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comparison pipeline.xml @ 24:15815a470e6b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author bgruening
date Wed, 09 Aug 2023 12:06:37 +0000
parents 449bd57f70f4
children
comparison
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23:3d3cde736675 24:15815a470e6b
1 <tool id="sklearn_build_pipeline" name="Pipeline Builder" version="@VERSION@" profile="20.05"> 1 <tool id="sklearn_build_pipeline" name="Pipeline Builder" version="@VERSION@" profile="@PROFILE@">
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" />
16 <configfile name="sklearn_pipeline_script"> 16 <configfile name="sklearn_pipeline_script">
17 <![CDATA[ 17 <![CDATA[
18 import imblearn 18 import imblearn
19 import json 19 import json
20 import pandas as pd 20 import pandas as pd
21 import pickle
22 import pprint 21 import pprint
23 import skrebate 22 import skrebate
24 import sys 23 import sys
25 import warnings 24 import warnings
26 from sklearn import ( 25 from sklearn import (
28 feature_selection, gaussian_process, kernel_approximation, metrics, 27 feature_selection, gaussian_process, kernel_approximation, metrics,
29 model_selection, naive_bayes, neighbors, pipeline, preprocessing, 28 model_selection, naive_bayes, neighbors, pipeline, preprocessing,
30 svm, linear_model, tree, discriminant_analysis) 29 svm, linear_model, tree, discriminant_analysis)
31 from sklearn.pipeline import make_pipeline 30 from sklearn.pipeline import make_pipeline
32 from imblearn.pipeline import make_pipeline as imb_make_pipeline 31 from imblearn.pipeline import make_pipeline as imb_make_pipeline
32 from galaxy_ml.model_persist import dump_model_to_h5, load_model_from_h5
33 from galaxy_ml.utils import (SafeEval, feature_selector, get_estimator, 33 from galaxy_ml.utils import (SafeEval, feature_selector, get_estimator,
34 try_get_attr, get_search_params, load_model) 34 try_get_attr, get_search_params)
35
36 ## TODO remove following imports after scikit-learn v0.22
37 from sklearn.experimental import enable_hist_gradient_boosting
38 35
39 36
40 N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1)) 37 N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1))
41 38
42 warnings.filterwarnings('ignore') 39 warnings.filterwarnings('ignore')
180 elif estimator_json['selected_module'] == 'sklearn.compose': 177 elif estimator_json['selected_module'] == 'sklearn.compose':
181 #if $final_estimator.estimator_selector.selected_module == 'sklearn.compose': 178 #if $final_estimator.estimator_selector.selected_module == 'sklearn.compose':
182 regressor_path = '$final_estimator.estimator_selector.regressor' 179 regressor_path = '$final_estimator.estimator_selector.regressor'
183 transformer_path = '$final_estimator.estimator_selector.transformer' 180 transformer_path = '$final_estimator.estimator_selector.transformer'
184 #end if 181 #end if
185 with open(regressor_path, 'rb') as f: 182 regressor = load_model_from_h5(regressor_path)
186 regressor = load_model(f) 183 transformer = load_model_from_h5(transformer_path)
187 with open(transformer_path, 'rb') as f:
188 transformer = load_model(f)
189 estimator = compose.TransformedTargetRegressor(regressor=regressor, transformer=transformer) 184 estimator = compose.TransformedTargetRegressor(regressor=regressor, transformer=transformer)
190 pipeline_steps.append( estimator ) 185 pipeline_steps.append( estimator )
191 else: 186 else:
192 estimator = get_estimator(estimator_json) 187 estimator = get_estimator(estimator_json)
193 pipeline_steps.append( estimator ) 188 pipeline_steps.append( estimator )
200 out_obj = imb_make_pipeline(*pipeline_steps) 195 out_obj = imb_make_pipeline(*pipeline_steps)
201 else: 196 else:
202 out_obj = make_pipeline(*pipeline_steps) 197 out_obj = make_pipeline(*pipeline_steps)
203 pprint.pprint(out_obj.named_steps) 198 pprint.pprint(out_obj.named_steps)
204 199
205 with open('$outfile', 'wb') as out_handler: 200 dump_model_to_h5(out_obj, '$outfile', verbose=0)
206 pickle.dump(out_obj, out_handler, pickle.HIGHEST_PROTOCOL) 201
207
