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comparison wrapper_arpa.xml @ 0:7548aa64d696 draft

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author biowebdb
date Wed, 03 Feb 2016 11:22:53 -0500
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1 <tool id="Arpa" name="Arpa">
2
3 <description>Arpa</description>
4 <requirements>
5 <requirement type="package" version="1.0.0">arpa_package</requirement>
6 </requirements>
7 <command interpreter="ruby">
8 wrapper_arpa.rb $output $input
9 "$tipo_script.data_type $aligner $trimmer $tipo_script.type_statistic_method.type_tree.program
10 #if $tipo_script.type_statistic_method.tree_select != "bayesian":
11 --bp $tipo_script.type_statistic_method.type_tree.bootstrap
12 #end if
13 #if $tipo_script.type_statistic_method.tree_select != "neighbor" and $tipo_script.type_statistic_method.tree_select != "maxparsi" and $tipo_script.type_statistic_method.type_tree.program != "-p phylip_ml":
14 $tipo_script.type_statistic_method.type_tree.evolut_model --nb $tipo_script.type_statistic_method.type_tree.nb_categ
15 #end if
16 #if $tipo_script.type_statistic_method.type_tree.program == "-p phyml":
17 --a $tipo_script.type_statistic_method.type_tree.gam_distribution
18 #end if
19 #if $tipo_script.data_type == "-t aa" and $tipo_script.type_statistic_method.type_tree.program == "-p phyml":
20 --in $tipo_script.type_statistic_method.type_tree.proportion
21 #end if
22 #if $tipo_script.type_statistic_method.tree_select == "bayesian":
23 --ngen $tipo_script.type_statistic_method.type_tree.ngeneration $tipo_script.type_statistic_method.type_tree.chains_run $tipo_script.type_statistic_method.type_tree.independent_analyses $tipo_script.type_statistic_method.type_tree.variation_model --printfreq $tipo_script.type_statistic_method.type_tree.chain_printed --samplefreq $tipo_script.type_statistic_method.type_tree.markov_chain --burnin $tipo_script.type_statistic_method.type_tree.samples_discarded
24 #end if
25 #if $tipo_script.type_statistic_method.type_tree.program == "-p raxml":
26 $tipo_script.type_statistic_method.type_tree.subst_rates
27 #end if
28 #if $tipo_script.data_type == "-t aa" and $tipo_script.type_statistic_method.type_tree.program == "-p raxml":
29 $tipo_script.type_statistic_method.type_tree.freq_raxml_aa
30 #end if
31 #if $tipo_script.data_type == "-t nucl" and $tipo_script.type_statistic_method.type_tree.program == "-p phyml":
32 --kappa $tipo_script.type_statistic_method.type_tree.trans_ratio
33 #end if
34 "
35 </command>
36
37 <inputs>
38
39 <param name="input" type="data" format="fasta" label="Fasta file"/>
40
41 <param name="aligner" type="select" label="Multiple Alignment">
42 <option value="-a alignm">Align-m</option>
43 <option selected="True" value="-a clustalw">Clustalw</option>
44 <option value="-a mafft">Mafft</option>
45 <option value="-a muscle">Muscle</option>
46 <option value="-a probcons">Probcons</option>
47 <option value="-a tcoffee">T-Coffee</option>
48 </param>
49
50 <param name="trimmer" type="select" label="Alignment trimming">
51 <option value="-c gblocks">G Blocks</option>
52 <option selected="True" value="-c total">Total</option>
53 <option value="-c trimal">TrimAl</option>
54 </param>
55
56 <conditional name="tipo_script">
57
58 <param name="data_type" type="select" label="Select Search">
59 <option value="">Select</option>
60 <option value="-t aa">Amino acid sequences</option>
61 <option value="-t nucl">DNA sequences</option>
62 </param>
63
64 <when value="-t aa">
65
66 <conditional name="type_statistic_method">
67
68 <param name="tree_select" type="select" label="Phylogenetic tree">
69 <option value="">Select</option>
70 <option value="maxlike">Maximum Likelihood</option>
71 <option value="neighbor">Neighbor-joining</option>
72 <option value="maxparsi">Maximum Parsimony</option>
73 <option value="bayesian">Bayesian Inference</option>
74 </param>
75
76 <when value="maxlike">
77 <conditional name="type_tree">
78 <param name="program" type="select" label="Maximum Likelihood">
79 <option value="">Select</option>
80 <option value="-p phyml">PhyML</option>
81 <option value="-p raxml">RAxML</option>
82 <option value="-p garli">GARLI</option>
83 <option value="-p phylip_ml">PHYLIP_ML</option>
