213 </param>
|
|
|
214 <when value="t_parker_choice">
|
|
|
215 <param name="thresh_park_value" value="0" type="float" label="Value" />
|
|
|
216 </when>
|
|
|
217 <when value="d_parker_choice">
|
|
|
218 </when>
|
|
|
219 </conditional>
|
|
|
220 </when>
|
|
|
221 </conditional>
|
|
|
222 <!-- Chou -->
|
|
|
223 <conditional name="chou_method">
|
|
|
224 <param name="chou_choice" type="boolean" checked="true" truevalue="chouyes" falsevalue="chouno" label="Use Chou & Fasman Beta-Turn Prediction method?" />
|
|
|
225 <when value="chouno">
|
|
|
226 </when>
|
|
|
227 <when value="chouyes">
|
|
|
228 <conditional name="chou_t">
|
|
|
229 <param name="t_chou" display="radio" type="select" label="Threshold" help="Define threshold for Chou & Fasman" >
|
|
|
230 <option value="d_chou_choice" selected="true">Default (calculated by method)</option>
|
|
|
231 <option value="t_chou_choice">Set Threshold</option>
|
|
|
232 </param>
|
|
|
233 <when value="t_chou_choice">
|
|
|
234 <param name="thresh_chou_value" value="0" type="float" label="Value" />
|
|
|
235 </when>
|
|
|
236 <when value="d_chou_choice">
|
|
|
237 </when>
|
|
|
238 </conditional>
|
|
|
239 </when>
|
|
|
240 </conditional>
|
|
|
241 <!-- Karplus -->
|
|
|
242 <conditional name="karplus_method">
|
|
|
243 <param name="karplus_choice" type="boolean" checked="true" truevalue="karplusyes" falsevalue="karplusno" label="Use Karplus & Schulz Flexibility Prediction method?" />
|
|
|
244 <when value="karplusno">
|
|
|
245 </when>
|
|
|
246 <when value="karplusyes">
|
|
|
247 <conditional name="karplus_t">
|
|
|
248 <param name="t_karplus" display="radio" type="select" label="Threshold" help="Define threshold for Karplus & Schulz" >
|
|
|
249 <option value="d_karplus_choice" selected="true">Default (calculated by method)</option>
|
|
|
250 <option value="t_karplus_choice">Set Threshold</option>
|
|
|
251 </param>
|
|
|
252 <when value="t_karplus_choice">
|
|
|
253 <param name="thresh_karplus_value" type="float" value="0" label="Value" />
|
|
|
254 </when>
|
|
|
255 <when value="d_karplus_choice">
|
|
|
256 </when>
|
|
|
257 </conditional>
|
|
|
258 </when>
|
|
|
259 </conditional>
|
|
|
260 <!-- Kolaskar -->
|
|
|
261 <conditional name="kolaskar_method">
|
|
|
262 <param name="kolaskar_choice" type="boolean" checked="true" truevalue="kolaskaryes" falsevalue="kolaskarno" label="Use Kolaskar & Tongaonkar Antigenicity method?" />
|
|
|
263 <when value="kolaskarno">
|
|
|
264 </when>
|
|
|
265 <when value="kolaskaryes">
|
|
|
266 <conditional name="kolaskar_t">
|
|
|
267 <param name="t_kolaskar" display="radio" type="select" label="Threshold" help="Define threshold for Kolaskar & Tongaonkar" >
|
|
|
268 <option value="d_kolaskar_choice" selected="true">Default (calculated by method)</option>
|
|
|
269 <option value="t_kolaskar_choice">Set Threshold</option>
|
|
|
270 </param>
|
|
|
271 <when value="t_kolaskar_choice">
|
|
|
272 <param name="thresh_kolaskar_value" type="float" value="0" label="Value" />
|
|
|
273 </when>
|
|
|
274 <when value="d_kolaskar_choice">
|
|
|
275 </when>
|
|
|
276 </conditional>
|
|
|
277 </when>
|
|
|
278 </conditional>
|
|
|
279 <!-- Insert Proteome -->
|
|
|
280 <conditional name="use_search">
|
|
|
281 <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?" />
|
|
|
282 <when value="dont">
|
|
|
283 </when>
|
|
|
284 <when value="use">
|
|
|
285 <repeat name="prot_input" title="Proteome" min="1">
|
|
|
286 <param type="data" name="prot_file" format="fasta" label="Proteome file" help="Protein sequences in fasta format" />
|
|
|
287 <param type="text" name="prot_name" label="Proteome name" help="Give a name to this dataset" >