208 #if $get_params
209 results = get_search_params(out_obj)
210 df = pd.DataFrame(results, columns=['', 'Parameter', 'Value'])
211 df.to_csv('$outfile_params', sep='\t', index=False)
212 #end if
213 ]]> 202 ]]>
214 </configfile> 203 </configfile>
215 </configfiles> 204 </configfiles>
216 <inputs> 205 <inputs>
217 <repeat name="pipeline_component" min="1" max="5" title="Pre-processing step"> 206 <repeat name="pipeline_component" min="1" max="5" title="Pre-processing step">
252 </when> 241 </when>
253 <when value="imblearn"> 242 <when value="imblearn">
254 <expand macro="imbalanced_learn_sampling" /> 243 <expand macro="imbalanced_learn_sampling" />
255 </when> 244 </when>
256 <when value="IRAPS"> 245 <when value="IRAPS">
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" /> 246 <expand macro="estimator_params_text"
247 label="Type in parameter settings for IRAPSCore if different from default:"
248 help="Default(=blank): n_iter=1000, responsive_thres=-1, resistant_thres=0, random_state=None. No double quotes" />
258 <param argument="p_thres" type="float" value="0.001" label="P value threshold" help="Float. default=0.001" /> 249 <param argument="p_thres" type="float" value="0.001" label="P value threshold" help="Float. default=0.001" />
259 <param argument="fc_thres" type="float" value="0.1" label="fold change threshold" help="Float. default=0.1" /> 250 <param argument="fc_thres" type="float" value="0.1" label="fold change threshold" help="Float. default=0.1" />
260 <param argument="occurrence" type="float" value="0.7" label="reservation factor" help="Float. default=0.7" /> 251 <param argument="occurrence" type="float" value="0.7" label="reservation factor" help="Float. default=0.7" />
261 <param argument="discretize" type="float" value="-1" label="The z_score threshold to discretize target value" help="Float. default=-1" /> 252 <param argument="discretize" type="float" value="-1" label="The z_score threshold to discretize target value" help="Float. default=-1" />
262 </when> 253 </when>
265 </when> 256 </when>
266 </conditional> 257 </conditional>
267 </repeat> 258 </repeat>
268 <section name="final_estimator" title="Final Estimator" expanded="true"> 259 <section name="final_estimator" title="Final Estimator" expanded="true">
269 <conditional name="estimator_selector"> 260 <conditional name="estimator_selector">
270 <param name="selected_module" type="select" label="Choose the module that contains target estimator:"> 261 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" >
271 <expand macro="estimator_module_options"> 262 <expand macro="estimator_module_options">
272 <option value="sklearn.compose">sklearn.compose</option> 263 <option value="sklearn.compose">sklearn.compose</option>
273 <option value="binarize_target">Binarize Target Classifier or Regressor</option> 264 <option value="binarize_target">Binarize Target Classifier or Regressor</option>
274 <option value="custom_estimator">Load a custom estimator</option> 265 <option value="custom_estimator">Load a custom estimator</option>
275 <option value="none">none -- The last component of pre-processing step will turn to a final estimator</option> 266 <option value="none">none -- The last component of pre-processing step will turn to a final estimator</option>
278 <expand macro="estimator_suboptions"> 269 <expand macro="estimator_suboptions">
279 <when value="sklearn.compose"> 270 <when value="sklearn.compose">
280 <param name="selected_estimator" type="select" label="Choose estimator class:"> 271 <param name="selected_estimator" type="select" label="Choose estimator class:">
281 <option value="TransformedTargetRegressor" selected="true">TransformedTargetRegressor</option> 272 <option value="TransformedTargetRegressor" selected="true">TransformedTargetRegressor</option>
282 </param> 273 </param>
283 <param name="regressor" type="data" format="zip" label="Choose the dataset containing the wrapped regressor" /> 274 <param name="regressor" type="data" format="h5mlm" label="Choose the dataset containing the wrapped regressor" />
