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comparison pipeline.xml @ 18:449bd57f70f4 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
author bgruening
date Tue, 13 Apr 2021 21:00:31 +0000
parents a7a047cf36d8
children 15815a470e6b
comparison
equal deleted inserted replaced
17:0eb811dde78c 18:449bd57f70f4
1 <tool id="sklearn_build_pipeline" name="Pipeline Builder" version="@VERSION@"> 1 <tool id="sklearn_build_pipeline" name="Pipeline Builder" version="@VERSION@" profile="20.05">
2 <description>an all-in-one platform to build pipeline, single estimator, preprocessor and custom wrappers</description> 2 <description>an all-in-one platform to build pipeline, single estimator, preprocessor and custom wrappers</description>
3 <macros> 3 <macros>
4 <import>main_macros.xml</import> 4 <import>main_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="python_requirements"/> 6 <expand macro="python_requirements" />
7 <expand macro="macro_stdio"/> 7 <expand macro="macro_stdio" />
8 <version_command>echo "@VERSION@"</version_command> 8 <version_command>echo "@VERSION@"</version_command>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 python "$sklearn_pipeline_script" '$inputs' 11 python "$sklearn_pipeline_script" '$inputs'
12 ]]> 12 ]]>
226 <option value="skrebate">SK-rebate Feature Selection</option> 226 <option value="skrebate">SK-rebate Feature Selection</option>
227 <option value="imblearn">Imbalanced-learn Sampling</option> 227 <option value="imblearn">Imbalanced-learn Sampling</option>
228 <option value="IRAPS">IRAPS -- feature selector and classifier</option> 228 <option value="IRAPS">IRAPS -- feature selector and classifier</option>
229 <option value="preprocessors">Bio-sequence Encoders</option> 229 <option value="preprocessors">Bio-sequence Encoders</option>
230 </param> 230 </param>
231 <when value="None"/> 231 <when value="None" />
232 <when value="pre_processor"> 232 <when value="pre_processor">
233 <conditional name="pre_processors"> 233 <conditional name="pre_processors">
234 <expand macro="sparse_preprocessors_ext" /> 234 <expand macro="sparse_preprocessors_ext" />
235 <expand macro="sparse_preprocessor_options_ext" /> 235 <expand macro="sparse_preprocessor_options_ext" />
236 </conditional> 236 </conditional>
237 </when> 237 </when>
238 <when value="feature_selection"> 238 <when value="feature_selection">
239 <expand macro="feature_selection_pipeline"/> 239 <expand macro="feature_selection_pipeline" />
240 </when> 240 </when>
241 <when value="decomposition"> 241 <when value="decomposition">
242 <expand macro="matrix_decomposition_all"/> 242 <expand macro="matrix_decomposition_all" />
243 </when> 243 </when>
244 <when value="kernel_approximation"> 244 <when value="kernel_approximation">
245 <expand macro="kernel_approximation_all"/> 245 <expand macro="kernel_approximation_all" />
246 </when> 246 </when>
247 <when value="FeatureAgglomeration"> 247 <when value="FeatureAgglomeration">
248 <expand macro="FeatureAgglomeration"/> 248 <expand macro="FeatureAgglomeration" />
249 </when> 249 </when>
250 <when value="skrebate"> 250 <when value="skrebate">
251 <expand macro="skrebate"/> 251 <expand macro="skrebate" />
252 </when> 252 </when>
253 <when value="imblearn"> 253 <when value="imblearn">
254 <expand macro="imbalanced_learn_sampling"/> 254 <expand macro="imbalanced_learn_sampling" />
255 </when> 255 </when>
256 <when value="IRAPS"> 256 <when value="IRAPS">
257 <expand macro="estimator_params_text" 257 <expand macro="estimator_params_text" label="Type in parameter settings for IRAPSCore if different from default:" help="Default(=blank): n_iter=1000, responsive_thres=-1, resistant_thres=0, random_state=None. No double quotes" />
258 label="Type in parameter settings for IRAPSCore if different from default:" 258 <param argument="p_thres" type="float" value="0.001" label="P value threshold" help="Float. default=0.001" />