|
|
|
288 <!-- Change spaces for '_' -->
|
|
|
289 <sanitizer>
|
|
|
290 <valid initial="string.printable">
|
|
|
291 <remove value=" "/>
|
|
|
292 </valid>
|
|
|
293 <mapping initial="none">
|
|
|
294 <add source=" " target="_"/>
|
|
|
295 </mapping>
|
|
|
296 </sanitizer>
|
|
|
297 <!-- Check if its an empty value-->
|
|
|
298 <validator type="empty_field" message="Basename required"/>
|
|
|
299 </param>
|
|
|
300 </repeat>
|
|
|
301 <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" />
|
|
|
302 <conditional name="blast">
|
|
|
303 <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" />
|
|
|
304 <when value="blastno">
|
|
|
305 </when>
|
|
|
306 <when value="blastyes">
|
|
|
307 <param name="blast_id" value="90" min="1" type="integer" label="Identity" help="[0-100] Minimal identity accepted to parse blast results" />
|
|
|
308 <param name="blast_cover" value="90" min="2" type="integer" label="Coverage" help="[0-100] Minimal coverage accepted to parse blast results" />
|
|
|
309 <param name="blast_wordsize" value="4" min="1" type="integer" label="Word-Size" help="Blast argument word-size" />
|
|
|
310 <param name="blast_task" type="select" label="Task" help="How blastp should run">
|
|
|
311 <option value="blastp-short" selected="True">Blastp-short</option>
|
|
|
312 <option value="blastp-fast">Blastp-fast</option>
|
|
|
313 <option value="blastp">Blastp</option>
|
|
|
314 </param>
|
|
|
315 </when>
|
|
|
316 </conditional>
|
|
|
317 </when>
|
|
|
318 </conditional>
|
|
|
319 <param name="basename" type="text" value="" label="Basename" help="Provide a name for this run (string text without special characters)" >
|
|
|
320 <!-- Change spaces for '_' -->
|
|
|
321 <sanitizer>
|
|
|
322 <valid initial="string.printable">
|
|
|
323 <remove value=" "/>
|
|
|
324 </valid>
|
|
|
325 <mapping initial="none">
|
|
|
326 <add source=" " target="_"/>
|
|
|
327 </mapping>
|
|
|
328 </sanitizer>
|
|
|
329 <!-- Check if its an empty value-->
|
|
|
330 <validator type="empty_field" message="Basename required"/>
|
|
|
331 </param>
|
|
|
332 </inputs>
|
|
|
333 <outputs>
|
|
|
334 <data name="epif_out" format="txt" from_work_dir="EpiBuilder" label="EpiBuilder Output Summary - ${basename}" />
|
|
|
335 <data name="ep_xls" format="xlsx" from_work_dir="EpiBuilder_report.xlsx" label="EpiBuilder Report - ${basename}" />
|
|
|
336 <collection type="list" label="EpiBuilder Files - ${basename}" name="epif_collection" >
|
|
|
337 <discover_datasets format="fasta" pattern="(?P<designation>.*)\.fasta" visible="false" />
|
|
|
338 <discover_datasets format="txt" pattern="(?P<designation>.*)\.tsv" visible="false" />
|
|
|
339 <discover_datasets format="txt" pattern="(?P<designation>.*)\.txt" visible="false" />
|
|
|
340 </collection>
|
|
|
341 <collection type="list" label="EpiBuilder Blast Run - ${basename}" name="blast_collection" >
|
|
|
342 <filter>use_search['search_use_bool'] is True and use_search['blast']['blast_search'] is True</filter>
|
|
|
343 <discover_datasets pattern="(?P<designation>.*)blast\.csv" visible="false" />
|
|
|
344 </collection>
|
|
|
345 </outputs>
|
|
|
346 <tests>
|
|
|
347 <test>
|
|
|
348 <!-- Test all methods threshold selected, command line version of input with proteome-->
|
|
|
349 <conditional name="bepi_type">
|
|
|
350 <param name="bepipred_origin" value="y"/>
|
|
|
351 <param name="bepi_out" value="input_bepi_online.csv"/>
|
|
|
352 </conditional>
|
|
|
353 <param name="tresh_bepi2" value="0.6"/>
|
|
|
354
|
|
|
355 <param name="min_length" value="10" />
|
|
|
356 <param name="max_length" value="30" />
|
|
|
357
|
|
|
358 <conditional name="emini_method">
