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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
author goeckslab
date Tue, 07 Jan 2025 22:45:58 +0000
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1 <tool id="ludwig_render_config" name="Ludwig Render Config" version="@VERSION@" profile="@PROFILE@">
2 <description>renders thefull config based on user input</description>
3 <macros>
4 <import>ludwig_macros.xml</import>
5 </macros>
6 <expand macro="python_requirements_gpu" />
7 <expand macro="macro_stdio" />
8 <version_command>echo "@VERSION@"</version_command>
9 <command>
10 <![CDATA[
11 python '$__tool_directory__/ludwig_render_config.py' '$inputs' '$output'
12 ]]>
13 </command>
14 <configfiles>
15 <inputs name="inputs" />
16 </configfiles>
17 <inputs>
18 <section name="input_features" title="Input Features" expanded="true">
19 <repeat name="input_feature" min="1" max="30" title="Input Feature">
20 <conditional name="input_feature_selector" >
21 <param name="type" type="select" label="Select an input feature type">
22 <option value="number" selected="true">number</option>
23 <option value="binary">binary</option>
24 <option value="category">category</option>
25 <option value="set">set</option>
26 <option value="bag">bag</option>
27 <option value="sequence">sequence</option>
28 <option value="text">text</option>
29 <option value="timeseries">timeseries</option>
30 <option value="audio">audio</option>
31 <option value="image">image</option>
32 <option value="date">date</option>
33 <option value="h3">h3</option>
34 <option value="vector">vector</option>
35 </param>
36 <when value="number">
37 <param argument="name" type="text" value="" label="Name"/>
38 <conditional name="encoder">
39 <param argument="type" type="select" label="Select an encoder">
40 <option value="passthrough" selected="true">passthrough</option>
41 <option value="dense">dense</option>
42 <option value="sparse">sparse</option>
43 </param>
44 <when value="passthrough" />
45 <when value="dense" />
46 <when value="sparse" />
47 </conditional>
48 </when>
49 <when value="binary">
50 <param argument="name" type="text" value="" label="Name"/>
51 <conditional name="encoder">
52 <param argument="type" type="select" label="Select an encoder">
53 <option value="passthrough" selected="true">passthrough</option>
54 <option value="dense">dense</option>
55 </param>
56 <when value="passthrough" />
57 <when value="dense" />
58 </conditional>
59 </when>
60 <when value="category">
61 <param argument="name" type="text" value="" label="Name"/>
62 <conditional name="encoder">
63 <param argument="type" type="select" label="Select an encoder">
64 <option value="passthrough" selected="true">passthrough</option>
65 <option value="dense">dense</option>
66 <option value="sparse">sparse</option>
67 </param>
68 <when value="passthrough" />
69 <when value="dense" />
70 <when value="sparse" />
71 </conditional>
72 </when>
73 <when value="set">
74 </when>
75 <when value="bag">
76 </when>
77 <when value="sequence">
78 <param argument="name" type="text" value="" label="Name"/>
79 <conditional name="encoder">
80 <param argument="type" type="select" label="Select an encoder">
81 <option value="parallel_cnn" selected="true">parallel_cnn</option>
82 <option value="embed">embed</option>
83 <option value="stacked_cnn">stacked_cnn</option>
84 <option value="stacked_parallel_cnn">stacked_parallel_cnn</option>
85 <option value="rnn">rnn</option>
86 <option value="cnnrnn">cnnrnn</option>
87 <option value="transformer">transformer</option>
88 <option value="passthrough">passthrough</option>
89 </param>
90 <when value="parallel_cnn" />
91 <when value="embed" />
92 <when value="stacked_cnn" />
93 <when value="stacked_parallel_cnn" />
94 <when value="rnn" />
95 <when value="cnnrnn" />
96 <when value="transformer" />
97 <when value="passthrough" />
98 </conditional>
99 </when>
100 <when value="text">
101 <param argument="name" type="text" value="" label="Name"/>
102 <conditional name="encoder">
103 <param argument="type" type="select" label="Select an encoder">
