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comparison WebServiceToolWorkflow/workflowclients/client_7.xml~ @ 0:d5cd409b8a18 default tip

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author ganjoo
date Tue, 07 Jun 2011 18:00:50 -0400
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-1:000000000000 0:d5cd409b8a18
1 <tool id="client_7" name="runclustalW2 ">
2 <description> Client for method: runclustalW2 , Web service: http://om.cs.uga.edu/demo/clusatlW2.wadl </description>
3 <command interpreter="python">
4 #client_1.py
5 $output
6 http://www.ebi.ac.uk/Tools/services/restclustalw2/run
7 email
8 #if $source0.source0_source=="user" $source0.user_param0 #else $source0.cached_param0 #end if
9 #if $cond_source.optional_param_source=="yes" type
10 #if $cond_source.source1.source1_source=="user" $cond_source.source1.user_param1 #else $cond_source.source1.cached_param1 #end if
11 title
12 #if $cond_source.source2.source2_source=="user" $cond_source.source2.user_param2 #else $cond_source.source2.cached_param2 #end if
13 output
14 #if $cond_source.source3.source3_source=="user" $cond_source.source3.user_param3 #else $cond_source.source3.cached_param3 #end if
15 alignments
16 #if $cond_source.source4.source4_source=="user" $cond_source.source4.user_param4 #else $cond_source.source4.cached_param4 #end if
17 outorder
18 #if $cond_source.source5.source5_source=="user" $cond_source.source5.user_param5 #else $cond_source.source5.cached_param5 #end if
19 sequence
20 #if $cond_source.source6.source6_source=="user" $cond_source.source6.user_param6 #else $cond_source.source6.cached_param6 #end if
21 ktup
22 #if $cond_source.source7.source7_source=="user" $cond_source.source7.user_param7 #else $cond_source.source7.cached_param7 #end if
23 window
24 #if $cond_source.source8.source8_source=="user" $cond_source.source8.user_param8 #else $cond_source.source8.cached_param8 #end if
25 score
26 #if $cond_source.source9.source9_source=="user" $cond_source.source9.user_param9 #else $cond_source.source9.cached_param9 #end if
27 topdiag
28 #if $cond_source.source10.source10_source=="user" $cond_source.source10.user_param10 #else $cond_source.source10.cached_param10 #end if
29 pairgap
30 #if $cond_source.source11.source11_source=="user" $cond_source.source11.user_param11 #else $cond_source.source11.cached_param11 #end if
31 pwmatrix
32 #if $cond_source.source12.source12_source=="user" $cond_source.source12.user_param12 #else $cond_source.source12.cached_param12 #end if
33 pwdnamatrix
34 #if $cond_source.source13.source13_source=="user" $cond_source.source13.user_param13 #else $cond_source.source13.cached_param13 #end if
35 pwgapopen
36 #if $cond_source.source14.source14_source=="user" $cond_source.source14.user_param14 #else $cond_source.source14.cached_param14 #end if
37 pwgapext
38 #if $cond_source.source15.source15_source=="user" $cond_source.source15.user_param15 #else $cond_source.source15.cached_param15 #end if
39 matrix
40 #if $cond_source.source16.source16_source=="user" $cond_source.source16.user_param16 #else $cond_source.source16.cached_param16 #end if
41 dnamatrix
42 #if $cond_source.source17.source17_source=="user" $cond_source.source17.user_param17 #else $cond_source.source17.cached_param17 #end if
43 gapopen
44 #if $cond_source.source18.source18_source=="user" $cond_source.source18.user_param18 #else $cond_source.source18.cached_param18 #end if
45 noendgaps
46 #if $cond_source.source19.source19_source=="user" $cond_source.source19.user_param19 #else $cond_source.source19.cached_param19 #end if
47 gapext
48 #if $cond_source.source20.source20_source=="user" $cond_source.source20.user_param20 #else $cond_source.source20.cached_param20 #end if
49 gapext
50 #if $cond_source.source21.source21_source=="user" $cond_source.source21.user_param21 #else $cond_source.source21.cached_param21 #end if
51 iteration
52 #if $cond_source.source22.source22_source=="user" $cond_source.source22.user_param22 #else $cond_source.source22.cached_param22 #end if
53 numiter
54 #if $cond_source.source23.source23_source=="user" $cond_source.source23.user_param23 #else $cond_source.source23.cached_param23 #end if
55 #else
56 #end if
57 </command>
58 <inputs>
59 <conditional name="source0">
60 <param name="source0_source" type="select" label="id Source">
61 <option value="cached" selected="true">Param value will be taken from previous step</option>
62 <option value="user">User will enter the param value</option>
63 </param>
64 <when value="user">
65 <param format="text" size = "150" name = "user_param0" type="text" label="Enter email" help="see tip below" />
66 </when>