259 help="Default(=blank): n_iter=1000, responsive_thres=-1, resistant_thres=0, random_state=None. No double quotes"/> 259 <param argument="fc_thres" type="float" value="0.1" label="fold change threshold" help="Float. default=0.1" />
260 <param argument="p_thres" type="float" value="0.001" label="P value threshold" help="Float. default=0.001"/> 260 <param argument="occurrence" type="float" value="0.7" label="reservation factor" help="Float. default=0.7" />
261 <param argument="fc_thres" type="float" value="0.1" label="fold change threshold" help="Float. default=0.1"/> 261 <param argument="discretize" type="float" value="-1" label="The z_score threshold to discretize target value" help="Float. default=-1" />
262 <param argument="occurrence" type="float" value="0.7" label="reservation factor" help="Float. default=0.7"/>
263 <param argument="discretize" type="float" value="-1" label="The z_score threshold to discretize target value" help="Float. default=-1"/>
264 </when> 262 </when>
265 <when value="preprocessors"> 263 <when value="preprocessors">
266 <expand macro="preprocessors_sequence_encoders"/> 264 <expand macro="preprocessors_sequence_encoders" />
267 </when> 265 </when>
268 </conditional> 266 </conditional>
269 </repeat> 267 </repeat>
270 <section name="final_estimator" title="Final Estimator" expanded="true"> 268 <section name="final_estimator" title="Final Estimator" expanded="true">
271 <conditional name="estimator_selector"> 269 <conditional name="estimator_selector">
272 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" > 270 <param name="selected_module" type="select" label="Choose the module that contains target estimator:">
273 <expand macro="estimator_module_options"> 271 <expand macro="estimator_module_options">
274 <option value="sklearn.compose">sklearn.compose</option> 272 <option value="sklearn.compose">sklearn.compose</option>
275 <option value="binarize_target">Binarize Target Classifier or Regressor</option> 273 <option value="binarize_target">Binarize Target Classifier or Regressor</option>
276 <option value="custom_estimator">Load a custom estimator</option> 274 <option value="custom_estimator">Load a custom estimator</option>
277 <option value="none">none -- The last component of pre-processing step will turn to a final estimator</option> 275 <option value="none">none -- The last component of pre-processing step will turn to a final estimator</option>
280 <expand macro="estimator_suboptions"> 278 <expand macro="estimator_suboptions">
281 <when value="sklearn.compose"> 279 <when value="sklearn.compose">
282 <param name="selected_estimator" type="select" label="Choose estimator class:"> 280 <param name="selected_estimator" type="select" label="Choose estimator class:">
283 <option value="TransformedTargetRegressor" selected="true">TransformedTargetRegressor</option> 281 <option value="TransformedTargetRegressor" selected="true">TransformedTargetRegressor</option>
284 </param> 282 </param>
285 <param name="regressor" type="data" format="zip" label="Choose the dataset containing the wrapped regressor"/> 283 <param name="regressor" type="data" format="zip" label="Choose the dataset containing the wrapped regressor" />
286 <param name="transformer" type="data" format="zip" label="Choose the dataset containing transformer"/> 284 <param name="transformer" type="data" format="zip" label="Choose the dataset containing transformer" />
287 </when> 285 </when>
288 <when value="binarize_target"> 286 <when value="binarize_target">
289 <param name="clf_or_regr" type="select" label="Classifier or Regressor:"> 287 <param name="clf_or_regr" type="select" label="Classifier or Regressor:">
290 <option value="BinarizeTargetClassifier">BinarizeTargetClassifier</option> 288 <option value="BinarizeTargetClassifier">BinarizeTargetClassifier</option>
291 <option value="BinarizeTargetRegressor">BinarizeTargetRegressor</option> 289 <option value="BinarizeTargetRegressor">BinarizeTargetRegressor</option>
292 </param> 290 </param>
