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comparison model_validation.xml @ 12:86b57b062f96 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
author bgruening
date Fri, 17 Aug 2018 12:24:20 -0400
parents 61844bce4115
children 10a9e2a63464
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11:61844bce4115 12:86b57b062f96
14 <configfiles> 14 <configfiles>
15 <inputs name="inputs" /> 15 <inputs name="inputs" />
16 <configfile name="sklearn_model_validation_script"> 16 <configfile name="sklearn_model_validation_script">
17 <![CDATA[ 17 <![CDATA[
18 import sys 18 import sys
19 import os
19 import json 20 import json
20 import pandas 21 import pandas
21 import re
22 import ast
23 import pickle
24 import numpy as np 22 import numpy as np
25 import sklearn.feature_selection
26 from sklearn import preprocessing, model_selection, svm, linear_model, ensemble, naive_bayes, tree, neighbors 23 from sklearn import preprocessing, model_selection, svm, linear_model, ensemble, naive_bayes, tree, neighbors
27 from sklearn.pipeline import Pipeline 24 from sklearn.pipeline import Pipeline
28 25
29 @COLUMNS_FUNCTION@ 26 execfile("$__tool_directory__/utils.py")
30 @GET_ESTIMATOR_FUNCTION@ 27
31 @FEATURE_SELECTOR_FUNCTION@ 28 safe_eval = SafeEval()
32 @SAFE_EVAL_FUNCTION@
33 @GET_CV_FUNCTION@
34
35 29
36 input_json_path = sys.argv[1] 30 input_json_path = sys.argv[1]
37 with open(input_json_path, "r") as param_handler: 31 with open(input_json_path, "r") as param_handler:
38 params = json.load(param_handler) 32 params = json.load(param_handler)
39 33
72 ) 66 )
73 y=y.ravel() 67 y=y.ravel()
74 68
75 options = params["model_validation_functions"]["options"] 69 options = params["model_validation_functions"]["options"]
76 options['cv'] = get_cv( options['cv'] ) 70 options['cv'] = get_cv( options['cv'] )
77 if 'scoring' in options and options['scoring'] == '': 71 options['n_jobs'] = N_JOBS
78 options['scoring'] = None 72 if 'scoring' in options:
73 options['scoring'] = get_scoring(options['scoring'])
79 if 'pre_dispatch' in options and options['pre_dispatch'] == '': 74 if 'pre_dispatch' in options and options['pre_dispatch'] == '':
80 options['pre_dispatch'] = None 75 options['pre_dispatch'] = None
81 76
82 pipeline_steps = [] 77 pipeline_steps = []
83 78
173 <when value="cross_validate"> 168 <when value="cross_validate">
174 <expand macro="estimator_selector_all" /> 169 <expand macro="estimator_selector_all" />
175 <section name="options" title="Other Options" expanded="false"> 170 <section name="options" title="Other Options" expanded="false">
176 <!--groups--> 171 <!--groups-->
177 <expand macro="model_validation_common_options"/> 172 <expand macro="model_validation_common_options"/>
178 <expand macro="scoring"/> 173 <expand macro="scoring_selection"/>
179 <!--fit_params--> 174 <!--fit_params-->
180 <expand macro="pre_dispatch"/> 175 <expand macro="pre_dispatch"/>
181 </section> 176 </section>
182 <param name="return_type" type="select" label="Select a return type"> 177 <param name="return_type" type="select" label="Select a return type">
183 <option value="test_score" selected="true">test_score</option> 178 <option value="test_score" selected="true">test_score</option>
202 <when value="cross_val_score"> 197 <when value="cross_val_score">
203 <expand macro="estimator_selector_all" /> 198 <expand macro="estimator_selector_all" />
204 <section name="options" title="Other Options" expanded="false"> 199 <section name="options" title="Other Options" expanded="false">
205 <!--groups--> 200 <!--groups-->
206 <expand macro="model_validation_common_options"/> 201 <expand macro="model_validation_common_options"/>
207 <expand macro="scoring"/> 202 <expand macro="scoring_selection"/>
208 <!--fit_params--> 203 <!--fit_params-->
209 <expand macro="pre_dispatch"/> 204 <expand macro="pre_dispatch"/>
210 </section> 205 </section>
211 </when> 206 </when>
212 <when value="learning_curve"> 207 <when value="learning_curve">
213 <expand macro="estimator_selector_all" /> 208 <expand macro="estimator_selector_all" />
214 <section name="options" title="Other Options" expanded="false"> 209 <section name="options" title="Other Options" expanded="false">
215 <!--groups--> 210 <!--groups-->
216 <expand macro="model_validation_common_options"/> 211 <expand macro="model_validation_common_options"/>
217 <param argument="train_sizes" type="text" value="np.linspace(0.1, 1.0, 5)" label="train_sizes" help="Relative or absolute numbers of training examples that will be used to generate the learning curve"/> 212 <param argument="train_sizes" type="text" value="np.linspace(0.1, 1.0, 5)" label="train_sizes" help="Relative or absolute numbers of training examples that will be used to generate the learning curve"/>
