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date Mon, 05 Jun 2023 02:44:43 +0000
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1 <tool id="edu.tamu.cpt2.helicalWheel.generateHelicalWheel" name="Helical Wheel" version="1.0">
2 <description>Generate and Plot a Protein Helical Wheel</description>
3 <macros>
4 <import>cpt-macros.xml</import>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements">
8 <requirement type="package">numpy</requirement>
9 <requirement type="package">pandas</requirement>
10 <requirement type="package" version="0.18.1">scikit-learn</requirement>
11 <requirement type="package">scipy</requirement>
12 <requirement type="package">matplotlib</requirement>
13 </expand>
14 <command detect_errors="aggressive"><![CDATA[
15 python '$__tool_directory__/generateHelicalWheel.py'
16 --sequence '$sequence'
17 --seqRange '$seqRange'
18 --t_size '$t_size'
19 --rotation '$rotation'
20 '$numbering'
21 --f_A "$sec_B.f_A"
22 --f_C "$sec_C.f_C"
23 --f_D "$sec_D.f_D"
24 --f_E "$sec_D.f_E"
25 --f_F "$sec_B.f_F"
26 --f_G "$sec_C.f_G"
27 --f_H "$sec_E.f_H"
28 --f_I "$sec_B.f_I"
29 --f_K "$sec_E.f_K"
30 --f_L "$sec_B.f_L"
31 --f_M "$sec_B.f_M"
32 --f_N "$sec_C.f_N"
33 --f_P "$sec_B.f_P"
34 --f_Q "$sec_C.f_Q"
35 --f_R "$sec_E.f_R"
36 --f_S "$sec_C.f_S"
37 --f_T "$sec_C.f_T"
38 --f_V "$sec_B.f_V"
39 --f_W "$sec_B.f_W"
40 --f_Y "$sec_C.f_Y"
41 --t_A "$sec_B.t_A"
42 --t_C "$sec_C.t_C"
43 --t_D "$sec_D.t_D"
44 --t_E "$sec_D.t_E"
45 --t_F "$sec_B.t_F"
46 --t_G "$sec_C.t_G"
47 --t_H "$sec_E.t_H"
48 --t_I "$sec_B.t_I"
49 --t_K "$sec_E.t_K"
50 --t_L "$sec_B.t_L"
51 --t_M "$sec_B.t_M"
52 --t_N "$sec_C.t_N"
53 --t_P "$sec_B.t_P"
54 --t_Q "$sec_C.t_Q"
55 --t_R "$sec_E.t_R"
56 --t_S "$sec_C.t_S"
57 --t_T "$sec_C.t_T"
58 --t_V "$sec_B.t_V"
59 --t_W "$sec_B.t_W"
60 --t_Y "$sec_C.t_Y"
61 --output '$output'
62 ]]></command>
63 <inputs>
64 <param label="Paste in exact sequence to be plotted" name="sequence" type="text"/>
65 <param label="Label Start Number" name="seqRange" type="integer" value="1" help="starting residue number to use for labels"/>
66 <param label="Amino Acid Text Size" name="t_size" type="integer" value="32" help="Alters the Text Size. Default is 32"/>
67 <param label="Rotation" name="rotation" type="integer" value="90" help="Rotates the helical wheel. Default is 90"/>
68 <param label="Label Numbering Text" name="numbering" type="boolean" help="number schema subscripts" truevalue="--numbering" falsevalue=""/>
69 <section name="sec_B" title="nonpolar ; hydrophobic">
70 <param name="f_A" type="color" label="Color for A" value="#ffcc33">
71 <sanitizer>
72 <valid initial="string.ascii_letters,string.digits">
73 <add value="#"/>
74 </valid>
75 </sanitizer>
76 </param>
77 <param name="t_A" type="color" label="Text color for A" value="#000000">
78 <sanitizer>
79 <valid initial="string.ascii_letters,string.digits">
80 <add value="#"/>
81 </valid>
82 </sanitizer>
83 </param>
84 <param name="f_F" type="color" label="Color for F" value="#ffcc33">
85 <sanitizer>
86 <valid initial="string.ascii_letters,string.digits">
87 <add value="#"/>
88 </valid>
89 </sanitizer>
90 </param>
91 <param name="t_F" type="color" label="Text color for F" value="#000000">
92 <sanitizer>
93 <valid initial="string.ascii_letters,string.digits">
94 <add value="#"/>
95 </valid>
96 </sanitizer>
97 </param>
98 <param name="f_I" type="color" label="Color for I" value="#ffcc33">
99 <sanitizer>
100 <valid initial="string.ascii_letters,string.digits">
101 <add value="#"/>
102 </valid>
103 </sanitizer>
104 </param>
105 <param name="t_I" type="color" label="Text color for I" value="#000000">
106 <sanitizer>
107 <valid initial="string.ascii_letters,string.digits">
108 <add value="#"/>
109 </valid>
110 </sanitizer>
111 </param>
112 <param name="f_L" type="color" label="Color for L" value="#ffcc33">
113 <sanitizer>
114 <valid initial="string.ascii_letters,string.digits">
115 <add value="#"/>
116 </valid>
117 </sanitizer>
118 </param>
119 <param name="t_L" type="color" label="Text color for L" value="#000000">
120 <sanitizer>
121 <valid initial="string.ascii_letters,string.digits">