104 <option value="parallel_cnn" selected="true">parallel_cnn</option>
105 <option value="embed">embed</option>
106 <option value="stacked_cnn">stacked_cnn</option>
107 <option value="stacked_parallel_cnn">stacked_parallel_cnn</option>
108 <option value="rnn">rnn</option>
109 <option value="cnnrnn">cnnrnn</option>
110 <option value="transformer">transformer</option>
111 <option value="passthrough">passthrough</option>
112 </param>
113 <when value="parallel_cnn" />
114 <when value="embed" />
115 <when value="stacked_cnn" />
116 <when value="stacked_parallel_cnn" />
117 <when value="rnn" />
118 <when value="cnnrnn" />
119 <when value="transformer" />
120 <when value="passthrough" />
121 </conditional>
122 </when>
123 <when value="timeseries">
124 </when>
125 <when value="audio">
126 <param argument="name" type="text" value="" label="Name"/>
127 <conditional name="encoder">
128 <param argument="type" type="select" label="Select an encoder">
129 <option value="parallel_cnn" selected="true">parallel_cnn</option>
130 <option value="embed">embed</option>
131 <option value="stacked_cnn">stacked_cnn</option>
132 <option value="stacked_parallel_cnn">stacked_parallel_cnn</option>
133 <option value="rnn">rnn</option>
134 <option value="cnnrnn">cnnrnn</option>
135 <option value="transformer">transformer</option>
136 <option value="passthrough">passthrough</option>
137 </param>
138 <when value="parallel_cnn" />
139 <when value="embed" />
140 <when value="stacked_cnn" />
141 <when value="stacked_parallel_cnn" />
142 <when value="rnn" />
143 <when value="cnnrnn" />
144 <when value="transformer" />
145 <when value="passthrough" />
146 </conditional>
147 </when>
148 <when value="image">
149 <param argument="name" type="text" value="" label="Name"/>
150 <conditional name="encoder">
151 <param argument="type" type="select" label="Select an encoder">
152 <option value="stacked_cnn" selected="true">stacked_cnn</option>
153 <option value="resnet">resnet</option>
154 <option value="mlp_mixer">mlp_mixer</option>
155 <option value="vit">vit</option>
156 </param>
157 <when value="stacked_cnn" />
158 <when value="resnet" />
159 <when value="mlp_mixer" />
160 <when value="vit" />
161 </conditional>
162 </when>
163 <when value="date">
164 <param argument="name" type="text" value="" label="Name"/>
165 <conditional name="encoder">
166 <param argument="type" type="select" label="Select an encoder">
167 <option value="embed" selected="true">embed</option>
168 <option value="wave">wave</option>
169 </param>
170 <when value="embed" />
171 <when value="wave" />
172 </conditional>
173 </when>
174 <when value="h3">
175 <param argument="name" type="text" value="" label="Name"/>
176 <conditional name="encoder">
177 <param argument="type" type="select" label="Select an encoder">
178 <option value="embed" selected="true">embed</option>
179 <option value="weighted_sum">weighted_sum</option>
180 <option value="rnn">rnn</option>
181 </param>
182 <when value="embed" />
183 <when value="weighted_sum" />
184 <when value="rnn" />
185 </conditional>
186 </when>
187 <when value="vector">
188 <param argument="name" type="text" value="" label="Name"/>
189 <conditional name="encoder">
190 <param argument="type" type="select" label="Select an encoder">
191 <option value="passthrough">passthrough</option>
192 <option value="dense" selected="true">dense</option>
193 </param>
194 <when value="passthrough" />
195 <when value="dense" />
196 </conditional>
197 </when>
198 </conditional>
199 </repeat>
200 </section>
201 <section name="output_features" title="Output Features" expanded="true">
202 <repeat name="output_feature" min="1" max="30" title="Output Feature">
203 <conditional name="output_feature_selector">
204 <param argument="type" type="select" label="Select an ouput feature type">
205 <option value="category" selected="true">category</option>
206 <option value="binary" >binary</option>
207 <option value="set" >set</option>
208 <option value="vector" >vector</option>
209 <option value="number" >number</option>
210 <option value="sequence" >sequence</option>