284 <param name="transformer" type="data" format="zip" label="Choose the dataset containing transformer" /> 275 <param name="transformer" type="data" format="h5mlm" label="Choose the dataset containing transformer" />
285 </when> 276 </when>
286 <when value="binarize_target"> 277 <when value="binarize_target">
287 <param name="clf_or_regr" type="select" label="Classifier or Regressor:"> 278 <param name="clf_or_regr" type="select" label="Classifier or Regressor:">
288 <option value="BinarizeTargetClassifier">BinarizeTargetClassifier</option> 279 <option value="BinarizeTargetClassifier">BinarizeTargetClassifier</option>
289 <option value="BinarizeTargetRegressor">BinarizeTargetRegressor</option> 280 <option value="BinarizeTargetRegressor">BinarizeTargetRegressor</option>
290 </param> 281 </param>
291 <param name="wrapped_estimator" type="data" format="zip" label="Choose the dataset containing the wrapped estimator or pipeline" /> 282 <param name="wrapped_estimator" type="data" format="h5mlm" label="Choose the dataset containing the wrapped estimator or pipeline" />
292 <param name='z_score' type="float" value="-1" optional="false" label="Discrize target values using z_score" /> 283 <param name='z_score' type="float" value="-1" optional="false" label="Discrize target values using z_score" />
293 <param name='value' type="float" value="" optional="true" label="Discretize target values using a fixed value instead" help="Optional. default: None." /> 284 <param name='value' type="float" value="" optional="true" label="Discretize target values using a fixed value instead" help="Optional. default: None." />
294 <param name="less_is_positive" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Are the detecting values smaller than others?" /> 285 <param name="less_is_positive" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Are the detecting values smaller than others?" />
295 </when> 286 </when>
296 <when value="custom_estimator"> 287 <when value="custom_estimator">
297 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline" /> 288 <param name="c_estimator" type="data" format="h5mlm" label="Choose the dataset containing the custom estimator or pipeline" />
298 </when> 289 </when>
299 <when value="none" /> 290 <when value="none" />
300 </expand> 291 </expand>
301 </conditional> 292 </conditional>
302 </section> 293 </section>
303 <!--param name="output_type" type="select" label="Output the final estimator instead?"> 294 <!--param name="output_type" type="select" label="Output the final estimator instead?">
304 <option value="Pipeline_Builder" selected="true">Pipeline</option> 295 <option value="Pipeline_Builder" selected="true">Pipeline</option>
305 <option value="Final_Estimator_Builder">Final Estimator</option> 296 <option value="Final_Estimator_Builder">Final Estimator</option>
306 </param>--> 297 </param>-->
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." />
308 </inputs> 298 </inputs>
309 <outputs> 299 <outputs>
310 <data format="zip" name="outfile" label="New Pipleline/Estimator" /> 300 <data format="h5mlm" name="outfile" label="New Pipleline/Estimator" />
311 <data format="tabular" name="outfile_params" label="get_params for Pipleline/Estimator">
312 <filter>get_params</filter>
313 </data>
314 </outputs> 301 </outputs>
315 <tests> 302 <tests>
316 <test> 303 <test>
317 <conditional name="component_selector"> 304 <conditional name="component_selector">
318 <param name="component_type" value="pre_processor" /> 305 <param name="component_type" value="pre_processor" />
326 <section name="final_estimator"> 313 <section name="final_estimator">
327 <conditional name="estimator_selector"> 314 <conditional name="estimator_selector">
328 <param name="selected_module" value="none" /> 315 <param name="selected_module" value="none" />
329 </conditional> 316 </conditional>
330 </section> 317 </section>
331 <output name="outfile" file="pipeline17" compare="sim_size" delta="30" /> 318 <output name="outfile" file="pipeline17" compare="sim_size" delta="5" />
332 </test> 319 </test>
333 <test> 320 <test>