67 <when value="cached">
68 <param name = "cached_param0" type="data" label="Choose the step from which to get the parameter id"/>
69 </when></conditional> <conditional name="cond_source">
70 <param name="optional_param_source" type="select" label="Display Additional Parameters">
71 <option value="no" selected="true">no</option>
72 <option value="yes">yes</option>
73 </param>
74 <when value="no">
75 </when>
76 <when value="yes">
77
78 <conditional name="source1">
79 <param name="source1_source" type="select" label="type Source">
80 <option value="cached" selected="true">Param value will be taken from previous step</option>
81 <option value="user">User will enter the param value</option>
82 </param>
83 <when value="user"><param name="user_param1" type="select" label="Select type" help="see tip below">
84 <option value="protein" selected="true">protein</option>
85 <option value="dna" >dna</option>
86 </param>
87 </when>
88 <when value="cached">
89 <param name = "cached_param1" type="data" label="Choose the step from which to get the parameter type"/>
90 </when></conditional>
91
92 <conditional name="source2">
93 <param name="source2_source" type="select" label="title Source">
94 <option value="cached" selected="true">Param value will be taken from previous step</option>
95 <option value="user">User will enter the param value</option>
96 </param>
97 <when value="user"><param format="text" size = "150" name = "user_param2" type="text" label="Enter title" help="see tip below" />
98 </when>
99 <when value="cached">
100 <param name = "cached_param2" type="data" label="Choose the step from which to get the parameter title"/>
101 </when></conditional>
102
103 <conditional name="source3">
104 <param name="source3_source" type="select" label="output Source">
105 <option value="cached" selected="true">Param value will be taken from previous step</option>
106 <option value="user">User will enter the param value</option>
107 </param>
108 <when value="user"><param name="user_param3" type="select" label="Select output" help="see tip below">
109 <option value="aln1" selected="true">aln1</option>
110 <option value="aln2" >aln2</option>
111 <option value="gcg" >gcg</option>
112 <option value="phylip" >phylip</option>
113 <option value="nexus" >nexus</option>
114 <option value="pir" >pir</option>
115 <option value="gde" >gde</option>
116 <option value="fasta" >fasta</option>
117 </param>
118 </when>
119 <when value="cached">
120 <param name = "cached_param3" type="data" label="Choose the step from which to get the parameter output"/>
121 </when></conditional>
122
123 <conditional name="source4">
124 <param name="source4_source" type="select" label="alignments Source">
125 <option value="cached" selected="true">Param value will be taken from previous step</option>
126 <option value="user">User will enter the param value</option>
127 </param>
128 <when value="user"><param name="user_param4" type="select" label="Select alignments" help="see tip below">
129 <option value="slow" selected="true">slow</option>
130 <option value="fast" >fast</option>
131 </param>
132 </when>
133 <when value="cached">
134 <param name = "cached_param4" type="data" label="Choose the step from which to get the parameter alignments"/>
135 </when></conditional>
136
137 <conditional name="source5">
138 <param name="source5_source" type="select" label="outorder Source">
139 <option value="cached" selected="true">Param value will be taken from previous step</option>
140 <option value="user">User will enter the param value</option>
141 </param>
142 <when value="user"><param name="user_param5" type="select" label="Select outorder" help="see tip below">
143 <option value="aligned" selected="true">aligned</option>
144 <option value="input" >input</option>
145 </param>
146 </when>
147 <when value="cached">
148 <param name = "cached_param5" type="data" label="Choose the step from which to get the parameter outorder"/>
149 </when></conditional>
150
151 <conditional name="source6">
152 <param name="source6_source" type="select" label="sequence Source">
153 <option value="cached" selected="true">Param value will be taken from previous step</option>
154 <option value="user">User will enter the param value</option>
155 </param>
156 <when value="user"><param format="text" size = "150" name = "user_param6" type="text" label="Enter sequence" help="see tip below" />
157 </when>
158 <when value="cached">
159 <param name = "cached_param6" type="data" label="Choose the step from which to get the parameter sequence"/>
160 </when></conditional>
161
162 <conditional name="source7">
163 <param name="source7_source" type="select" label="ktup Source">