211 <option value="text" >text</option>
212 </param>
213 <when value="category">
214 <param argument="name" type="text" value="" />
215 <conditional name="decoder">
216 <param argument="type" type="select" label="Select a decoder type">
217 <option value="classifier" selected="true">classifier</option>
218 <option value="passthrough">passthrough</option>
219 </param>
220 <when value="classifier">
221 <param argument="num_fc_layers" type="integer" value="0" help="The number of stacked fully connected layers that the input to the feature passes through" min="0" max="20" />
222 <param argument="output_size" type="integer" value="256" help="The Size of the output of a fully connected layer." min="1" max="1024" />
223 <param argument="fc_dropout" type="float" value="0" help="Dropout rate" min="0" max="1" />
224 </when>
225 <when value="passthrough" />
226 </conditional>
227 <conditional name="loss">
228 <param argument="type" type="select" label="Select a loss type">
229 <option value="softmax_cross_entropy" selected="true">softmax_cross_entropy</option>
230 </param>
231 <when value="softmax_cross_entropy" />
232 </conditional>
233 <param argument="top_k" type="integer" value="3" help="The number of categories to consider when computing the first k measure." min="2" max="10" />
234 </when>
235 <when value="binary">
236 <param argument="name" type="text" value="" />
237 <conditional name="decoder">
238 <param argument="type" type="select" label="Select a decoder type">
239 <option value="regressor" selected="true">regressor</option>
240 <option value="passthrough">passthrough</option>
241 </param>
242 <when value="regressor">
243 <param argument="num_fc_layers" type="integer" value="0" help="The number of stacked fully connected layers that the input to the feature passes through" min="1" max="20" />
244 <param argument="output_size" type="integer" value="256" help="The Size of the output of a fully connected layer." min="1" max="1024" />
245 <param argument="fc_dropout" type="float" value="0" help="Dropout rate" min="0" max="1" />
246 </when>
247 <when value="passthrough" />
248 </conditional>
249 <conditional name="loss">
250 <param argument="type" type="select" label="Select a loss type">
251 <option value="binary_weighted_cross_entropy" selected="true">binary_weighted_cross_entropy</option>
252 </param>
253 <when value="binary_weighted_cross_entropy">
254 <param argument="positive_class_weight" type="integer" value="1" help="Multiplies the loss for the positive class, increasing its importance" min="1" max="100" />
255 </when>
256 </conditional>
257 <param argument="threshold" type="float" value="0.5" help="The threshold above which the predicted output of the sigmoid will be mapped to 1." min="0" max="1.0" />
258 </when>
259 <when value="set">
260 <param argument="name" type="text" value="" />
261 <conditional name="decoder">
262 <param argument="type" type="select" label="Select a decoder type">
263 <option value="classifier" selected="true">classifier</option>
264 <option value="passthrough">passthrough</option>
265 </param>
266 <when value="classifier">
267 <param argument="num_fc_layers" type="integer" value="0" help="The number of stacked fully connected layers that the input to the feature passes through" min="1" max="20" />
268 <param argument="output_size" type="integer" value="256" help="The Size of the output of a fully connected layer." min="1" max="1024" />
269 <param argument="fc_dropout" type="float" value="0" help="Dropout rate" min="0" max="1" />
270 </when>
271 <when value="passthrough" />
272 </conditional>
273 <conditional name="loss">
274 <param argument="type" type="select" label="Select a loss type">
275 <option value="sigmoid_cross_entropy" selected="true">sigmoid_cross_entropy</option>
276 </param>
277 <when value="sigmoid_cross_entropy" />
278 </conditional>
279 </when>
280 <when value="vector">
281 <param argument="name" type="text" value="" />
282 <conditional name="decoder">
283 <param argument="type" type="select" label="Select a decoder type">