293 <param name="wrapped_estimator" type="data" format="zip" label="Choose the dataset containing the wrapped estimator or pipeline"/> 291 <param name="wrapped_estimator" type="data" format="zip" label="Choose the dataset containing the wrapped estimator or pipeline" />
294 <param name='z_score' type="float" value="-1" optional="false" label="Discrize target values using z_score"/> 292 <param name='z_score' type="float" value="-1" optional="false" label="Discrize target values using z_score" />
295 <param name='value' type="float" value="" optional="true" label="Discretize target values using a fixed value instead" help="Optional. default: None."/> 293 <param name='value' type="float" value="" optional="true" label="Discretize target values using a fixed value instead" help="Optional. default: None." />
296 <param name="less_is_positive" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Are the detecting values smaller than others?"/> 294 <param name="less_is_positive" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Are the detecting values smaller than others?" />
297 </when> 295 </when>
298 <when value="custom_estimator"> 296 <when value="custom_estimator">
299 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline"/> 297 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline" />
300 </when> 298 </when>
301 <when value="none"/> 299 <when value="none" />
302 </expand> 300 </expand>
303 </conditional> 301 </conditional>
304 </section> 302 </section>
305 <!--param name="output_type" type="select" label="Output the final estimator instead?"> 303 <!--param name="output_type" type="select" label="Output the final estimator instead?">
306 <option value="Pipeline_Builder" selected="true">Pipeline</option> 304 <option value="Pipeline_Builder" selected="true">Pipeline</option>
307 <option value="Final_Estimator_Builder">Final Estimator</option> 305 <option value="Final_Estimator_Builder">Final Estimator</option>
308 </param>--> 306 </param>-->
309 <param name="get_params" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Output parameters for searchCV?" 307 <param name="get_params" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Output parameters for searchCV?" help="Optional. Tunable parameters could be obtained through `estimator_attributes` tool." />
310 help="Optional. Tunable parameters could be obtained through `estimator_attributes` tool."/>
311 </inputs> 308 </inputs>
312 <outputs> 309 <outputs>
313 <data format="zip" name="outfile" label="New Pipleline/Estimator"/> 310 <data format="zip" name="outfile" label="New Pipleline/Estimator" />
314 <data format="tabular" name="outfile_params" label="get_params for Pipleline/Estimator"> 311 <data format="tabular" name="outfile_params" label="get_params for Pipleline/Estimator">
315 <filter>get_params</filter> 312 <filter>get_params</filter>
316 </data> 313 </data>
317 </outputs> 314 </outputs>
318 <tests> 315 <tests>
319 <test> 316 <test>
320 <conditional name="component_selector"> 317 <conditional name="component_selector">
321 <param name="component_type" value="pre_processor"/> 318 <param name="component_type" value="pre_processor" />
322 <conditional name="pre_processors"> 319 <conditional name="pre_processors">
323 <param name="selected_pre_processor" value="QuantileTransformer"/> 320 <param name="selected_pre_processor" value="QuantileTransformer" />
324 <section name="options"> 321 <section name="options">
325 <param name="random_state" value="10"/> 322 <param name="random_state" value="10" />
326 </section> 323 </section>
327 </conditional> 324 </conditional>
328 </conditional> 325 </conditional>
329 <section name="final_estimator"> 326 <section name="final_estimator">
330 <conditional name="estimator_selector"> 327 <conditional name="estimator_selector">
331 <param name="selected_module" value="none"/> 328 <param name="selected_module" value="none" />
332 </conditional> 329 </conditional>
333 </section> 330 </section>