164 <option value="cached" selected="true">Param value will be taken from previous step</option>
165 <option value="user">User will enter the param value</option>
166 </param>
167 <when value="user"><param name="user_param7" type="select" label="Select ktup" help="see tip below">
168 <option value="1" selected="true">1</option>
169 <option value="2" >2</option>
170 <option value="3" >3</option>
171 <option value="4" >4</option>
172 <option value="5" >5</option>
173 </param>
174 </when>
175 <when value="cached">
176 <param name = "cached_param7" type="data" label="Choose the step from which to get the parameter ktup"/>
177 </when></conditional>
178
179 <conditional name="source8">
180 <param name="source8_source" type="select" label="window Source">
181 <option value="cached" selected="true">Param value will be taken from previous step</option>
182 <option value="user">User will enter the param value</option>
183 </param>
184 <when value="user"><param name="user_param8" type="select" label="Select window" help="see tip below">
185 <option value="10" >10</option>
186 <option value="9" >9</option>
187 <option value="8" >8</option>
188 <option value="7" >7</option>
189 <option value="6" >6</option>
190 <option value="5" selected="true">5</option>
191 <option value="4" >4</option>
192 <option value="3" >3</option>
193 <option value="2" >2</option>
194 <option value="1" >1</option>
195 <option value="0" >0</option>
196 </param>
197 </when>
198 <when value="cached">
199 <param name = "cached_param8" type="data" label="Choose the step from which to get the parameter window"/>
200 </when></conditional>
201
202 <conditional name="source9">
203 <param name="source9_source" type="select" label="score Source">
204 <option value="cached" selected="true">Param value will be taken from previous step</option>
205 <option value="user">User will enter the param value</option>
206 </param>
207 <when value="user"><param name="user_param9" type="select" label="Select score" help="see tip below">
208 <option value="percent" selected="true">percent</option>
209 <option value="absolute" >absolute</option>
210 </param>
211 </when>
212 <when value="cached">
213 <param name = "cached_param9" type="data" label="Choose the step from which to get the parameter score"/>
214 </when></conditional>
215
216 <conditional name="source10">
217 <param name="source10_source" type="select" label="topdiag Source">
218 <option value="cached" selected="true">Param value will be taken from previous step</option>
219 <option value="user">User will enter the param value</option>
220 </param>
221 <when value="user"><param name="user_param10" type="select" label="Select topdiag" help="see tip below">
222 <option value="10" >10</option>
223 <option value="9" >9</option>
224 <option value="8" >8</option>
225 <option value="7" >7</option>
226 <option value="6" >6</option>
227 <option value="5" selected="true">5</option>
228 <option value="4" >4</option>
229 <option value="3" >3</option>
230 <option value="2" >2</option>
231 <option value="1" >1</option>
232 </param>
233 </when>
234 <when value="cached">
235 <param name = "cached_param10" type="data" label="Choose the step from which to get the parameter topdiag"/>
236 </when></conditional>
237
238 <conditional name="source11">
239 <param name="source11_source" type="select" label="pairgap Source">
240 <option value="cached" selected="true">Param value will be taken from previous step</option>
241 <option value="user">User will enter the param value</option>
242 </param>
243 <when value="user"><param name="user_param11" type="select" label="Select pairgap" help="see tip below">
244 <option value="1" >1</option>
245 <option value="2" >2</option>
246 <option value="3" selected="true">3</option>
247 <option value="4" >4</option>
248 <option value="5" >5</option>
249 <option value="10" >10</option>
250 <option value="25" >25</option>
251 <option value="50" >50</option>
252 <option value="100" >100</option>
253 <option value="250" >250</option>
254 <option value="500" >500</option>
255 </param>
256 </when>
257 <when value="cached">
258 <param name = "cached_param11" type="data" label="Choose the step from which to get the parameter pairgap"/>
259 </when></conditional>
260
261 <conditional name="source12">
262 <param name="source12_source" type="select" label="pwmatrix 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 name="user_param12" type="select" label="Select pwmatrix" help="see tip below">
267 <option value="blosum" >blosum</option>
268 <option value="pam" >pam</option>
269 <option value="gonnet" selected="true">gonnet</option>