122 <add value="#"/>
123 </valid>
124 </sanitizer>
125 </param>
126 <param name="f_M" type="color" label="Color for M" value="#ffcc33">
127 <sanitizer>
128 <valid initial="string.ascii_letters,string.digits">
129 <add value="#"/>
130 </valid>
131 </sanitizer>
132 </param>
133 <param name="t_M" type="color" label="Text color for M" value="#000000">
134 <sanitizer>
135 <valid initial="string.ascii_letters,string.digits">
136 <add value="#"/>
137 </valid>
138 </sanitizer>
139 </param>
140 <param name="f_P" type="color" label="Color for P" value="#ffcc33">
141 <sanitizer>
142 <valid initial="string.ascii_letters,string.digits">
143 <add value="#"/>
144 </valid>
145 </sanitizer>
146 </param>
147 <param name="t_P" type="color" label="Text color for P" value="#000000">
148 <sanitizer>
149 <valid initial="string.ascii_letters,string.digits">
150 <add value="#"/>
151 </valid>
152 </sanitizer>
153 </param>
154 <param name="f_V" type="color" label="Color for V" value="#ffcc33">
155 <sanitizer>
156 <valid initial="string.ascii_letters,string.digits">
157 <add value="#"/>
158 </valid>
159 </sanitizer>
160 </param>
161 <param name="t_V" type="color" label="Text color for V" value="#000000">
162 <sanitizer>
163 <valid initial="string.ascii_letters,string.digits">
164 <add value="#"/>
165 </valid>
166 </sanitizer>
167 </param>
168 <param name="f_W" type="color" label="Color for W" value="#ffcc33">
169 <sanitizer>
170 <valid initial="string.ascii_letters,string.digits">
171 <add value="#"/>
172 </valid>
173 </sanitizer>
174 </param>
175 <param name="t_W" type="color" label="Text color for W" value="#000000">
176 <sanitizer>
177 <valid initial="string.ascii_letters,string.digits">
178 <add value="#"/>
179 </valid>
180 </sanitizer>
181 </param>
182 </section>
183 <section name="sec_C" title="polar ; uncharged">
184 <param name="f_C" type="color" label="Color for C" value="#b5b5b5">
185 <sanitizer>
186 <valid initial="string.ascii_letters,string.digits">
187 <add value="#"/>
188 </valid>
189 </sanitizer>
190 </param>
191 <param name="t_C" type="color" label="Text color for C" value="#000000">
192 <sanitizer>
193 <valid initial="string.ascii_letters,string.digits">
194 <add value="#"/>
195 </valid>
196 </sanitizer>
197 </param>
198 <param name="f_G" type="color" label="Color for G" value="#b5b5b5">
199 <sanitizer>
200 <valid initial="string.ascii_letters,string.digits">
201 <add value="#"/>
202 </valid>
203 </sanitizer>
204 </param>
205 <param name="t_G" type="color" label="Text color for G" value="#000000">
206 <sanitizer>
207 <valid initial="string.ascii_letters,string.digits">
208 <add value="#"/>
209 </valid>
210 </sanitizer>
211 </param>
212 <param name="f_N" type="color" label="Color for N" value="#b5b5b5">
213 <sanitizer>
214 <valid initial="string.ascii_letters,string.digits">
215 <add value="#"/>
216 </valid>
217 </sanitizer>
218 </param>
219 <param name="t_N" type="color" label="Text color for N" value="#000000">
220 <sanitizer>
221 <valid initial="string.ascii_letters,string.digits">
222 <add value="#"/>
223 </valid>
224 </sanitizer>
225 </param>
226 <param name="f_Q" type="color" label="Color for Q" value="#b5b5b5">
227 <sanitizer>
228 <valid initial="string.ascii_letters,string.digits">
229 <add value="#"/>
230 </valid>
231 </sanitizer>
232 </param>
233 <param name="t_Q" type="color" label="Text color for Q" value="#000000">
234 <sanitizer>
235 <valid initial="string.ascii_letters,string.digits">
236 <add value="#"/>
237 </valid>
238 </sanitizer>
239 </param>
240 <param name="f_S" type="color" label="Color for S" value="#b5b5b5">
241 <sanitizer>
242 <valid initial="string.ascii_letters,string.digits">
243 <add value="#"/>
244 </valid>
245 </sanitizer>
246 </param>
247 <param name="t_S" type="color" label="Text color for S" value="#000000">
248 <sanitizer>
249 <valid initial="string.ascii_letters,string.digits">
250 <add value="#"/>
251 </valid>
252 </sanitizer>
253 </param>
254 <param name="f_T" type="color" label="Color for T" value="#b5b5b5">
255 <sanitizer>
256 <valid initial="string.ascii_letters,string.digits">
257 <add value="#"/>
258 </valid>
259 </sanitizer>
