Mercurial > repos > uga-galaxy-group > webservice_toolsuite_v1_1

comparison WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_61.xml~ @ 0:049760c677de default tip

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Galaxy WSExtensions added successfully
author uga-galaxy-group
date Tue, 05 Jul 2011 19:34:18 -0400
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-1:000000000000 0:049760c677de
1 <tool id="client_61" name="run">
2 <description> Client for operation : run , Web service : clustalw2.clustalw2_services </description>
3 <command interpreter="python">
4 client_1.py
5 #if $cond_source.optional_param_source=="no":
6 $output
7 $servicetype
8 $url
9 $method
10 clustalw2.clustalw2_services run
11 "_email"
12 #if $source0.source0_source=="user":
13 $source0.user_param0
14 #else:
15 fileInput
16 $source0.cached_param0
17 #end if
18 #else:
19 $output
20 $servicetype
21 $url
22 $method
23 clustalw2.clustalw2_services run
24 "_email"
25 #if $source0.source0_source=="user":
26 $source0.user_param0
27 #else:
28 fileInput
29 $source0.cached_param0
30 #end if
31 "_parameters|_sequence"
32 #if $cond_source.source1.source1_source=="user":
33 $cond_source.source1.user_param1
34 #else:
35 fileInput
36 $cond_source.source1.cached_param1
37 #end if
38 "_parameters|_pwmatrix"
39 #if $cond_source.source2.source2_source=="user":
40 $cond_source.source2.user_param2
41 #else:
42 fileInput
43 $cond_source.source2.cached_param2
44 #end if
45 "_parameters|_dnamatrix"
46 #if $cond_source.source3.source3_source=="user":
47 $cond_source.source3.user_param3
48 #else:
49 fileInput
50 $cond_source.source3.cached_param3
51 #end if
52 "_parameters|_gapopen"
53 #if $cond_source.source4.source4_source=="user":
54 $cond_source.source4.user_param4
55 #else:
56 fileInput
57 $cond_source.source4.cached_param4
58 #end if
59 "_parameters|_pairgap"
60 #if $cond_source.source5.source5_source=="user":
61 $cond_source.source5.user_param5
62 #else:
63 fileInput
64 $cond_source.source5.cached_param5
65 #end if
66 "_parameters|_pwdnamatrix"
67 #if $cond_source.source6.source6_source=="user":
68 $cond_source.source6.user_param6
69 #else:
70 fileInput
71 $cond_source.source6.cached_param6
72 #end if
73 "_parameters|_outorder"
74 #if $cond_source.source7.source7_source=="user":
75 $cond_source.source7.user_param7
76 #else:
77 fileInput
78 $cond_source.source7.cached_param7
79 #end if
80 "_parameters|_iteration"
81 #if $cond_source.source8.source8_source=="user":
82 $cond_source.source8.user_param8
83 #else:
84 fileInput
85 $cond_source.source8.cached_param8
86 #end if
87 "_parameters|_noendgaps"
88 #if $cond_source.source9.source9_source=="user":
89 $cond_source.source9.user_param9
90 #else:
91 fileInput
92 $cond_source.source9.cached_param9
93 #end if
94 "_parameters|_pwgapopen"
95 #if $cond_source.source10.source10_source=="user":
96 $cond_source.source10.user_param10
97 #else:
98 fileInput
99 $cond_source.source10.cached_param10
100 #end if
101 "_parameters|_ktup"
102 #if $cond_source.source11.source11_source=="user":
103 $cond_source.source11.user_param11
104 #else:
105 fileInput
106 $cond_source.source11.cached_param11
107 #end if
108 "_parameters|_alignment"
109 #if $cond_source.source12.source12_source=="user":
110 $cond_source.source12.user_param12
111 #else:
112 fileInput
113 $cond_source.source12.cached_param12
114 #end if
115 "_parameters|_matrix"
116 #if $cond_source.source13.source13_source=="user":
117 $cond_source.source13.user_param13
118 #else:
119 fileInput
120 $cond_source.source13.cached_param13
121 #end if
122 "_parameters|_score"
123 #if $cond_source.source14.source14_source=="user":
124 $cond_source.source14.user_param14
125 #else:
126 fileInput
127 $cond_source.source14.cached_param14
128 #end if
129 "_title"
130 #if $cond_source.source15.source15_source=="user":
131 $cond_source.source15.user_param15
132 #else:
133 fileInput
134 $cond_source.source15.cached_param15
135 #end if
136 "_parameters|_gapext"
137 #if $cond_source.source16.source16_source=="user":
138 $cond_source.source16.user_param16
139 #else:
140 fileInput
141 $cond_source.source16.cached_param16
142 #end if
143 "_parameters|_clustering"
144 #if $cond_source.source17.source17_source=="user":
145 $cond_source.source17.user_param17
146 #else:
147 fileInput
148 $cond_source.source17.cached_param17