270 <option value="id" >id</option>
271 </param>
272 </when>
273 <when value="cached">
274 <param name = "cached_param12" type="data" label="Choose the step from which to get the parameter pwmatrix"/>
275 </when></conditional>
276
277 <conditional name="source13">
278 <param name="source13_source" type="select" label="pwdnamatrix Source">
279 <option value="cached" selected="true">Param value will be taken from previous step</option>
280 <option value="user">User will enter the param value</option>
281 </param>
282 <when value="user"><param name="user_param13" type="select" label="Select pwdnamatrix" help="see tip below">
283 <option value="iub" selected="true">iub</option>
284 <option value="clustalw" >clustalw</option>
285 </param>
286 </when>
287 <when value="cached">
288 <param name = "cached_param13" type="data" label="Choose the step from which to get the parameter pwdnamatrix"/>
289 </when></conditional>
290
291 <conditional name="source14">
292 <param name="source14_source" type="select" label="pwgapopen Source">
293 <option value="cached" selected="true">Param value will be taken from previous step</option>
294 <option value="user">User will enter the param value</option>
295 </param>
296 <when value="user"><param name="user_param14" type="select" label="Select pwgapopen" help="see tip below">
297 <option value="100" >100</option>
298 <option value="50" >50</option>
299 <option value="25" >25</option>
300 <option value="10" selected="true">10</option>
301 <option value="5" >5</option>
302 <option value="2" >2</option>
303 <option value="1" >1</option>
304 </param>
305 </when>
306 <when value="cached">
307 <param name = "cached_param14" type="data" label="Choose the step from which to get the parameter pwgapopen"/>
308 </when></conditional>
309
310 <conditional name="source15">
311 <param name="source15_source" type="select" label="pwgapext Source">
312 <option value="cached" selected="true">Param value will be taken from previous step</option>
313 <option value="user">User will enter the param value</option>
314 </param>
315 <when value="user"><param name="user_param15" type="select" label="Select pwgapext" help="see tip below">
316 <option value="0.05" >0.05</option>
317 <option value="0.1" selected="true">0.1</option>
318 <option value="0.5" >0.5</option>
319 <option value="1.0" >1.0</option>
320 <option value="2.5" >2.5</option>
321 <option value="5.0" >5.0</option>
322 <option value="7.5" >7.5</option>
323 <option value="10.0" >10.0</option>
324 </param>
325 </when>
326 <when value="cached">
327 <param name = "cached_param15" type="data" label="Choose the step from which to get the parameter pwgapext"/>
328 </when></conditional>
329
330 <conditional name="source16">
331 <param name="source16_source" type="select" label="matrix Source">
332 <option value="cached" selected="true">Param value will be taken from previous step</option>
333 <option value="user">User will enter the param value</option>
334 </param>
335 <when value="user"><param name="user_param16" type="select" label="Select matrix" help="see tip below">
336 <option value="blosum" >blosum</option>
337 <option value="pam" >pam</option>
338 <option value="gonnet" selected="true">gonnet</option>
339 <option value="id" >id</option>
340 </param>
341 </when>
342 <when value="cached">
343 <param name = "cached_param16" type="data" label="Choose the step from which to get the parameter matrix"/>
344 </when></conditional>
345
346 <conditional name="source17">
347 <param name="source17_source" type="select" label="dnamatrix Source">
348 <option value="cached" selected="true">Param value will be taken from previous step</option>
349 <option value="user">User will enter the param value</option>
350 </param>
351 <when value="user"><param name="user_param17" type="select" label="Select dnamatrix" help="see tip below">
352 <option value="iub" selected="true">iub</option>
353 <option value="clustalw" >clustalw</option>
354 </param>
355 </when>
356 <when value="cached">
357 <param name = "cached_param17" type="data" label="Choose the step from which to get the parameter dnamatrix"/>
358 </when></conditional>
359
360 <conditional name="source18">
361 <param name="source18_source" type="select" label="gapopen Source">
362 <option value="cached" selected="true">Param value will be taken from previous step</option>
363 <option value="user">User will enter the param value</option>
364 </param>
365 <when value="user"><param name="user_param18" type="select" label="Select gapopen" help="see tip below">
366 <option value="100" >100</option>
367 <option value="50" >50</option>