334 <conditional name="component_selector"> 321 <conditional name="component_selector">
335 <param name="component_type" value="pre_processor" /> 322 <param name="component_type" value="pre_processor" />
336 <conditional name="pre_processors"> 323 <conditional name="pre_processors">
338 </conditional> 325 </conditional>
339 </conditional> 326 </conditional>
340 <section name="final_estimator"> 327 <section name="final_estimator">
341 <conditional name="estimator_selector"> 328 <conditional name="estimator_selector">
342 <param name="selected_module" value="sklearn.compose" /> 329 <param name="selected_module" value="sklearn.compose" />
343 <param name="regressor" value="RandomForestRegressor01.zip" ftype="zip" /> 330 <param name="regressor" value="RandomForestRegressor01.h5mlm" ftype="h5mlm" />
344 <param name="transformer" value="pipeline17" ftype="zip" /> 331 <param name="transformer" value="pipeline17" ftype="h5mlm" />
345 </conditional> 332 </conditional>
346 </section> 333 </section>
347 <param name="get_params" value="true" /> 334 <output name="outfile" file="pipeline18" compare="sim_size" delta="5" />
348 <output name="outfile_params" file="pipeline_params18" ftype="tabular" />
349 </test> 335 </test>
350 <test> 336 <test>
351 <repeat name="pipeline_component"> 337 <repeat name="pipeline_component">
352 <conditional name="component_selector"> 338 <conditional name="component_selector">
353 <param name="component_type" value="pre_processor" /> 339 <param name="component_type" value="pre_processor" />
366 </conditional> 352 </conditional>
367 </repeat> 353 </repeat>
368 <param name="selected_module" value="svm" /> 354 <param name="selected_module" value="svm" />
369 <param name="selected_estimator" value="SVR" /> 355 <param name="selected_estimator" value="SVR" />
370 <param name="text_params" value="kernel='linear'" /> 356 <param name="text_params" value="kernel='linear'" />
371 <output name="outfile" file="pipeline01" compare="sim_size" delta="30" /> 357 <output name="outfile" file="pipeline01" compare="sim_size" delta="5" />
372 </test> 358 </test>
373 <test> 359 <test>
374 <conditional name="component_selector"> 360 <conditional name="component_selector">
375 <param name="component_type" value="pre_processor" /> 361 <param name="component_type" value="pre_processor" />
376 <conditional name="pre_processors"> 362 <conditional name="pre_processors">
377 <param name="selected_pre_processor" value="RobustScaler" /> 363 <param name="selected_pre_processor" value="RobustScaler" />
378 </conditional> 364 </conditional>
379 </conditional> 365 </conditional>
380 <param name="selected_module" value="linear_model" /> 366 <param name="selected_module" value="linear_model" />
381 <param name="selected_estimator" value="LassoCV" /> 367 <param name="selected_estimator" value="LassoCV" />
382 <output name="outfile" file="pipeline02" compare="sim_size" delta="30" /> 368 <output name="outfile" file="pipeline02" compare="sim_size" delta="5" />
383 </test> 369 </test>
384 <test> 370 <test>
385 <conditional name="component_selector"> 371 <conditional name="component_selector">
386 <param name="component_type" value="pre_processor" /> 372 <param name="component_type" value="pre_processor" />
387 <conditional name="pre_processors"> 373 <conditional name="pre_processors">
388 <param name="selected_pre_processor" value="RobustScaler" /> 374 <param name="selected_pre_processor" value="RobustScaler" />
389 </conditional> 375 </conditional>
390 </conditional> 376 </conditional>
391 <param name="selected_module" value="xgboost" /> 377 <param name="selected_module" value="xgboost" />
392 <param name="selected_estimator" value="XGBClassifier" /> 378 <param name="selected_estimator" value="XGBClassifier" />
393 <output name="outfile" file="pipeline03" compare="sim_size" delta="30" /> 379 <output name="outfile" file="pipeline03" compare="sim_size" delta="5" />
394 </test> 380 </test>
395 <test> 381 <test>
396 <conditional name="component_selector"> 382 <conditional name="component_selector">
397 <param name="component_type" value="feature_selection" /> 383 <param name="component_type" value="feature_selection" />