149 #end if
150 "_parameters|_numiter"
151 #if $cond_source.source18.source18_source=="user":
152 $cond_source.source18.user_param18
153 #else:
154 fileInput
155 $cond_source.source18.cached_param18
156 #end if
157 "_parameters|_pwgapext"
158 #if $cond_source.source19.source19_source=="user":
159 $cond_source.source19.user_param19
160 #else:
161 fileInput
162 $cond_source.source19.cached_param19
163 #end if
164 "_parameters|_topdiags"
165 #if $cond_source.source20.source20_source=="user":
166 $cond_source.source20.user_param20
167 #else:
168 fileInput
169 $cond_source.source20.cached_param20
170 #end if
171 "_parameters|_window"
172 #if $cond_source.source21.source21_source=="user":
173 $cond_source.source21.user_param21
174 #else:
175 fileInput
176 $cond_source.source21.cached_param21
177 #end if
178 "_parameters|_gapdist"
179 #if $cond_source.source22.source22_source=="user":
180 $cond_source.source22.user_param22
181 #else:
182 fileInput
183 $cond_source.source22.cached_param22
184 #end if
185 "_parameters|_type"
186 #if $cond_source.source23.source23_source=="user":
187 $cond_source.source23.user_param23
188 #else:
189 fileInput
190 $cond_source.source23.cached_param23
191 #end if
192 "_parameters|_output"
193 #if $cond_source.source24.source24_source=="user":
194 $cond_source.source24.user_param24
195 #else:
196 fileInput
197 $cond_source.source24.cached_param24
198 #end if
199 #end if
200 </command>
201 <inputs>
202 <param name="servicetype" type="hidden" value="SOAP" />
203 <param name="url" type="hidden" value="http://www.ebi.ac.uk/Tools/services/soap/clustalw2?wsdl" />
204 <param name="method" type="hidden" value="run" />
205 <conditional name="source0">
206 <param name="source0_source" type="select" label="email Source">
207 <option value="cached" selected="true">Param value will be taken from previous step</option>
208 <option value="user">User will enter the param value</option>
209 </param>
210 <when value="user">
211 <param format="text" size = "150" name = "user_param0" type="text" label="Enter email" help="see tip below" />
212 </when>
213 <when value="cached">
214 <param name = "cached_param0" type="data" label="Choose the step from which to get the parameter email"/>
215 </when>
216 </conditional> <conditional name="cond_source">
217 <param name="optional_param_source" type="select" label="Display Additional Parameters">
218 <option value="no" selected="true">no</option>
219 <option value="yes">yes</option>
220 </param>
221 <when value="no">
222 </when>
223 <when value="yes">
224
225 <conditional name="source1">
226 <param name="source1_source" type="select" label="sequence Source">
227 <option value="cached" selected="true">Param value will be taken from previous step</option>
228 <option value="user">User will enter the param value</option>
229 </param>
230 <when value="user"><param format="text" size = "150" name = "user_param1" type="text" label="Enter sequence" help="see tip below" />
231 </when>
232 <when value="cached">
233 <param name = "cached_param1" type="data" label="Choose the step from which to get the parameter sequence"/>
234 </when>
235 </conditional>
236
237 <conditional name="source2">
238 <param name="source2_source" type="select" label="pwmatrix Source">
239 <option value="cached" selected="true">Param value will be taken from previous step</option>
240 <option value="user">User will enter the param value</option>
241 </param>
242 <when value="user"><param format="text" size = "150" name = "user_param2" type="text" label="Enter pwmatrix" help="see tip below" />
243 </when>
244 <when value="cached">
245 <param name = "cached_param2" type="data" label="Choose the step from which to get the parameter pwmatrix"/>
246 </when>
247 </conditional>
248
249 <conditional name="source3">
250 <param name="source3_source" type="select" label="dnamatrix Source">
251 <option value="cached" selected="true">Param value will be taken from previous step</option>
252 <option value="user">User will enter the param value</option>
253 </param>
254 <when value="user"><param format="text" size = "150" name = "user_param3" type="text" label="Enter dnamatrix" help="see tip below" />
255 </when>
256 <when value="cached">
257 <param name = "cached_param3" type="data" label="Choose the step from which to get the parameter dnamatrix"/>