368 <option value="25" >25</option>
369 <option value="10" selected="true">10</option>
370 <option value="5" >5</option>
371 <option value="2" >2</option>
372 <option value="1" >1</option>
373 </param>
374 </when>
375 <when value="cached">
376 <param name = "cached_param18" type="data" label="Choose the step from which to get the parameter gapopen"/>
377 </when></conditional>
378
379 <conditional name="source19">
380 <param name="source19_source" type="select" label="noendgaps Source">
381 <option value="cached" selected="true">Param value will be taken from previous step</option>
382 <option value="user">User will enter the param value</option>
383 </param>
384 <when value="user"><param name="user_param19" type="select" label="Select noendgaps" help="see tip below">
385 <option value="false" selected="true">false</option>
386 <option value="true" >true</option>
387 </param>
388 </when>
389 <when value="cached">
390 <param name = "cached_param19" type="data" label="Choose the step from which to get the parameter noendgaps"/>
391 </when></conditional>
392
393 <conditional name="source20">
394 <param name="source20_source" type="select" label="gapext 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 name="user_param20" type="select" label="Select gapext" help="see tip below">
399 <option value="0.05" >0.05</option>
400 <option value="0.20" selected="true">0.20</option>
401 <option value="0.5" >0.5</option>
402 <option value="1.0" >1.0</option>
403 <option value="2.5" >2.5</option>
404 <option value="5.0" >5.0</option>
405 <option value="7.5" >7.5</option>
406 <option value="10.0" >10.0</option>
407 </param>
408 </when>
409 <when value="cached">
410 <param name = "cached_param20" type="data" label="Choose the step from which to get the parameter gapext"/>
411 </when></conditional>
412
413 <conditional name="source21">
414 <param name="source21_source" type="select" label="gapext Source">
415 <option value="cached" selected="true">Param value will be taken from previous step</option>
416 <option value="user">User will enter the param value</option>
417 </param>
418 <when value="user"><param name="user_param21" type="select" label="Select gapext" help="see tip below">
419 <option value="10" >10</option>
420 <option value="9" >9</option>
421 <option value="8" >8</option>
422 <option value="7" >7</option>
423 <option value="6" >6</option>
424 <option value="5" selected="true">5</option>
425 <option value="4" >4</option>
426 <option value="3" >3</option>
427 <option value="2" >2</option>
428 <option value="1" >1</option>
429 </param>
430 </when>
431 <when value="cached">
432 <param name = "cached_param21" type="data" label="Choose the step from which to get the parameter gapext"/>
433 </when></conditional>
434
435 <conditional name="source22">
436 <param name="source22_source" type="select" label="iteration Source">
437 <option value="cached" selected="true">Param value will be taken from previous step</option>
438 <option value="user">User will enter the param value</option>
439 </param>
440 <when value="user"><param name="user_param22" type="select" label="Select iteration" help="see tip below">
441 <option value="none" >none</option>
442 <option value="tree" >tree</option>
443 <option value="alignment" >alignment</option>
444 </param>
445 </when>
446 <when value="cached">
447 <param name = "cached_param22" type="data" label="Choose the step from which to get the parameter iteration"/>
448 </when></conditional>
449
450 <conditional name="source23">
451 <param name="source23_source" type="select" label="numiter Source">
452 <option value="cached" selected="true">Param value will be taken from previous step</option>
453 <option value="user">User will enter the param value</option>
454 </param>
455 <when value="user"><param name="user_param23" type="select" label="Select numiter" help="see tip below">
456 <option value="1" selected="true">1</option>
457 <option value="2" >2</option>
458 <option value="3" >3</option>
459 <option value="4" >4</option>
460 <option value="5" >5</option>
461 <option value="6" >6</option>
462 <option value="7" >7</option>
463 <option value="8" >8</option>
464 <option value="9" >9</option>
465 <option value="10" >10</option>
466 </param>
467 </when>
468 <when value="cached">
469 <param name = "cached_param23" type="data" label="Choose the step from which to get the parameter numiter"/>
470 </when></conditional>
471 </when>
472 </conditional>
473 </inputs>
474 <outputs>
475 <data format="tabular" name="output" />
476 </outputs>
477 <help>
478
479 .. class:: infomark
480
481 **TIP:** email type is xsd:string
482 </help>
483 </tool>