398 <conditional name="fs_algorithm_selector"> 384 <conditional name="fs_algorithm_selector">
407 </conditional> 393 </conditional>
408 <section name="final_estimator"> 394 <section name="final_estimator">
409 <param name="selected_module" value="svm" /> 395 <param name="selected_module" value="svm" />
410 <param name="selected_estimator" value="LinearSVC" /> 396 <param name="selected_estimator" value="LinearSVC" />
411 </section> 397 </section>
412 <output name="outfile" file="pipeline04" compare="sim_size" delta="30" /> 398 <output name="outfile" file="pipeline04" compare="sim_size" delta="5" />
413 </test> 399 </test>
414 <test> 400 <test>
415 <conditional name="component_selector"> 401 <conditional name="component_selector">
416 <param name="component_type" value="None" /> 402 <param name="component_type" value="None" />
417 </conditional> 403 </conditional>
418 <param name="selected_module" value="ensemble" /> 404 <param name="selected_module" value="ensemble" />
419 <param name="selected_estimator" value="RandomForestRegressor" /> 405 <param name="selected_estimator" value="RandomForestRegressor" />
420 <param name="text_params" value="n_estimators=100, random_state=42" /> 406 <param name="text_params" value="n_estimators=100, random_state=42" />
421 <param name="get_params" value="true" /> 407 <output name="outfile" file="pipeline05" compare="sim_size" delta="5" />
422 <output name="outfile" file="pipeline05" compare="sim_size" delta="30" />
423 <output name="outfile_params" file="pipeline_params05.tabular" ftype="tabular" />
424 </test> 408 </test>
425 <test> 409 <test>
426 <conditional name="component_selector"> 410 <conditional name="component_selector">
427 <param name="component_type" value="decomposition" /> 411 <param name="component_type" value="decomposition" />
428 <conditional name="matrix_decomposition_selector"> 412 <conditional name="matrix_decomposition_selector">
429 <param name="select_algorithm" value="PCA" /> 413 <param name="select_algorithm" value="PCA" />
430 </conditional> 414 </conditional>
431 </conditional> 415 </conditional>
432 <param name="selected_module" value="ensemble" /> 416 <param name="selected_module" value="ensemble" />
433 <param name="selected_estimator" value="AdaBoostRegressor" /> 417 <param name="selected_estimator" value="AdaBoostRegressor" />
434 <output name="outfile" file="pipeline06" compare="sim_size" delta="30" /> 418 <output name="outfile" file="pipeline06" compare="sim_size" delta="5" />
435 </test> 419 </test>
436 <test> 420 <test>
437 <conditional name="component_selector"> 421 <conditional name="component_selector">
438 <param name="component_type" value="kernel_approximation" /> 422 <param name="component_type" value="kernel_approximation" />
439 <conditional name="kernel_approximation_selector"> 423 <conditional name="kernel_approximation_selector">
440 <param name="select_algorithm" value="RBFSampler" /> 424 <param name="select_algorithm" value="RBFSampler" />
441 <param name="text_params" value="n_components=10, gamma=2.0" /> 425 <param name="text_params" value="n_components=10, gamma=2.0" />
442 </conditional> 426 </conditional>
443 </conditional> 427 </conditional>
444 <param name="selected_module" value="ensemble" /> 428 <param name="selected_module" value="ensemble" />
445 <param name="selected_estimator" value="AdaBoostClassifier" /> 429 <param name="selected_estimator" value="AdaBoostClassifier" />
446 <output name="outfile" file="pipeline07" compare="sim_size" delta="30" /> 430 <output name="outfile" file="pipeline07" compare="sim_size" delta="5" />
447 </test> 431 </test>
448 <test> 432 <test>
449 <conditional name="component_selector"> 433 <conditional name="component_selector">
450 <param name="component_type" value="FeatureAgglomeration" /> 434 <param name="component_type" value="FeatureAgglomeration" />
451 <conditional name="FeatureAgglomeration_selector"> 435 <conditional name="FeatureAgglomeration_selector">
452 <param name="select_algorithm" value="FeatureAgglomeration" /> 436 <param name="select_algorithm" value="FeatureAgglomeration" />