258 </when>
259 </conditional>
260
261 <conditional name="source4">
262 <param name="source4_source" type="select" label="gapopen Source">
263 <option value="cached" selected="true">Param value will be taken from previous step</option>
264 <option value="user">User will enter the param value</option>
265 </param>
266 <when value="user"><param format="text" size = "150" name = "user_param4" type="text" label="Enter gapopen" help="see tip below" />
267 </when>
268 <when value="cached">
269 <param name = "cached_param4" type="data" label="Choose the step from which to get the parameter gapopen"/>
270 </when>
271 </conditional>
272
273 <conditional name="source5">
274 <param name="source5_source" type="select" label="pairgap Source">
275 <option value="cached" selected="true">Param value will be taken from previous step</option>
276 <option value="user">User will enter the param value</option>
277 </param>
278 <when value="user"><param format="text" size = "150" name = "user_param5" type="text" label="Enter pairgap" help="see tip below" />
279 </when>
280 <when value="cached">
281 <param name = "cached_param5" type="data" label="Choose the step from which to get the parameter pairgap"/>
282 </when>
283 </conditional>
284
285 <conditional name="source6">
286 <param name="source6_source" type="select" label="pwdnamatrix Source">
287 <option value="cached" selected="true">Param value will be taken from previous step</option>
288 <option value="user">User will enter the param value</option>
289 </param>
290 <when value="user"><param format="text" size = "150" name = "user_param6" type="text" label="Enter pwdnamatrix" help="see tip below" />
291 </when>
292 <when value="cached">
293 <param name = "cached_param6" type="data" label="Choose the step from which to get the parameter pwdnamatrix"/>
294 </when>
295 </conditional>
296
297 <conditional name="source7">
298 <param name="source7_source" type="select" label="outorder Source">
299 <option value="cached" selected="true">Param value will be taken from previous step</option>
300 <option value="user">User will enter the param value</option>
301 </param>
302 <when value="user"><param format="text" size = "150" name = "user_param7" type="text" label="Enter outorder" help="see tip below" />
303 </when>
304 <when value="cached">
305 <param name = "cached_param7" type="data" label="Choose the step from which to get the parameter outorder"/>
306 </when>
307 </conditional>
308
309 <conditional name="source8">
310 <param name="source8_source" type="select" label="iteration Source">
311 <option value="cached" selected="true">Param value will be taken from previous step</option>
312 <option value="user">User will enter the param value</option>
313 </param>
314 <when value="user"><param format="text" size = "150" name = "user_param8" type="text" label="Enter iteration" help="see tip below" />
315 </when>
316 <when value="cached">
317 <param name = "cached_param8" type="data" label="Choose the step from which to get the parameter iteration"/>
318 </when>
319 </conditional>
320
321 <conditional name="source9">
322 <param name="source9_source" type="select" label="noendgaps Source">
323 <option value="cached" selected="true">Param value will be taken from previous step</option>
324 <option value="user">User will enter the param value</option>
325 </param>
326 <when value="user"><param format="text" size = "150" name = "user_param9" type="text" label="Enter noendgaps" help="see tip below" />
327 </when>
328 <when value="cached">
329 <param name = "cached_param9" type="data" label="Choose the step from which to get the parameter noendgaps"/>
330 </when>
331 </conditional>
332
333 <conditional name="source10">
334 <param name="source10_source" type="select" label="pwgapopen Source">
335 <option value="cached" selected="true">Param value will be taken from previous step</option>
336 <option value="user">User will enter the param value</option>
337 </param>
338 <when value="user"><param format="text" size = "150" name = "user_param10" type="text" label="Enter pwgapopen" help="see tip below" />
339 </when>
340 <when value="cached">
341 <param name = "cached_param10" type="data" label="Choose the step from which to get the parameter pwgapopen"/>
342 </when>
343 </conditional>
344
345 <conditional name="source11">