284 <option value="projector" selected="true">projector</option>
285 <option value="passthrough">passthrough</option>
286 </param>
287 <when value="projector">
288 <param argument="softmax" type="boolean" value="false" help="Whether to apply a softmax at the end of the decoder?" />
289 <param argument="num_fc_layers" type="integer" value="0" help="The number of stacked fully connected layers that the input to the feature passes through" min="0" max="20" />
290 <param argument="output_size" type="integer" value="256" help="The Size of the output of a fully connected layer." min="1" max="1024" />
291 <param argument="fc_dropout" type="float" value="0" help="Dropout rate" min="0" max="1" />
292 </when>
293 <when value="passthrough" />
294 </conditional>
295 <conditional name="loss">
296 <param argument="type" type="select" label="Select a loss type">
297 <option value="mean_squared_error" selected="true">mean_squared_error</option>
298 <option value="mean_absolute_error">mean_absolute_error</option>
299 <option value="softmax_cross_entropy">softmax_cross_entropy (use this only if softmax is true)</option>
300 </param>
301 <when value="mean_squared_error" />
302 <when value="mean_absolute_error" />
303 <when value="softmax_cross_entropy" />
304 </conditional>
305 </when>
306 <when value="number">
307 <param argument="name" type="text" value="" />
308 <conditional name="decoder">
309 <param argument="type" type="select" label="Select a decoder type">
310 <option value="regressor" selected="true">regressor</option>
311 <option value="passthrough">passthrough</option>
312 </param>
313 <when value="regressor">
314 <param argument="num_fc_layers" type="integer" value="0" help="The number of stacked fully connected layers that the input to the feature passes through" min="1" max="20" />
315 <param argument="output_size" type="integer" value="256" help="The Size of the output of a fully connected layer." min="1" max="1024" />
316 <param argument="fc_dropout" type="float" value="0" help="Dropout rate" min="0" max="1" />
317 </when>
318 <when value="passthrough" />
319 </conditional>
320 <conditional name="loss">
321 <param argument="type" type="select" label="Select a loss type">
322 <option value="mean_squared_error" selected="true">mean_squared_error</option>
323 <option value="mean_absolute_error">mean_absolute_error</option>
324 <option value="root_mean_squared_error">root_mean_squared_error</option>
325 <option value="root_mean_squared_percentage_error">root_mean_squared_percentage_error</option>
326 </param>
327 <when value="mean_squared_error" />
328 <when value="mean_absolute_error" />
329 <when value="root_mean_squared_error" />
330 <when value="root_mean_squared_percentage_error" />
331 </conditional>
332 </when>
333 <when value="sequence">
334 <param argument="name" type="text" value="" />
335 <conditional name="decoder">
336 <param argument="type" type="select" label="Select a decoder type">
337 <option value="generator" selected="true">generator</option>
338 <option value="tagger">tagger</option>
339 <option value="passthrough">passthrough</option>
340 </param>
341 <when value="generator">
342 <param argument="cell_type" type="select" label="Selct the type of recurrent cell to use" >
343 <option value="gru" selected="true">gru</option>
344 <option value="rnn">rnn</option>
345 <option value="lstm">lstm</option>
346 </param>
347 <param argument="num_fc_layers" type="integer" value="0" help="The number of stacked fully connected layers that the input to the feature passes through" min="1" max="20" />
348 <param argument="output_size" type="integer" value="256" help="The Size of the output of a fully connected layer." min="1" max="1024" />
349 <param argument="fc_dropout" type="float" value="0" help="Dropout rate" min="0" max="1" />
350 </when>
351 <when value="tagger">
352 <param argument="use_attention" type="boolean" value="false" help="Whether to apply a multi-head self attention layer before prediction?" />
353 <param argument="use_bias" type="boolean" value="true" help="whether the layer uses a bias vector?" />