|
|
|
359 <param name="emini_choice" value="eminiyes"/>
|
|
|
360 <conditional name="emini_t">
|
|
|
361 <param name="t_emini" value="t_emini_choice"/>
|
|
|
362 <param name="thresh_em_value" value="0.8" />
|
|
|
363 </conditional>
|
|
|
364 </conditional>
|
|
|
365
|
|
|
366 <conditional name="parker_method">
|
|
|
367 <param name="parker_choice" value="parkeryes"/>
|
|
|
368 <conditional name="parker_t">
|
|
|
369 <param name="t_parker" value="t_parker_choice"/>
|
|
|
370 <param name="thresh_park_value" value="0.8" />
|
|
|
371 </conditional>
|
|
|
372 </conditional>
|
|
|
373
|
|
|
374 <conditional name="chou_method">
|
|
|
375 <param name="chou_choice" value="chouyes"/>
|
|
|
376 <conditional name="chou_t">
|
|
|
377 <param name="t_chou" value="t_chou_choice"/>
|
|
|
378 <param name="thresh_chou_value" value="0.8" />
|
|
|
379 </conditional>
|
|
|
380 </conditional>
|
|
|
381
|
|
|
382 <conditional name="karplus_method">
|
|
|
383 <param name="karplus_choice" value="karplusyes"/>
|
|
|
384 <conditional name="karplus_t">
|
|
|
385 <param name="t_karplus" value="t_karplus_choice"/>
|
|
|
386 <param name="thresh_karplus_value" value="0.8" />
|
|
|
387 </conditional>
|
|
|
388 </conditional>
|
|
|
389
|
|
|
390
|
|
|
391 <conditional name="kolaskar_method">
|
|
|
392 <param name="kolaskar_choice" value="kolaskaryes"/>
|
|
|
393 <conditional name="kolaskar_t">
|
|
|
394 <param name="t_kolaskar" value="t_kolaskar_choice"/>
|
|
|
395 <param name="thresh_kolaskar_value" value="0.8" />
|
|
|
396 </conditional>
|
|
|
397 </conditional>
|
|
|
398 <!-- This first part test all methods-->
|
|
|
399
|
|
|
400 <conditional name="use_search">
|
|
|
401 <param name="search_use_bool" value="use" />
|
|
|
402 <repeat name="prot_input">
|
|
|
403 <param name="prot_name" value="test_proteom" />
|
|
|
404 <param name="prot_file" value="proteom.fasta" />
|
|
|
405 </repeat>
|
|
|
406 <param name="check_use_hit" value="usehit"/>
|
|
|
407 <conditional name="blast">
|
|
|
408 <param name="blast_search" value="blastyes" />
|
|
|
409 <param name="blast_id" value="90" />
|
|
|
410 <param name="blast_cover" value="90" />
|
|
|
411 <param name="blast_wordsize" value="4" />
|
|
|
412 <param name="blast_task" value="blastp-short" />
|
|
|
413 </conditional>
|
|
|
414 </conditional>
|
|
|
415
|
|
|
416 <param name="basename" value="online" />
|
|
|
417
|
|
|
418 <output name="epif_out" file="online-EpiBuilder.txt" />
|
|
|
419 <output name="ep_xls" file="online-EpiBuilder.xlsx" />
|
|
|
420 <output_collection name= "epif_collection">
|
|
|
421 <element name="ep_prot_sum" file="online-EpiBuilder-protein-summary.tsv" />
|
|
|
422 <element name="ep_top" file="online-EpiBuilder-topology.tsv" />
|
|
|
423 <element name="ep_score" file="online-EpiBuilder-socre.tsv" />
|
|
|
424 <element name="ep_detail" file="online-EpiBuilder-epitope-detail.tsv" />
|
|
|
425 <element name="ep_parameters" file="online-EpiBuilder-parameters.tsv" />
|
|
|
426 <element name="ep_fasta" file="online-EpiBuilder-fasta.fasta" />
|
|
|
427 </output_collection>
|
|
|
428 <output_collection name="blast_collection" >
|
|
|
429 <element name="test_proteom" file="online-test_proteom_blast.csv" ftype="csv" />
|
|
|
430 </output_collection >
|
|
|
431 </test>
|
|
|
432
|
|
|
433 <test>
|
|
|
434 <!-- Test all methods threshold selected, online version of input with proteome-->
|
|
|
435 <conditional name="bepi_type">
|
|
|
436 <param name="bepipred_origin" value="y"/>
|
|
|
437 <param name="bepi_out" value="input_bcell_command_line.txt"/>
|
|
|
438 </conditional>
|
|
|
439
|
|
|
440 <param name="bepipred_origin" value="n"/>
|
|
|