346 <param name="source11_source" type="select" label="ktup Source">
347 <option value="cached" selected="true">Param value will be taken from previous step</option>
348 <option value="user">User will enter the param value</option>
349 </param>
350 <when value="user"><param format="text" size = "150" name = "user_param11" type="text" label="Enter ktup" help="see tip below" />
351 </when>
352 <when value="cached">
353 <param name = "cached_param11" type="data" label="Choose the step from which to get the parameter ktup"/>
354 </when>
355 </conditional>
356
357 <conditional name="source12">
358 <param name="source12_source" type="select" label="alignment Source">
359 <option value="cached" selected="true">Param value will be taken from previous step</option>
360 <option value="user">User will enter the param value</option>
361 </param>
362 <when value="user"><param format="text" size = "150" name = "user_param12" type="text" label="Enter alignment" help="see tip below" />
363 </when>
364 <when value="cached">
365 <param name = "cached_param12" type="data" label="Choose the step from which to get the parameter alignment"/>
366 </when>
367 </conditional>
368
369 <conditional name="source13">
370 <param name="source13_source" type="select" label="matrix Source">
371 <option value="cached" selected="true">Param value will be taken from previous step</option>
372 <option value="user">User will enter the param value</option>
373 </param>
374 <when value="user"><param format="text" size = "150" name = "user_param13" type="text" label="Enter matrix" help="see tip below" />
375 </when>
376 <when value="cached">
377 <param name = "cached_param13" type="data" label="Choose the step from which to get the parameter matrix"/>
378 </when>
379 </conditional>
380
381 <conditional name="source14">
382 <param name="source14_source" type="select" label="score Source">
383 <option value="cached" selected="true">Param value will be taken from previous step</option>
384 <option value="user">User will enter the param value</option>
385 </param>
386 <when value="user"><param format="text" size = "150" name = "user_param14" type="text" label="Enter score" help="see tip below" />
387 </when>
388 <when value="cached">
389 <param name = "cached_param14" type="data" label="Choose the step from which to get the parameter score"/>
390 </when>
391 </conditional>
392
393 <conditional name="source15">
394 <param name="source15_source" type="select" label="title Source">
395 <option value="cached" selected="true">Param value will be taken from previous step</option>
396 <option value="user">User will enter the param value</option>
397 </param>
398 <when value="user"><param format="text" size = "150" name = "user_param15" type="text" label="Enter title" help="see tip below" />
399 </when>
400 <when value="cached">
401 <param name = "cached_param15" type="data" label="Choose the step from which to get the parameter title"/>
402 </when>
403 </conditional>
404
405 <conditional name="source16">
406 <param name="source16_source" type="select" label="gapext Source">
407 <option value="cached" selected="true">Param value will be taken from previous step</option>
408 <option value="user">User will enter the param value</option>
409 </param>
410 <when value="user"><param format="text" size = "150" name = "user_param16" type="text" label="Enter gapext" help="see tip below" />
411 </when>
412 <when value="cached">
413 <param name = "cached_param16" type="data" label="Choose the step from which to get the parameter gapext"/>
414 </when>
415 </conditional>
416
417 <conditional name="source17">
418 <param name="source17_source" type="select" label="clustering Source">
419 <option value="cached" selected="true">Param value will be taken from previous step</option>
420 <option value="user">User will enter the param value</option>
421 </param>
422 <when value="user"><param format="text" size = "150" name = "user_param17" type="text" label="Enter clustering" help="see tip below" />
423 </when>
424 <when value="cached">
425 <param name = "cached_param17" type="data" label="Choose the step from which to get the parameter clustering"/>
426 </when>
427 </conditional>
428
429 <conditional name="source18">
430 <param name="source18_source" type="select" label="numiter Source">