453 <param name="text_params" value="n_clusters=3, affinity='euclidean'" /> 437 <param name="text_params" value="n_clusters=3, affinity='euclidean'" />
454 </conditional> 438 </conditional>
455 </conditional> 439 </conditional>
456 <param name="selected_module" value="ensemble" /> 440 <param name="selected_module" value="ensemble" />
457 <param name="selected_estimator" value="AdaBoostClassifier" /> 441 <param name="selected_estimator" value="AdaBoostClassifier" />
458 <output name="outfile" file="pipeline08" compare="sim_size" delta="30" /> 442 <output name="outfile" file="pipeline08" compare="sim_size" delta="20" />
459 </test> 443 </test>
460 <test> 444 <test>
461 <conditional name="component_selector"> 445 <conditional name="component_selector">
462 <param name="component_type" value="skrebate" /> 446 <param name="component_type" value="skrebate" />
463 <conditional name="skrebate_selector"> 447 <conditional name="skrebate_selector">
464 <param name="select_algorithm" value="ReliefF" /> 448 <param name="select_algorithm" value="ReliefF" />
465 <param name="text_params" value="n_features_to_select=3, n_neighbors=100" /> 449 <param name="text_params" value="n_features_to_select=3, n_neighbors=100" />
466 </conditional> 450 </conditional>
467 </conditional> 451 </conditional>
468 <param name="selected_module" value="ensemble" /> 452 <param name="selected_module" value="ensemble" />
469 <param name="selected_estimator" value="RandomForestRegressor" /> 453 <param name="selected_estimator" value="RandomForestRegressor" />
470 <output name="outfile" file="pipeline09" compare="sim_size" delta="30" /> 454 <output name="outfile" file="pipeline09" compare="sim_size" delta="5" />
471 </test> 455 </test>
472 <test> 456 <test>
473 <conditional name="component_selector"> 457 <conditional name="component_selector">
474 <param name="component_type" value="imblearn" /> 458 <param name="component_type" value="imblearn" />
475 <conditional name="imblearn_selector"> 459 <conditional name="imblearn_selector">
476 <param name="select_algorithm" value="under_sampling.EditedNearestNeighbours" /> 460 <param name="select_algorithm" value="under_sampling.EditedNearestNeighbours" />
477 </conditional> 461 </conditional>
478 </conditional> 462 </conditional>
479 <param name="selected_module" value="ensemble" /> 463 <param name="selected_module" value="ensemble" />
480 <param name="selected_estimator" value="RandomForestClassifier" /> 464 <param name="selected_estimator" value="RandomForestClassifier" />
481 <output name="outfile" file="pipeline11" compare="sim_size" delta="30" /> 465 <output name="outfile" file="pipeline11" compare="sim_size" delta="5" />
482 </test> 466 </test>
483 <test expect_failure="true"> 467 <test expect_failure="true">
484 <conditional name="component_selector"> 468 <conditional name="component_selector">
485 <param name="component_type" value="None" /> 469 <param name="component_type" value="None" />
486 </conditional> 470 </conditional>
503 <section name="final_estimator"> 487 <section name="final_estimator">
504 <conditional name="estimator_selector"> 488 <conditional name="estimator_selector">
505 <param name="selected_module" value="none" /> 489 <param name="selected_module" value="none" />
506 </conditional> 490 </conditional>
507 </section> 491 </section>
508 <output name="outfile" file="pipeline12" compare="sim_size" delta="30" /> 492 <output name="outfile" file="pipeline12" compare="sim_size" delta="5" />
509 </test> 493 </test>
510 <test> 494 <test>
511 <conditional name="component_selector"> 495 <conditional name="component_selector">
512 <param name="component_type" value="None" /> 496 <param name="component_type" value="None" />
513 </conditional> 497 </conditional>
514 <param name="selected_module" value="ensemble" /> 498 <param name="selected_module" value="ensemble" />
515 <param name="selected_estimator" value="RandomForestClassifier" /> 499 <param name="selected_estimator" value="RandomForestClassifier" />