441 <param name="tresh_bepi2" value="0.6"/>
|
|
|
442
|
|
|
443 <param name="min_length" value="10" />
|
|
|
444 <param name="max_length" value="30" />
|
|
|
445
|
|
|
446 <conditional name="emini_method">
|
|
|
447 <param name="emini_choice" value="eminiyes"/>
|
|
|
448 <conditional name="emini_t">
|
|
|
449 <param name="t_emini" value="t_emini_choice"/>
|
|
|
450 <param name="thresh_em_value" value="0.8" />
|
|
|
451 </conditional>
|
|
|
452 </conditional>
|
|
|
453
|
|
|
454 <conditional name="parker_method">
|
|
|
455 <param name="parker_choice" value="parkeryes"/>
|
|
|
456 <conditional name="parker_t">
|
|
|
457 <param name="t_parker" value="t_parker_choice"/>
|
|
|
458 <param name="thresh_park_value" value="0.8" />
|
|
|
459 </conditional>
|
|
|
460 </conditional>
|
|
|
461
|
|
|
462 <conditional name="chou_method">
|
|
|
463 <param name="chou_choice" value="chouyes"/>
|
|
|
464 <conditional name="chou_t">
|
|
|
465 <param name="t_chou" value="t_chou_choice"/>
|
|
|
466 <param name="thresh_chou_value" value="0.8" />
|
|
|
467 </conditional>
|
|
|
468 </conditional>
|
|
|
469
|
|
|
470 <conditional name="karplus_method">
|
|
|
471 <param name="karplus_choice" value="karplusyes"/>
|
|
|
472 <conditional name="karplus_t">
|
|
|
473 <param name="t_karplus" value="t_karplus_choice"/>
|
|
|
474 <param name="thresh_karplus_value" value="0.8" />
|
|
|
475 </conditional>
|
|
|
476 </conditional>
|
|
|
477
|
|
|
478
|
|
|
479 <conditional name="kolaskar_method">
|
|
|
480 <param name="kolaskar_choice" value="kolaskaryes"/>
|
|
|
481 <conditional name="kolaskar_t">
|
|
|
482 <param name="t_kolaskar" value="t_kolaskar_choice"/>
|
|
|
483 <param name="thresh_kolaskar_value" value="0.8" />
|
|
|
484 </conditional>
|
|
|
485 </conditional>
|
|
|
486 <!-- This first part test all methods-->
|
|
|
487
|
|
|
488 <conditional name="use_search">
|
|
|
489 <param name="search_use_bool" value="use"/>
|
|
|
490 <repeat name="prot_input">
|
|
|
491 <param name="prot_name" value="test_proteom" />
|
|
|
492 <param name="prot_file" value="proteom.fasta" />
|
|
|
493 </repeat>
|
|
|
494 <param name="check_use_hit" value="usehit"/>
|
|
|
495 <conditional name="blast">
|
|
|
496 <param name="blast_search" value="blastyes" />
|
|
|
497 <param name="blast_id" value="90" />
|
|
|
498 <param name="blast_cover" value="90"/>
|
|
|
499 <param name="blast_wordsize" value="4" />
|
|
|
500 <param name="blast_task" value="blastp-short" />
|
|
|
501 </conditional>
|
|
|
502 </conditional>
|
|
|
503
|
|
|
504 <param name="basename" value="command" />
|
|
|
505
|
|
|
506 <output name="epif_out" file="command-EpiBuilder.txt" />
|
|
|
507 <output name="ep_xls" file="command-EpiBuilder.xlsx" />
|
|
|
508 <output_collection name= "epif_collection">
|
|
|
509 <element name="ep_prot_sum" file="command-EpiBuilder-protein-summary.tsv" />
|
|
|
510 <element name="ep_top" file="command-EpiBuilder-topology.tsv" />
|
|
|
511 <element name="ep_score" file="command-EpiBuilder-socre.tsv" />
|
|
|
512 <element name="ep_detail" file="command-EpiBuilder-epitope-detail.tsv" />
|
|
|
513 <element name="ep_parameters" file="command-EpiBuilder-parameters.tsv" />
|
|
|
514 <element name="ep_fasta" file="command-EpiBuilder-fasta.fasta" />
|
|
|
515 </output_collection>
|
|
|
516 <output_collection name="blast_collection" >
|
|
|
517 <element name="test_proteom" file="command-test_proteom_blast.csv" ftype="csv" />
|
|
|
518 </output_collection >
|
|
|
519 </test>
|
|
|
520 </tests>
|
|
|
521 <help>
|
|
|
522 **How to Run**
|
|
|
523
|
|
|
524 First, you must have a file with epitopes predicted by Bepipred 2.0 or have one job submmited into bepipred's server.