84 <option value="-p weighbor">WEIGHBOR</option>
85 </param>
86
87 <when value="-p phyml">
88 <param name="evolut_model" type="select" label="Evolutionary model">
89 <option value="--mg BLOSUM62">BLOSUM62</option>
90 <option value="--mg CPREV">CPREV</option>
91 <option value="--mg Dayhoff">Dayhoff</option>
92 <option value="--mg DCMut">DCMut</option>
93 <option value="--mg GTR">GTR</option>
94 <option selected="True" value="--mg JTT">JTT</option>
95 <option value="--mg MtMam">MtMam</option>
96 <option value="--mg MtREV">MtREV</option>
97 <option value="--mg RtREV">RtREV</option>
98 <option value="--mg VT">VT</option>
99 <option value="--mg WAG">WAG</option>
100 </param>
101
102 <param name="bootstrap" label="bootstrap [10 - 1000]" type="integer" value="100"/>
103
104 <param name="nb_categ" label="Substitution Rate Categories [1 - 20]" type="integer" value="4"/>
105
106 <param name="gam_distribution" label="Gamma Distribution [1 - 20]" type="integer" value="1"/>
107
108 <param name="proportion" label="proportion of invariable sites [0 - 20]" type="integer" value="0"/>
109
110 </when>
111
112 <when value="-p raxml">
113 <param name="evolut_model" type="select" label="Evolutionary model">
114 <option value="--mg BLOSUM62">BLOSUM62</option>
115 <option value="--mg CPREV">CPREV</option>
116 <option selected="True" value="--mg Dayhoff">Dayhoff</option>
117 <option value="--mg DCMut">DCMut</option>
118 <option value="--mg GTR">GTR</option>
119 <option value="--mg JTT">JTT</option>
120 <option value="--mg MtMam">MtMam</option>
121 <option value="--mg MtREV">MtREV</option>
122 <option value="--mg RtREV">RtREV</option>
123 <option value="--mg VT">VT</option>
124 <option value="--mg WAG">WAG</option>
125 </param>
126
127 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
128
129 <param name="nb_categ" label="Substitution Rate Categories [1 - 20]" type="integer" value="4"/>
130
131 <param name="subst_rates" type="select" label="Substitution Rates">
132 <option value="--rates_raxml_aa PROTGAMMA">PROTGAMMA</option>
133 </param>
134
135 <param name="freq_raxml_aa" type="select" label="Empirical Base Frequencies">
136 <option value="--freq_raxml_aa F">F</option>
137 </param>
138
139 </when>
140
141
142 <when value="-p garli">
143 <param name="evolut_model" type="select" label="Evolutionary model">
144 <option value="--mg Dayhoff">Dayhoff</option>
145 <option value="--mg jones">jones</option>
146 <option value="--mg MtMam">MtMam</option>
147 <option value="--mg MtREV">MtREV</option>
148 <option selected="True" value="--mg poisson">poisson</option>
149 <option value="--mg WAG">WAG</option>
150 </param>
151
152 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
153
154 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>
155
156 </when>
157
158 <when value="-p phylip_ml">
159 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
160 </when>
161
162
163 <when value="-p weighbor">
164 <param name="evolut_model" type="select" label="Evolutionary model">
165 <option value="--mg BLOSUM62">BLOSUM62</option>
166 <option value="--mg Dayhoff">Dayhoff</option>
167 <option value="--mg JTT">JTT</option>
168 <option value="--mg MTREV24">MTREV24</option>
169 <option value="--mg VT">VT</option>
170 <option selected="True" value="--mg WAG">WAG</option>
171 </param>
172
173 <param name="bootstrap" label="bootstrap [10 - 1000]" type="integer" value="100"/>
174
175 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="6"/>
176
177 </when>
178
179 </conditional>
180
181 </when>
182
183
184 <when value="neighbor">
185 <conditional name="type_tree">
186 <param name="program" type="select" label="Neighbor-joining">
187 <option selected="True" value="-p phylip_nj">PHYLIP_NJ</option>
188 </param>
189
190 <when value="-p phylip_nj">
191 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
192 </when>
193
194 </conditional>
195 </when>
196
197 <when value="maxparsi">
198 <conditional name="type_tree">
199 <param name="program" type="select" label="Maximum Parsimony">
200 <option selected="True" value="-p phylip_mp">PHYLIP_MP</option>
201 </param>
202
203 <when value="-p phylip_mp">
204 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="500"/>
205 </when>
206
207 </conditional>
208 </when>
209