334 <output name="outfile" file="pipeline17" compare="sim_size" delta="5"/> 331 <output name="outfile" file="pipeline17" compare="sim_size" delta="30" />
335 </test> 332 </test>
336 <test> 333 <test>
337 <conditional name="component_selector"> 334 <conditional name="component_selector">
338 <param name="component_type" value="pre_processor"/> 335 <param name="component_type" value="pre_processor" />
339 <conditional name="pre_processors"> 336 <conditional name="pre_processors">
340 <param name="selected_pre_processor" value="PowerTransformer"/> 337 <param name="selected_pre_processor" value="PowerTransformer" />
341 </conditional> 338 </conditional>
342 </conditional> 339 </conditional>
343 <section name="final_estimator"> 340 <section name="final_estimator">
344 <conditional name="estimator_selector"> 341 <conditional name="estimator_selector">
345 <param name="selected_module" value="sklearn.compose"/> 342 <param name="selected_module" value="sklearn.compose" />
346 <param name="regressor" value="RandomForestRegressor01.zip" ftype="zip"/> 343 <param name="regressor" value="RandomForestRegressor01.zip" ftype="zip" />
347 <param name="transformer" value="pipeline17" ftype="zip"/> 344 <param name="transformer" value="pipeline17" ftype="zip" />
348 </conditional> 345 </conditional>
349 </section> 346 </section>
350 <param name="get_params" value="true"/> 347 <param name="get_params" value="true" />
351 <output name="outfile_params" file="pipeline_params18" ftype="tabular"/> 348 <output name="outfile_params" file="pipeline_params18" ftype="tabular" />
352 </test> 349 </test>
353 <test> 350 <test>
354 <repeat name="pipeline_component"> 351 <repeat name="pipeline_component">
355 <conditional name="component_selector"> 352 <conditional name="component_selector">
356 <param name="component_type" value="pre_processor"/> 353 <param name="component_type" value="pre_processor" />
357 <conditional name="pre_processors"> 354 <conditional name="pre_processors">
358 <param name="selected_pre_processor" value="RobustScaler"/> 355 <param name="selected_pre_processor" value="RobustScaler" />
359 </conditional> 356 </conditional>
360 </conditional> 357 </conditional>
361 </repeat> 358 </repeat>
362 <repeat name="pipeline_component"> 359 <repeat name="pipeline_component">
363 <conditional name="component_selector"> 360 <conditional name="component_selector">
364 <param name="component_type" value="feature_selection"/> 361 <param name="component_type" value="feature_selection" />
365 <conditional name="fs_algorithm_selector"> 362 <conditional name="fs_algorithm_selector">
366 <param name="selected_algorithm" value="SelectKBest"/> 363 <param name="selected_algorithm" value="SelectKBest" />
367 <param name="score_func" value="f_classif"/> 364 <param name="score_func" value="f_classif" />
368 </conditional> 365 </conditional>
369 </conditional> 366 </conditional>
370 </repeat> 367 </repeat>
371 <param name="selected_module" value="svm"/> 368 <param name="selected_module" value="svm" />
372 <param name="selected_estimator" value="SVR"/> 369 <param name="selected_estimator" value="SVR" />
373 <param name="text_params" value="kernel='linear'"/> 370 <param name="text_params" value="kernel='linear'" />
374 <output name="outfile" file="pipeline01" compare="sim_size" delta="5"/> 371 <output name="outfile" file="pipeline01" compare="sim_size" delta="30" />
375 </test> 372 </test>
376 <test> 373 <test>
377 <conditional name="component_selector"> 374 <conditional name="component_selector">
378 <param name="component_type" value="pre_processor"/> 375 <param name="component_type" value="pre_processor" />
379 <conditional name="pre_processors"> 376 <conditional name="pre_processors">
380 <param name="selected_pre_processor" value="RobustScaler"/> 377 <param name="selected_pre_processor" value="RobustScaler" />
381 </conditional> 378 </conditional>
382 </conditional> 379 </conditional>
383 <param name="selected_module" value="linear_model"/> 380 <param name="selected_module" value="linear_model" />