260 </param>
261 <param name="t_T" type="color" label="Text color for T" value="#000000">
262 <sanitizer>
263 <valid initial="string.ascii_letters,string.digits">
264 <add value="#"/>
265 </valid>
266 </sanitizer>
267 </param>
268 <param name="f_Y" type="color" label="Color for Y" value="#b5b5b5">
269 <sanitizer>
270 <valid initial="string.ascii_letters,string.digits">
271 <add value="#"/>
272 </valid>
273 </sanitizer>
274 </param>
275 <param name="t_Y" type="color" label="Text color for Y" value="#000000">
276 <sanitizer>
277 <valid initial="string.ascii_letters,string.digits">
278 <add value="#"/>
279 </valid>
280 </sanitizer>
281 </param>
282 </section>
283 <section name="sec_D" title="polar ; acidic (negatively charged)">
284 <param name="f_D" type="color" label="Color for D" value="#db270f">
285 <sanitizer>
286 <valid initial="string.ascii_letters,string.digits">
287 <add value="#"/>
288 </valid>
289 </sanitizer>
290 </param>
291 <param name="t_D" type="color" label="Text color for D" value="#FFFFFF">
292 <sanitizer>
293 <valid initial="string.ascii_letters,string.digits">
294 <add value="#"/>
295 </valid>
296 </sanitizer>
297 </param>
298 <param name="f_E" type="color" label="Color for E" value="#db270f">
299 <sanitizer>
300 <valid initial="string.ascii_letters,string.digits">
301 <add value="#"/>
302 </valid>
303 </sanitizer>
304 </param>
305 <param name="t_E" type="color" label="Text color for E" value="#FFFFFF">
306 <sanitizer>
307 <valid initial="string.ascii_letters,string.digits">
308 <add value="#"/>
309 </valid>
310 </sanitizer>
311 </param>
312 </section>
313 <section name="sec_E" title="polar ; basic (positive charge)">
314 <param name="f_H" type="color" label="Color for H" value="#12d5fc">
315 <sanitizer>
316 <valid initial="string.ascii_letters,string.digits">
317 <add value="#"/>
318 </valid>
319 </sanitizer>
320 </param>
321 <param name="t_H" type="color" label="Text color for H" value="#000000">
322 <sanitizer>
323 <valid initial="string.ascii_letters,string.digits">
324 <add value="#"/>
325 </valid>
326 </sanitizer>
327 </param>
328 <param name="f_K" type="color" label="Color for K" value="#12d5fc">
329 <sanitizer>
330 <valid initial="string.ascii_letters,string.digits">
331 <add value="#"/>
332 </valid>
333 </sanitizer>
334 </param>
335 <param name="t_K" type="color" label="Text color for K" value="#000000">
336 <sanitizer>
337 <valid initial="string.ascii_letters,string.digits">
338 <add value="#"/>
339 </valid>
340 </sanitizer>
341 </param>
342 <param name="f_R" type="color" label="Color for R" value="#12d5fc">
343 <sanitizer>
344 <valid initial="string.ascii_letters,string.digits">
345 <add value="#"/>
346 </valid>
347 </sanitizer>
348 </param>
349 <param name="t_R" type="color" label="Text color for R" value="#000000">
350 <sanitizer>
351 <valid initial="string.ascii_letters,string.digits">
352 <add value="#"/>
353 </valid>
354 </sanitizer>
355 </param>
356 </section>
357 </inputs>
358 <outputs>
359 <data format="png" name="output" label="_helicalWheel.png"/>
360 </outputs>
361 <help><![CDATA[
362 **What it does**
363 INPUT : Peptide Sequence
364 PARAMETERS :
365 primary parameters :
366 > Paste in exact sequence to be plotted - Input Sequence of desired helical wheel plot
367 > Label Start Number - Numerical value that represents the beginning of the sequence (default 1)
368 > Amino Acid Text Size - Size of text for helical wheel (default 32)
369 > Rotation - Degrees to rotate helical wheel (defaul 90)
370 color parameters :
371 > Background Color and Text Color Selections
372 METHOD : Using the core features from the modlAMP python module, a helical wheel projection is constructed.
373 OUTPUT : _helicalWheel.png
374 NOTES : Peptide lengths longer than 36 residues will not properly graph.
375 ]]></help>
376 <citations>
377 <citation type="doi">10.1093/bioinformatics/btx285</citation>
378 <citation type="bibtex">
379 @unpublished{galaxyTools,
380 author = {C. Ross},
381 title = {CPT Galaxy Tools},
382 year = {2020-},
383 note = {https://github.com/tamu-cpt/galaxy-tools/}
384 }
385 </citation>
386 </citations>
387 </tool>