210 <when value="bayesian">
211 <conditional name="type_tree">
212 <param name="program" type="select" label="Bayesian Inference">
213 <option value="-p mrbayes">MrBayes</option>
214 </param>
215
216 <when value="-p mrbayes">
217 <param name="evolut_model" type="select" label="Evolutionary model">
218 <option value="--mg BLOSUM">BLOSUM</option>
219 <option value="--mg CPREV">CPREV</option>
220 <option value="--mg Dayhoff">Dayhoff</option>
221 <option value="--mg equalin">equalin</option>
222 <option value="--mg GTR">GTR</option>
223 <option value="--mg jones">jones</option>
224 <option value="--mg MtMam">MtMam</option>
225 <option value="--mg MtREV">MtREV</option>
226 <option selected="True" value="--mg poisson">poisson</option>
227 <option value="--mg RtREV">RtREV</option>
228 <option value="--mg VT">VT</option>
229 <option value="--mg WAG">WAG</option>
230 </param>
231
232 <param name="ngeneration" label="Generation Number[10 - 1000000]" type="integer" value="1000"/>
233
234 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>
235
236 <param name="chain_printed" label="Chain Printed[1 - 1000]" type="integer" value="100"/>
237
238 <param name="markov_chain" label="Markov Chain Sampled[1 - 1000]" type="integer" value="100"/>
239
240 <param name="chains_run" type="select" label="Chains Run">
241 <option value="--nchains 0">0</option>
242 <option value="--nchains 1">1</option>
243 <option value="--nchains 2">2</option>
244 <option value="--nchains 3">3</option>
245 <option selected="True" value="--nchains 4">4</option>
246 </param>
247
248 <param name="samples_discarded" label="Number of Samples Discarded[10 - 1000]" type="integer" value="10"/>
249
250 <param name="independent_analyses" type="select" label="Number of independent Analyses">
251 <option selected="True" value="--nruns 2">2</option>
252 </param>
253
254 <param name="variation_model" type="select" label="Rate Variation Model">
255 <option selected="True" value="--rates_mrbayes Equal">Equal</option>
256 </param>
257 </when>
258 </conditional>
259 </when>
260 </conditional>
261 </when>
262
263
264
265 <when value="-t nucl">
266
267 <conditional name="type_statistic_method">
268 <param name="tree_select" type="select" label="Phylogenetic tree">
269 <option value="">Select</option>
270 <option value="maxlike">Maximum Likelihood</option>
271 <option value="neighbor">Neighbor-joining</option>
272 <option value="maxparsi">Maximum Parsimony</option>
273 <option value="bayesian">Bayesian Inference</option>
274 </param>
275 <when value="maxlike">
276 <conditional name="type_tree">
277
278 <param name="program" type="select" label="Maximum Likelihood">
279 <option value="">Select</option>
280 <option value="-p phyml">PhyML</option>
281 <option value="-p raxml">RAxML</option>
282 <option value="-p garli">GARLI</option>
283 <option value="-p phylip_ml">PHYLIP_ML</option>
284 <option value="-p weighbor">WEIGHBOR</option>
285 </param>
286
287 <when value="-p phyml">
288 <param name="evolut_model" type="select" label="Evolutionary model">
289 <option value="--mg Custom">Custom</option>
290 <option value="--mg F81">F81</option>
291 <option value="--mg F84">F84</option>
292 <option value="--mg GTR">GTR</option>
293 <option selected="True" value="--mg HKY">HKY</option>
294 <option value="--mg JC69">JC69</option>
295 <option value="--mg K2P">K2P</option>
296 <option value="--mg TN93">TN93</option>
297 </param>
298
299 <param name="bootstrap" label="bootstrap [10 - 1000]" type="integer" value="100"/>
300
301 <param name="nb_categ" label="Substitution Rate Categories [1 - 20]" type="integer" value="4"/>
302
303 <param name="gam_distribution" label="Gamma Distribution [1 - 20]" type="integer" value="1"/>
304
305 <param name="trans_ratio" label="Transition / transversion ratio [0 - 20]" type="integer" value="4"/>
306
307 </when>
308
309 <when value="-p raxml">
310 <param name="evolut_model" type="select" label="Evolutionary model">
311 <option selected="True" value="--mg GTR">GTR</option>
312 </param>
313
314 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
315
316 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>
317
318 <param name="subst_rates" type="select" label="Substitution Rates">