384 <param name="selected_estimator" value="LassoCV"/> 381 <param name="selected_estimator" value="LassoCV" />
385 <output name="outfile" file="pipeline02" compare="sim_size" delta="5"/> 382 <output name="outfile" file="pipeline02" compare="sim_size" delta="30" />
386 </test> 383 </test>
387 <test> 384 <test>
388 <conditional name="component_selector"> 385 <conditional name="component_selector">
389 <param name="component_type" value="pre_processor"/> 386 <param name="component_type" value="pre_processor" />
390 <conditional name="pre_processors"> 387 <conditional name="pre_processors">
391 <param name="selected_pre_processor" value="RobustScaler"/> 388 <param name="selected_pre_processor" value="RobustScaler" />
392 </conditional> 389 </conditional>
393 </conditional> 390 </conditional>
394 <param name="selected_module" value="xgboost"/> 391 <param name="selected_module" value="xgboost" />
395 <param name="selected_estimator" value="XGBClassifier"/> 392 <param name="selected_estimator" value="XGBClassifier" />
396 <output name="outfile" file="pipeline03" compare="sim_size" delta="5"/> 393 <output name="outfile" file="pipeline03" compare="sim_size" delta="30" />
397 </test> 394 </test>
398 <test> 395 <test>
399 <conditional name="component_selector"> 396 <conditional name="component_selector">
400 <param name="component_type" value="feature_selection"/> 397 <param name="component_type" value="feature_selection" />
401 <conditional name="fs_algorithm_selector"> 398 <conditional name="fs_algorithm_selector">
402 <param name="selected_algorithm" value="SelectFromModel"/> 399 <param name="selected_algorithm" value="SelectFromModel" />
403 <conditional name="model_inputter"> 400 <conditional name="model_inputter">
404 <conditional name="estimator_selector"> 401 <conditional name="estimator_selector">
405 <param name="selected_module" value="ensemble"/> 402 <param name="selected_module" value="ensemble" />
406 <param name="selected_estimator" value="AdaBoostClassifier"/> 403 <param name="selected_estimator" value="AdaBoostClassifier" />
407 </conditional> 404 </conditional>
408 </conditional> 405 </conditional>
409 </conditional> 406 </conditional>
410 </conditional> 407 </conditional>
411 <section name="final_estimator"> 408 <section name="final_estimator">
412 <param name="selected_module" value="svm"/> 409 <param name="selected_module" value="svm" />
413 <param name="selected_estimator" value="LinearSVC"/> 410 <param name="selected_estimator" value="LinearSVC" />
414 </section> 411 </section>
415 <output name="outfile" file="pipeline04" compare="sim_size" delta="5"/> 412 <output name="outfile" file="pipeline04" compare="sim_size" delta="30" />
416 </test> 413 </test>
417 <test> 414 <test>
418 <conditional name="component_selector"> 415 <conditional name="component_selector">
419 <param name="component_type" value="None"/> 416 <param name="component_type" value="None" />
420 </conditional> 417 </conditional>
421 <param name="selected_module" value="ensemble"/> 418 <param name="selected_module" value="ensemble" />
422 <param name="selected_estimator" value="RandomForestRegressor"/> 419 <param name="selected_estimator" value="RandomForestRegressor" />
423 <param name="text_params" value="n_estimators=100, random_state=42"/> 420 <param name="text_params" value="n_estimators=100, random_state=42" />
424 <param name="get_params" value="true"/> 421 <param name="get_params" value="true" />
425 <output name="outfile" file="pipeline05" compare="sim_size" delta="5"/> 422 <output name="outfile" file="pipeline05" compare="sim_size" delta="30" />
426 <output name="outfile_params" file="pipeline_params05.tabular" ftype="tabular"/> 423 <output name="outfile_params" file="pipeline_params05.tabular" ftype="tabular" />
427 </test> 424 </test>
428 <test> 425 <test>
429 <conditional name="component_selector"> 426 <conditional name="component_selector">