354 <param argument="attention_embedding_size" type="integer" value="256" help="The embedding size of the multi-head self attention layer." min="1" max="1024" />
355 <param argument="attention_num_heads" type="integer" value="8" help="The number of attention heads in the multi-head self attention layer." min="1" max="16"/>
356 <param argument="num_fc_layers" type="integer" value="0" help="The number of stacked fully connected layers that the input to the feature passes through" min="1" max="20" />
357 <param argument="output_size" type="integer" value="256" help="The Size of the output of a fully connected layer." min="1" max="1024" />
358 <param argument="fc_dropout" type="float" value="0" help="Dropout rate" min="0" max="1" />
359 </when>
360 <when value="passthrough" />
361 </conditional>
362 <conditional name="loss">
363 <param argument="type" type="select" label="Select a loss type">
364 <option value="sequence_softmax_cross_entropy" selected="true">sequence_softmax_cross_entropy</option>
365 </param>
366 <when value="sequence_softmax_cross_entropy" />
367 </conditional>
368 </when>
369 <when value="text">
370 <param argument="name" type="text" value="" />
371 <conditional name="decoder">
372 <param argument="type" type="select" label="Select a decoder type">
373 <option value="generator" selected="true">generator</option>
374 <option value="tagger">tagger</option>
375 <option value="passthrough">passthrough</option>
376 </param>
377 <when value="generator">
378 <param argument="cell_type" type="select" label="Selct the type of recurrent cell to use" >
379 <option value="gru" selected="true">gru</option>
380 <option value="rnn">rnn</option>
381 <option value="lstm">lstm</option>
382 </param>
383 <param argument="num_fc_layers" type="integer" value="0" help="The number of stacked fully connected layers that the input to the feature passes through" min="1" max="20" />
384 <param argument="output_size" type="integer" value="256" help="The Size of the output of a fully connected layer." min="1" max="1024" />
385 <param argument="fc_dropout" type="float" value="0" help="Dropout rate" min="0" max="1" />
386 </when>
387 <when value="tagger">
388 <param argument="use_attention" type="boolean" value="false" help="Whether to apply a multi-head self attention layer before prediction?" />
389 <param argument="use_bias" type="boolean" value="true" help="whether the layer uses a bias vector?" />
390 <param argument="attention_embedding_size" type="integer" value="256" help="The embedding size of the multi-head self attention layer." min="1" max="1024" />
391 <param argument="attention_num_heads" type="integer" value="8" help="The number of attention heads in the multi-head self attention layer." min="1" max="16"/> <param argument="num_fc_layers" type="integer" value="0" help="The number of stacked fully connected layers that the input to the feature passes through" min="1" max="20" />
392 <param argument="output_size" type="integer" value="256" help="The Size of the output of a fully connected layer." min="1" max="1024" />
393 <param argument="fc_dropout" type="float" value="0" help="Dropout rate" min="0" max="1" />
394 </when>
395 <when value="passthrough" />
396 </conditional>
397 <conditional name="loss">
398 <param argument="type" type="select" label="Select a loss type">
399 <option value="sequence_softmax_cross_entropy" selected="true">sequence_softmax_cross_entropy</option>
400 </param>
401 <when value="sequence_softmax_cross_entropy" />
402 </conditional>
403 </when>
404 </conditional>
405 </repeat>
406 </section>
407 <section name="combiner" title="Combiner" expanded="false">
408 <param name="type" type="select" label="Select a combiner type">
409 <option value="concat" selected="true">concat</option>
410 <option value="sequence_concat">sequence_concat</option>
411 <option value="sequence">sequence</option>
412 <option value="tabnet">tabnet</option>
413 <option value="transformer">transformer</option>
414 <option value="tabtransformer">tabtransformer</option>