319 <option selected="True" value="--rates_raxml_nucl GAMMA">GAMMA</option>
320 </param>
321
322 </when>
323
324
325 <when value="-p garli">
326 <param name="evolut_model" type="select" label="Evolutionary model">
327 <option value="--mg F81">F81</option>
328 <option value="--mg GTR">GTR</option>
329 <option value="--mg HKY">HKY</option>
330 <option selected="True" value="--mg JC">JC</option>
331 <option value="--mg K3P">K3P</option>
332 <option value="--mg K80">K80</option>
333 <option value="--mg SYM">SYM</option>
334 <option value="--mg TIM">TIM</option>
335 <option value="--mg TrN">TrN</option>
336 <option value="--mg TVM">TVM</option>
337 </param>
338
339 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
340
341 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>
342
343 </when>
344
345 <when value="-p phylip_ml">
346 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
347 </when>
348
349
350 <when value="-p weighbor">
351 <param name="evolut_model" type="select" label="Evolutionary model">
352 <option value="--mg GTR">GTR</option>
353 <option selected="True" value="--mg HKY">HKY</option>
354 <option value="--mg TN">TN</option>
355 </param>
356
357 <param name="bootstrap" label="bootstrap [10 - 1000]" type="integer" value="100"/>
358
359 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>
360
361 </when>
362
363 </conditional>
364 </when>
365
366
367 <when value="neighbor">
368 <conditional name="type_tree">
369 <param name="program" type="select" label="Neighbor-joining">
370 <option selected="True" value="-p phylip_nj">PHYLIP_NJ</option>
371 </param>
372
373 <when value="-p phylip_nj">
374 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
375 </when>
376
377 </conditional>
378 </when>
379
380 <when value="maxparsi">
381 <conditional name="type_tree">
382 <param name="program" type="select" label="Maximum Parsimony">
383 <option selected="True" value="-p phylip_mp">PHYLIP_MP</option>
384 </param>
385
386 <when value="-p phylip_mp">
387 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="500"/>
388 </when>
389
390 </conditional>
391 </when>
392
393 <when value="bayesian">
394 <conditional name="type_tree">
395 <param name="program" type="select" label="Bayesian Inference">
396 <option selected="True" value="-p mrbayes">MrBayes</option>
397 </param>
398
399 <when value="-p mrbayes">
400 <param name="evolut_model" type="select" label="Evolutionary model">
401 <option value="--mg F81">F81</option>
402 <option value="--mg GTR">GTR</option>
403 <option value="--mg HKY">HKY</option>
404 <option value="--mg HKY85">HKY85</option>
405 <option selected="--mg True" value="JC">JC</option>
406 <option value="--mg JC69">JC69</option>
407 <option value="--mg K3P">K3P</option>
408 <option value="--mg K80">K80</option>
409 <option value="--mg SYM">SYM</option>
410 <option value="--mg TIM">TIM</option>
411 <option value="--mg TrN">TrN</option>
412 <option value="--mg TVM">TVM</option>
413 </param>
414
415 <param name="ngeneration" label="Generation Number[10 - 1000000]" type="integer" value="1000"/>
416
417 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>
418
419 <param name="chain_printed" label="Chain Printed[1 - 1000]" type="integer" value="100"/>
420
421 <param name="markov_chain" label="Markov Chain Sampled[1 - 1000]" type="integer" value="100"/>
422
423 <param name="chains_run" type="select" label="Chains Run:">
424 <option selected="True" value="--nchains 4">4</option>
425 </param>
426
427 <param name="samples_discarded" label="Number of Samples Discarded[0 - 20]" type="integer" value="10"/>
428
429 <param name="independent_analyses" type="select" label="Number of independent Analyses">
430 <option selected="True" value="--nruns 2">2</option>
431 </param>
432
433 <param name="variation_model" type="select" label="Rate Variation Model">
434 <option selected="True" value="--rates_mrbayes Equal">Equal</option>
435 </param>
436 </when>
437 </conditional>
438 </when>
439 </conditional>
440
441 </when>
442
443 </conditional>
444 </inputs>
445
446 <outputs>
447 <data format="txt" name="output" />
448 </outputs>
449
450 <tests>
451 <test>
452 <param name="input" value=""/>
453 <output name="out_file1" file=""/>
454 </test>
455 </tests>
456
457 <help>
458 </help>
459
460 </tool>