430 <param name="component_type" value="decomposition"/> 427 <param name="component_type" value="decomposition" />
431 <conditional name="matrix_decomposition_selector"> 428 <conditional name="matrix_decomposition_selector">
432 <param name="select_algorithm" value="PCA"/> 429 <param name="select_algorithm" value="PCA" />
433 </conditional> 430 </conditional>
434 </conditional> 431 </conditional>
435 <param name="selected_module" value="ensemble"/> 432 <param name="selected_module" value="ensemble" />
436 <param name="selected_estimator" value="AdaBoostRegressor"/> 433 <param name="selected_estimator" value="AdaBoostRegressor" />
437 <output name="outfile" file="pipeline06" compare="sim_size" delta="5"/> 434 <output name="outfile" file="pipeline06" compare="sim_size" delta="30" />
438 </test> 435 </test>
439 <test> 436 <test>
440 <conditional name="component_selector"> 437 <conditional name="component_selector">
441 <param name="component_type" value="kernel_approximation"/> 438 <param name="component_type" value="kernel_approximation" />
442 <conditional name="kernel_approximation_selector"> 439 <conditional name="kernel_approximation_selector">
443 <param name="select_algorithm" value="RBFSampler"/> 440 <param name="select_algorithm" value="RBFSampler" />
444 <param name="text_params" value="n_components=10, gamma=2.0"/> 441 <param name="text_params" value="n_components=10, gamma=2.0" />
445 </conditional> 442 </conditional>
446 </conditional> 443 </conditional>
447 <param name="selected_module" value="ensemble"/> 444 <param name="selected_module" value="ensemble" />
448 <param name="selected_estimator" value="AdaBoostClassifier"/> 445 <param name="selected_estimator" value="AdaBoostClassifier" />
449 <output name="outfile" file="pipeline07" compare="sim_size" delta="5"/> 446 <output name="outfile" file="pipeline07" compare="sim_size" delta="30" />
450 </test> 447 </test>
451 <test> 448 <test>
452 <conditional name="component_selector"> 449 <conditional name="component_selector">
453 <param name="component_type" value="FeatureAgglomeration"/> 450 <param name="component_type" value="FeatureAgglomeration" />
454 <conditional name="FeatureAgglomeration_selector"> 451 <conditional name="FeatureAgglomeration_selector">
455 <param name="select_algorithm" value="FeatureAgglomeration"/> 452 <param name="select_algorithm" value="FeatureAgglomeration" />
456 <param name="text_params" value="n_clusters=3, affinity='euclidean'"/> 453 <param name="text_params" value="n_clusters=3, affinity='euclidean'" />
457 </conditional> 454 </conditional>
458 </conditional> 455 </conditional>
459 <param name="selected_module" value="ensemble"/> 456 <param name="selected_module" value="ensemble" />
460 <param name="selected_estimator" value="AdaBoostClassifier"/> 457 <param name="selected_estimator" value="AdaBoostClassifier" />
461 <output name="outfile" file="pipeline08" compare="sim_size" delta="20"/> 458 <output name="outfile" file="pipeline08" compare="sim_size" delta="30" />
462 </test> 459 </test>
463 <test> 460 <test>
464 <conditional name="component_selector"> 461 <conditional name="component_selector">
465 <param name="component_type" value="skrebate"/> 462 <param name="component_type" value="skrebate" />
466 <conditional name="skrebate_selector"> 463 <conditional name="skrebate_selector">
467 <param name="select_algorithm" value="ReliefF"/> 464 <param name="select_algorithm" value="ReliefF" />
468 <param name="text_params" value="n_features_to_select=3, n_neighbors=100"/> 465 <param name="text_params" value="n_features_to_select=3, n_neighbors=100" />
469 </conditional> 466 </conditional>
470 </conditional> 467 </conditional>
471 <param name="selected_module" value="ensemble"/> 468 <param name="selected_module" value="ensemble" />
472 <param name="selected_estimator" value="RandomForestRegressor"/> 469 <param name="selected_estimator" value="RandomForestRegressor" />