516 <output name="outfile" file="RandomForestClassifier.zip" compare="sim_size" delta="30" /> 500 <output name="outfile" file="RandomForestClassifier.h5mlm" compare="sim_size" delta="5" />
517 </test> 501 </test>
518 <test> 502 <test>
519 <conditional name="component_selector"> 503 <conditional name="component_selector">
520 <param name="component_type" value="IRAPS" /> 504 <param name="component_type" value="IRAPS" />
521 </conditional> 505 </conditional>
522 <section name="final_estimator"> 506 <section name="final_estimator">
523 <conditional name="estimator_selector"> 507 <conditional name="estimator_selector">
524 <param name="selected_module" value="none" /> 508 <param name="selected_module" value="none" />
525 </conditional> 509 </conditional>
526 </section> 510 </section>
527 <output name="outfile" file="pipeline14" compare="sim_size" delta="30" /> 511 <output name="outfile" file="pipeline14" compare="sim_size" delta="5" />
528 </test> 512 </test>
529 <test> 513 <test>
530 <conditional name="component_selector"> 514 <conditional name="component_selector">
531 <param name="component_type" value="None" /> 515 <param name="component_type" value="None" />
532 </conditional> 516 </conditional>
533 <section name="final_estimator"> 517 <section name="final_estimator">
534 <conditional name="estimator_selector"> 518 <conditional name="estimator_selector">
535 <param name="selected_module" value="binarize_target" /> 519 <param name="selected_module" value="binarize_target" />
536 <param name="clf_or_regr" value="BinarizeTargetClassifier" /> 520 <param name="clf_or_regr" value="BinarizeTargetClassifier" />
537 <param name="wrapped_estimator" value="RandomForestClassifier.zip" ftype="zip" /> 521 <param name="wrapped_estimator" value="RandomForestClassifier.h5mlm" ftype="h5mlm" />
538 </conditional> 522 </conditional>
539 </section> 523 </section>
540 <output name="outfile" file="pipeline15" compare="sim_size" delta="30" /> 524 <output name="outfile" file="pipeline15" compare="sim_size" delta="5" />
541 </test> 525 </test>
542 <test> 526 <test>
543 <conditional name="component_selector"> 527 <conditional name="component_selector">
544 <param name="component_type" value="preprocessors" /> 528 <param name="component_type" value="preprocessors" />
545 <conditional name="encoder_selection"> 529 <conditional name="encoder_selection">
549 </conditional> 533 </conditional>
550 </conditional> 534 </conditional>
551 <section name="final_estimator"> 535 <section name="final_estimator">
552 <conditional name="estimator_selector"> 536 <conditional name="estimator_selector">
553 <param name="selected_module" value="custom_estimator" /> 537 <param name="selected_module" value="custom_estimator" />
554 <param name="c_estimator" value="keras_model02" ftype="zip" /> 538 <param name="c_estimator" value="keras_model02" ftype="h5mlm" />
555 </conditional> 539 </conditional>
556 </section> 540 </section>
557 <output name="outfile" file="pipeline16" compare="sim_size" delta="30" /> 541 <output name="outfile" file="pipeline16" compare="sim_size" delta="5" />
558 </test> 542 </test>
559 </tests> 543 </tests>
560 <help> 544 <help>
561 <![CDATA[ 545 <![CDATA[
562 **What it does** 546 **What it does**
581 565
582 - `BinarizeTargetRegressor`_ 566 - `BinarizeTargetRegressor`_
583 567
584 **Output** 568 **Output**
585 569
586 - Pickled pipeline/estimator object 570 - Pipeline/estimator object
587 571
588 - Hyperparameter of the ojbect (optional) 572 - Hyperparameter of the object (optional)
589 573
590 574
591 .. _`Scikit-learn pipeline Pipeline`: http://scikit-learn.org/stable/modules/generated/sklearn.pipeline.Pipeline.html 575 .. _`Scikit-learn pipeline Pipeline`: http://scikit-learn.org/stable/modules/generated/sklearn.pipeline.Pipeline.html
592 .. _`svm`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.svm 576 .. _`svm`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.svm
593 .. _`linear_model`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.linear_model 577 .. _`linear_model`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.linear_model