|
|
|
525
|
|
|
526 .. class:: warningmark
|
|
|
527
|
|
|
528 Input this file (or jobID) and specify if Bepipred 2.0 was ran online or command-line based through bcell standalone suite.
|
|
|
529
|
|
|
530 Select methods that you want to check your epitopes for validation.
|
|
|
531
|
|
|
532 Give a threshold for each method (or use default threshold).
|
|
|
533
|
|
|
534 Optionaly, you can search validated epitopes in proteomes datasets, as many as you wish.
|
|
|
535
|
|
|
536 .. class:: warningmark
|
|
|
537
|
|
|
538 If you want to search using Blastp, this software and Makeblastdb must be avaliable on your server's $PATH.
|
|
|
539
|
|
|
540 -----
|
|
|
541
|
|
|
542 **Outputs**
|
|
|
543
|
|
|
544
|
|
|
545 **Summary** : Prediction overview
|
|
|
546
|
|
|
547 **Protein Summary** : Show proteins that have epitopes predicted
|
|
|
548
|
|
|
549 **Fasta** : Epitopes' sequences
|
|
|
550
|
|
|
551 **Topology** : Show epitope match in each method, aminoacid per aminoacid
|
|
|
552
|
|
|
553 **Score** : Detailed score for aminoacids
|
|
|
554
|
|
|
555 **Epitope Detail** : Properties of each predicted epitope
|
|
|
556
|
|
|
557 **Parameters** : Softwares, thresholds and parameters used for prediction
|
|
|
558
|
|
|
559 **Xls Report** : Table with epitope detail, protein summary, topology and scores
|
|
|
560
|
|
|
561 **Collection with blast files** : All blast results for each proteome
|
|
|
562
|
|
|
563
|
|
|
564 -----
|
|
|
565
|
|
|
566 .. class:: infomark
|
|
|
567
|
|
|
568 **For more information, checkout our GitHub page**: https://github.com/bioinfo-ufsc/EpiBuilder
|
|
|
569
|
|
|
570 -----
|
|
|
571
|
|
|
572 Please cite methods used in your analysis, available bellow
|
|
|
573
|
|
|
574 | Bioinformatics Lab - UFSC - 2021
|
|
|
575
|
|
|
576 </help>
|
|
|
577 <citations>
|
|
|
578 <citation type="doi">10.1093/nar/gkx346</citation>
|
|
|
579 <citation type="doi">10.1016/0014-5793(90)80535-q</citation>
|
|
|
580 <citation type="doi">10.1002/9780470122921.ch2</citation>
|
|
|
581 <citation type="doi">10.1021/bi00367a013</citation>
|
|
|
582 <citation type="doi">https://doi.org/10.1007/BF01195768</citation>
|
|
|
583 <citation type="doi">doi:10.1128/jvi.55.3.836-839.1985</citation>
|
|
|
584 <citation type="doi">10.1371/journal.pcbi.1006791</citation>
|
|
|
585 <citation type="doi">https://doi.org/10.1093/nar/gky379</citation>
|
|
|
586 </citations>
|
|
|
587 </tool>
|