473 <output name="outfile" file="pipeline09" compare="sim_size" delta="5"/> 470 <output name="outfile" file="pipeline09" compare="sim_size" delta="30" />
474 </test> 471 </test>
475 <test> 472 <test>
476 <conditional name="component_selector"> 473 <conditional name="component_selector">
477 <param name="component_type" value="imblearn"/> 474 <param name="component_type" value="imblearn" />
478 <conditional name="imblearn_selector"> 475 <conditional name="imblearn_selector">
479 <param name="select_algorithm" value="under_sampling.EditedNearestNeighbours"/> 476 <param name="select_algorithm" value="under_sampling.EditedNearestNeighbours" />
480 </conditional> 477 </conditional>
481 </conditional> 478 </conditional>
482 <param name="selected_module" value="ensemble"/> 479 <param name="selected_module" value="ensemble" />
483 <param name="selected_estimator" value="RandomForestClassifier"/> 480 <param name="selected_estimator" value="RandomForestClassifier" />
484 <output name="outfile" file="pipeline11" compare="sim_size" delta="5"/> 481 <output name="outfile" file="pipeline11" compare="sim_size" delta="30" />
485 </test> 482 </test>
486 <test expect_failure="true"> 483 <test expect_failure="true">
487 <conditional name="component_selector"> 484 <conditional name="component_selector">
488 <param name="component_type" value="None"/> 485 <param name="component_type" value="None" />
489 </conditional> 486 </conditional>
490 <param name="selected_module" value="ensemble"/> 487 <param name="selected_module" value="ensemble" />
491 <param name="selected_estimator" value="RandomForestRegressor"/> 488 <param name="selected_estimator" value="RandomForestRegressor" />
492 <param name="text_params" value="n_estimators=__import__('os').system('ls ~')"/> 489 <param name="text_params" value="n_estimators=__import__('os').system('ls ~')" />
493 </test> 490 </test>
494 <test> 491 <test>
495 <conditional name="component_selector"> 492 <conditional name="component_selector">
496 <param name="component_type" value="feature_selection"/> 493 <param name="component_type" value="feature_selection" />
497 <conditional name="fs_algorithm_selector"> 494 <conditional name="fs_algorithm_selector">
498 <param name="selected_algorithm" value="RFE"/> 495 <param name="selected_algorithm" value="RFE" />
499 <conditional name="estimator_selector"> 496 <conditional name="estimator_selector">
500 <param name="selected_module" value="xgboost"/> 497 <param name="selected_module" value="xgboost" />
501 <param name="selected_estimator" value="XGBRegressor"/> 498 <param name="selected_estimator" value="XGBRegressor" />
502 <param name="text_params" value="random_state=0"/> 499 <param name="text_params" value="random_state=0" />
503 </conditional> 500 </conditional>
504 </conditional> 501 </conditional>
505 </conditional> 502 </conditional>
506 <section name="final_estimator"> 503 <section name="final_estimator">
507 <conditional name="estimator_selector"> 504 <conditional name="estimator_selector">
508 <param name="selected_module" value="none"/> 505 <param name="selected_module" value="none" />
509 </conditional> 506 </conditional>
510 </section> 507 </section>
511 <output name="outfile" file="pipeline12" compare="sim_size" delta="5"/> 508 <output name="outfile" file="pipeline12" compare="sim_size" delta="30" />
512 </test> 509 </test>
513 <test> 510 <test>
514 <conditional name="component_selector"> 511 <conditional name="component_selector">
515 <param name="component_type" value="None"/> 512 <param name="component_type" value="None" />
516 </conditional> 513 </conditional>
517 <param name="selected_module" value="ensemble"/> 514 <param name="selected_module" value="ensemble" />
518 <param name="selected_estimator" value="RandomForestClassifier"/> 515 <param name="selected_estimator" value="RandomForestClassifier" />
519 <output name="outfile" file="RandomForestClassifier.zip" compare="sim_size" delta="5"/> 516 <output name="outfile" file="RandomForestClassifier.zip" compare="sim_size" delta="30" />