415 <option value="comparator">comparator</option>
416 <option value="project_aggregate">project_aggregate</option>
417 </param>
418 </section>
419 <section name="trainer" title="Trainer" expanded="true">
420 <conditional name="trainer" >
421 <param name="model_type" type="select" label="Select the model type">
422 <option value="ecd" selected="true">ecd</option>
423 <option value="gbm">gbm</option>
424 </param>
425 <when value="ecd">
426 <param argument="batch_size" type="integer" value="128" help="Batch size" min="1" max="4096" />
427 <param argument="epochs" type="integer" value="100" help="Number of epochs" min="1" max="1000" />
428 <conditional name="optimizer">
429 <param name="type" type="select" label="Select an optimizer">
430 <option value="adam" selected="true">adam</option>
431 <option value="sgd">sgd</option>
432 <option value="adadelta">adadelta</option>
433 <option value="adamw">adamw</option>
434 <option value="adagrad">adagrad</option>
435 <option value="adamax">adamax</option>
436 <option value="ftrl">ftrl</option>
437 <option value="nadam">nadam</option>
438 <option value="rmsprop">rmsprop</option>
439 </param>
440 <when value="adam" />
441 <when value="sgd" />
442 <when value="adadelta" />
443 <when value="adamw" />
444 <when value="adagrad" />
445 <when value="adamax" />
446 <when value="ftrl" />
447 <when value="nadam" />
448 <when value="rmsprop" />
449 </conditional>
450 <param argument="learning_rate" type="float" value="0.001" help="Learning rate" min="0" max="1.0" />
451 <param argument="early_stop" type="integer" value="5" help="Number of epochs of patience without an improvement on the validation measure before the training is stopped." min="1" max="20"/>
452 </when>
453 <when value="gbm">
454 <param argument="boosting_type" type="select" label="Select the type of boosting algorithm" >
455 <option value="gbdt" selected="true">gbdt</option>
456 <option value="rf">rf`</option>
457 <option value="dart">dart</option>
458 <option value="goss">goss</option>
459 </param>
460 <param argument="num_boost_round" type="integer" value="1000" help="Number of boosting rounds to perform." min="1" max="5000" />
461 <param argument="learning_rate" type="float" value="0.03" help="Learning rate." min="0.0001" max="1.0" />
462 <param argument="lambda_l1" type="float" value="0.25" help="L1 regularization factor." min="0" max="10.0" />
463 <param argument="lambda_l2" type="float" value="0.2" help="L2 regularization factor." min="0" max="10.0" />
464 <param argument="max_depth" type="integer" value="18" help="Maximum depth of a tree. A negative value means no limit." min="3" max="50" />
465 <param argument="early_stop" type="integer" value="5" help="Number of epochs of patience without an improvement on the validation measure before the training is stopped." min="1" max="20" />
466 </when>
467 </conditional>
468 </section>
469 <!-- <section name="preprocessing" title="Preprocessing" expanded="false">
470 </section> -->
471 <conditional name="hyperopt">
472 <param name="do_hyperopt" type="select" label="Whether to do hyperparameter optimization?">
473 <option value="false" selected="true">No</option>
474 <option value="true">Yes</option>
475 </param>
476 <when value="true">
477 <section name="hyperopt" title="Hyperparameter Optimization configuration" expanded="false">
478 <conditional name="executor">
479 <param argument="type" type="select" label="Select the executor type" >
480 <option value="ray" selected="true">ray</option>
481 </param>
482 <when value="ray" />
483 </conditional>
484 </section>
485 </when>
486 <when value="false" />
487 </conditional>
488 </inputs>
489 <outputs>
490 <data format="yaml" name="output" label="${tool.name}" />
491 </outputs>
492 <tests>
493 <test expect_num_outputs="1">
494 <output name="output" file="render_config01.yml" />
495 </test>
496 </tests>
497 <help>
498 <![CDATA[
499 **What it does**
500 Render a Ludwig config template.
501
502
503 **Output**
504 A yaml file.
505
506 ]]>
507 </help>
508 <expand macro="macro_citations" />
509 </tool>