218 <expand macro="scoring"/> 213 <expand macro="scoring_selection"/>
219 <param argument="exploit_incremental_learning" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="exploit_incremental_learning" help="Whether to apply incremental learning to speed up fitting of the estimator if supported"/> 214 <param argument="exploit_incremental_learning" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="exploit_incremental_learning" help="Whether to apply incremental learning to speed up fitting of the estimator if supported"/>
220 <expand macro="pre_dispatch"/> 215 <expand macro="pre_dispatch"/>
221 <expand macro="shuffle" checked="false" label="shuffle" help="Whether to shuffle training data before taking prefixes"/> 216 <expand macro="shuffle" checked="false" label="shuffle" help="Whether to shuffle training data before taking prefixes"/>
222 <expand macro="random_state"/> 217 <expand macro="random_state"/>
223 </section> 218 </section>
230 <when value="permutation_test_score"> 225 <when value="permutation_test_score">
231 <expand macro="estimator_selector_all" /> 226 <expand macro="estimator_selector_all" />
232 <section name="options" title="Other Options" expanded="false"> 227 <section name="options" title="Other Options" expanded="false">
233 <!--groups--> 228 <!--groups-->
234 <expand macro="model_validation_common_options"/> 229 <expand macro="model_validation_common_options"/>
235 <expand macro="scoring"/> 230 <expand macro="scoring_selection"/>
236 <param name="n_permutations" type="integer" value="100" optional="true" label="n_permutations" help="Number of times to permute y"/> 231 <param name="n_permutations" type="integer" value="100" optional="true" label="n_permutations" help="Number of times to permute y"/>
237 <expand macro="random_state"/> 232 <expand macro="random_state"/>
238 </section> 233 </section>
239 <param name="return_type" type="select" label="Select a return type"> 234 <param name="return_type" type="select" label="Select a return type">
240 <option value="score" selected="true">score</option> 235 <option value="score" selected="true">score</option>
247 <section name="options" title="Other Options" expanded="false"> 242 <section name="options" title="Other Options" expanded="false">
248 <param name="param_name" type="text" value="gamma" label="param_name" help="Name of the parameter that will be varied"/> 243 <param name="param_name" type="text" value="gamma" label="param_name" help="Name of the parameter that will be varied"/>
249 <param name="param_range" type="text" value="np.logspace(-6, -1, 5)" label="param_range" help="The values of the parameter that will be evaluated."/> 244 <param name="param_range" type="text" value="np.logspace(-6, -1, 5)" label="param_range" help="The values of the parameter that will be evaluated."/>
250 <!--groups--> 245 <!--groups-->
251 <expand macro="model_validation_common_options"/> 246 <expand macro="model_validation_common_options"/>
252 <expand macro="scoring"/> 247 <expand macro="scoring_selection"/>
253 <expand macro="pre_dispatch"/> 248 <expand macro="pre_dispatch"/>
254 </section> 249 </section>
255 <param name="return_type" type="select" label="Select a return type"> 250 <param name="return_type" type="select" label="Select a return type">
256 <option value="train_scores" selected="true">train_scores</option> 251 <option value="train_scores" selected="true">train_scores</option>
257 <option value="test_scores">test_scores</option> 252 <option value="test_scores">test_scores</option>
318 </test> 313 </test>
319 <test> 314 <test>
320 <param name="selected_function" value="validation_curve"/> 315 <param name="selected_function" value="validation_curve"/>
321 <param name="selected_module" value="svm"/> 316 <param name="selected_module" value="svm"/>
322 <param name="selected_estimator" value="SVC"/> 317 <param name="selected_estimator" value="SVC"/>
323 <param name="text_params" value="'kernel': 'linear'"/> 318 <param name="text_params" value="kernel='linear'"/>
324 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> 319 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
325 <param name="header1" value="true" /> 320 <param name="header1" value="true" />
326 <param name="selected_column_selector_option" value="all_columns"/> 321 <param name="selected_column_selector_option" value="all_columns"/>
327 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> 322 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
328 <param name="header2" value="true" /> 323 <param name="header2" value="true" />