520 </test> 517 </test>
521 <test> 518 <test>
522 <conditional name="component_selector"> 519 <conditional name="component_selector">
523 <param name="component_type" value="IRAPS"/> 520 <param name="component_type" value="IRAPS" />
524 </conditional> 521 </conditional>
525 <section name="final_estimator"> 522 <section name="final_estimator">
526 <conditional name="estimator_selector"> 523 <conditional name="estimator_selector">
527 <param name="selected_module" value="none"/> 524 <param name="selected_module" value="none" />
528 </conditional> 525 </conditional>
529 </section> 526 </section>
530 <output name="outfile" file="pipeline14" compare="sim_size" delta="5"/> 527 <output name="outfile" file="pipeline14" compare="sim_size" delta="30" />
531 </test> 528 </test>
532 <test> 529 <test>
533 <conditional name="component_selector"> 530 <conditional name="component_selector">
534 <param name="component_type" value="None"/> 531 <param name="component_type" value="None" />
535 </conditional> 532 </conditional>
536 <section name="final_estimator"> 533 <section name="final_estimator">
537 <conditional name="estimator_selector"> 534 <conditional name="estimator_selector">
538 <param name="selected_module" value="binarize_target"/> 535 <param name="selected_module" value="binarize_target" />
539 <param name="clf_or_regr" value="BinarizeTargetClassifier"/> 536 <param name="clf_or_regr" value="BinarizeTargetClassifier" />
540 <param name="wrapped_estimator" value="RandomForestClassifier.zip" ftype="zip"/> 537 <param name="wrapped_estimator" value="RandomForestClassifier.zip" ftype="zip" />
541 </conditional> 538 </conditional>
542 </section> 539 </section>
543 <output name="outfile" file="pipeline15" compare="sim_size" delta="5"/> 540 <output name="outfile" file="pipeline15" compare="sim_size" delta="30" />
544 </test> 541 </test>
545 <test> 542 <test>
546 <conditional name="component_selector"> 543 <conditional name="component_selector">
547 <param name="component_type" value="preprocessors"/> 544 <param name="component_type" value="preprocessors" />
548 <conditional name="encoder_selection"> 545 <conditional name="encoder_selection">
549 <param name="encoder_type" value="GenomeOneHotEncoder"/> 546 <param name="encoder_type" value="GenomeOneHotEncoder" />
550 <param name="seq_length" value="1000"/> 547 <param name="seq_length" value="1000" />
551 <param name="padding" value="True"/> 548 <param name="padding" value="True" />
552 </conditional> 549 </conditional>
553 </conditional> 550 </conditional>
554 <section name="final_estimator"> 551 <section name="final_estimator">
555 <conditional name="estimator_selector"> 552 <conditional name="estimator_selector">
556 <param name="selected_module" value="custom_estimator"/> 553 <param name="selected_module" value="custom_estimator" />
557 <param name="c_estimator" value="keras_model02" ftype="zip"/> 554 <param name="c_estimator" value="keras_model02" ftype="zip" />
558 </conditional> 555 </conditional>
559 </section> 556 </section>
560 <output name="outfile" file="pipeline16" compare="sim_size" delta="5"/> 557 <output name="outfile" file="pipeline16" compare="sim_size" delta="30" />
561 </test> 558 </test>
562 </tests> 559 </tests>
563 <help> 560 <help>
564 <![CDATA[ 561 <![CDATA[
565 **What it does** 562 **What it does**
614 .. _`BinarizeTargetRegressor`: https://goeckslab.github.io/Galaxy-ML/APIs/binarize-target/#binarizetargetregressor 611 .. _`BinarizeTargetRegressor`: https://goeckslab.github.io/Galaxy-ML/APIs/binarize-target/#binarizetargetregressor
615 612
616 ]]> 613 ]]>
617 </help> 614 </help>
618 <expand macro="sklearn_citation"> 615 <expand macro="sklearn_citation">
619 <expand macro="skrebate_citation"/> 616 <expand macro="skrebate_citation" />
620 <expand macro="xgboost_citation"/> 617 <expand macro="xgboost_citation" />
621 <expand macro="imblearn_citation"/> 618 <expand macro="imblearn_citation" />
622 </expand> 619 </expand>
623 </tool> 620 </tool>