431 <option value="cached" selected="true">Param value will be taken from previous step</option>
432 <option value="user">User will enter the param value</option>
433 </param>
434 <when value="user"><param format="text" size = "150" name = "user_param18" type="text" label="Enter numiter" help="see tip below" />
435 </when>
436 <when value="cached">
437 <param name = "cached_param18" type="data" label="Choose the step from which to get the parameter numiter"/>
438 </when>
439 </conditional>
440
441 <conditional name="source19">
442 <param name="source19_source" type="select" label="pwgapext Source">
443 <option value="cached" selected="true">Param value will be taken from previous step</option>
444 <option value="user">User will enter the param value</option>
445 </param>
446 <when value="user"><param format="text" size = "150" name = "user_param19" type="text" label="Enter pwgapext" help="see tip below" />
447 </when>
448 <when value="cached">
449 <param name = "cached_param19" type="data" label="Choose the step from which to get the parameter pwgapext"/>
450 </when>
451 </conditional>
452
453 <conditional name="source20">
454 <param name="source20_source" type="select" label="topdiags Source">
455 <option value="cached" selected="true">Param value will be taken from previous step</option>
456 <option value="user">User will enter the param value</option>
457 </param>
458 <when value="user"><param format="text" size = "150" name = "user_param20" type="text" label="Enter topdiags" help="see tip below" />
459 </when>
460 <when value="cached">
461 <param name = "cached_param20" type="data" label="Choose the step from which to get the parameter topdiags"/>
462 </when>
463 </conditional>
464
465 <conditional name="source21">
466 <param name="source21_source" type="select" label="window Source">
467 <option value="cached" selected="true">Param value will be taken from previous step</option>
468 <option value="user">User will enter the param value</option>
469 </param>
470 <when value="user"><param format="text" size = "150" name = "user_param21" type="text" label="Enter window" help="see tip below" />
471 </when>
472 <when value="cached">
473 <param name = "cached_param21" type="data" label="Choose the step from which to get the parameter window"/>
474 </when>
475 </conditional>
476
477 <conditional name="source22">
478 <param name="source22_source" type="select" label="gapdist Source">
479 <option value="cached" selected="true">Param value will be taken from previous step</option>
480 <option value="user">User will enter the param value</option>
481 </param>
482 <when value="user"><param format="text" size = "150" name = "user_param22" type="text" label="Enter gapdist" help="see tip below" />
483 </when>
484 <when value="cached">
485 <param name = "cached_param22" type="data" label="Choose the step from which to get the parameter gapdist"/>
486 </when>
487 </conditional>
488
489 <conditional name="source23">
490 <param name="source23_source" type="select" label="type Source">
491 <option value="cached" selected="true">Param value will be taken from previous step</option>
492 <option value="user">User will enter the param value</option>
493 </param>
494 <when value="user"><param format="text" size = "150" name = "user_param23" type="text" label="Enter type" help="see tip below" />
495 </when>
496 <when value="cached">
497 <param name = "cached_param23" type="data" label="Choose the step from which to get the parameter type"/>
498 </when>
499 </conditional>
500
501 <conditional name="source24">
502 <param name="source24_source" type="select" label="output Source">
503 <option value="cached" selected="true">Param value will be taken from previous step</option>
504 <option value="user">User will enter the param value</option>
505 </param>
506 <when value="user"><param format="text" size = "150" name = "user_param24" type="text" label="Enter output" help="see tip below" />
507 </when>
508 <when value="cached">
509 <param name = "cached_param24" type="data" label="Choose the step from which to get the parameter output"/>
510 </when>
511 </conditional>
512 </when>
513 </conditional>
514 </inputs>
515 <outputs>
516 <data format="tabular" name="output" />
517 </outputs>
518 <help>
519
520 .. class:: infomark
521
522 **TIP:** About email: type is String
523 </help>
524 </tool>