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comparison feature_selection.xml @ 29:93f3b307485f draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
author bgruening
date Tue, 13 Apr 2021 18:21:34 +0000
parents c2cd3219543a
children 61edd9e5c17f
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28:6d21b03e00a1 29:93f3b307485f
1 <tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@"> 1 <tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@" profile="20.05">
2 <description>module, including univariate filter selection methods and recursive feature elimination algorithm</description> 2 <description>module, including univariate filter selection methods and recursive feature elimination algorithm</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 <!--TODO: Add imblearn package support--> 7 <!--TODO: Add imblearn package support-->
8 <expand macro="macro_stdio"/> 8 <expand macro="macro_stdio" />
9 <version_command>echo "@VERSION@"</version_command> 9 <version_command>echo "@VERSION@"</version_command>
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 python "$feature_selection_script" '$inputs' 12 python "$feature_selection_script" '$inputs'
13 ]]> 13 ]]>
148 148
149 ]]> 149 ]]>
150 </configfile> 150 </configfile>
151 </configfiles> 151 </configfiles>
152 <inputs> 152 <inputs>
153 <expand macro="feature_selection_fs"/> 153 <expand macro="feature_selection_fs" />
154 <param name="save" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Save the fitted selector?"/> 154 <param name="save" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Save the fitted selector?" />
155 <expand macro="sl_mixed_input_plus_sequence"/> 155 <expand macro="sl_mixed_input_plus_sequence" />
156 </inputs> 156 </inputs>
157 <outputs> 157 <outputs>
158 <data format="tabular" name="outfile" /> 158 <data format="tabular" name="outfile" />
159 <data format="zip" name="outfile_selector" label="${fs_algorithm_selector.selected_algorithm}"> 159 <data format="zip" name="outfile_selector" label="${fs_algorithm_selector.selected_algorithm}">
160 <filter>save</filter> 160 <filter>save</filter>
161 </data> 161 </data>
162 </outputs> 162 </outputs>
163 <tests> 163 <tests>
164 <test> 164 <test>
165 <param name="selected_algorithm" value="SelectFromModel"/> 165 <param name="selected_algorithm" value="SelectFromModel" />
166 <param name="input_mode" value="new"/> 166 <param name="input_mode" value="new" />
167 <param name="selected_module" value="ensemble"/> 167 <param name="selected_module" value="ensemble" />
168 <param name="selected_estimator" value="RandomForestRegressor"/> 168 <param name="selected_estimator" value="RandomForestRegressor" />
169 <param name="text_params" value="n_estimators=10, random_state=10"/> 169 <param name="text_params" value="n_estimators=10, random_state=10" />
170 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> 170 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
171 <param name="header1" value="false"/> 171 <param name="header1" value="false" />
172 <param name="col1" value="1,2,3,4,5"/> 172 <param name="col1" value="1,2,3,4,5" />
173 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> 173 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
174 <param name="col2" value="6"/> 174 <param name="col2" value="6" />
175 <param name="header2" value="false"/> 175 <param name="header2" value="false" />
176 <output name="outfile" file="feature_selection_result01"/> 176 <output name="outfile" file="feature_selection_result01" />
177 </test> 177 </test>
178 <test> 178 <test>
179 <param name="selected_algorithm" value="GenericUnivariateSelect"/> 179 <param name="selected_algorithm" value="GenericUnivariateSelect" />
180 <param name="param" value="20"/> 180 <param name="param" value="20" />
181 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> 181 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
182 <param name="header1" value="True"/> 182 <param name="header1" value="True" />
183 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> 183 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
184 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> 184 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
185 <param name="col2" value="1"/> 185 <param name="col2" value="1" />
186 <param name="header2" value="True"/> 186 <param name="header2" value="True" />
187 <output name="outfile" file="feature_selection_result02"/> 187 <output name="outfile" file="feature_selection_result02" />
188 </test> 188 </test>
189 <test> 189 <test>
190 <param name="selected_algorithm" value="SelectPercentile"/> 190 <param name="selected_algorithm" value="SelectPercentile" />
191 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> 191 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
192 <param name="header1" value="True"/> 192 <param name="header1" value="True" />
193 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> 193 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
194 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> 194 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
195 <param name="col2" value="1"/> 195 <param name="col2" value="1" />
196 <param name="header2" value="True"/> 196 <param name="header2" value="True" />
197 <output name="outfile" file="feature_selection_result03"/> 197 <output name="outfile" file="feature_selection_result03" />
198 </test> 198 </test>
199 <test> 199 <test>
200 <param name="selected_algorithm" value="SelectKBest"/> 200 <param name="selected_algorithm" value="SelectKBest" />
201 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> 201 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
202 <param name="header1" value="True"/> 202 <param name="header1" value="True" />
203 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> 203 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
204 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> 204 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
205 <param name="col2" value="1"/> 205 <param name="col2" value="1" />
206 <param name="header2" value="True"/> 206 <param name="header2" value="True" />
207 <output name="outfile" file="feature_selection_result04"/> 207 <output name="outfile" file="feature_selection_result04" />
208 </test> 208 </test>
209 <test> 209 <test>
210 <param name="selected_algorithm" value="SelectFpr"/> 210 <param name="selected_algorithm" value="SelectFpr" />
211 <param name="alpha" value="0.05"/> 211 <param name="alpha" value="0.05" />
212 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> 212 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
213 <param name="header1" value="True"/> 213 <param name="header1" value="True" />
214 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> 214 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
215 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> 215 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
216 <param name="col2" value="1"/> 216 <param name="col2" value="1" />
217 <param name="header2" value="True"/> 217 <param name="header2" value="True" />
218 <output name="outfile" file="feature_selection_result05"/> 218 <output name="outfile" file="feature_selection_result05" />
219 </test> 219 </test>
220 <test> 220 <test>
221 <param name="selected_algorithm" value="SelectFdr"/> 221 <param name="selected_algorithm" value="SelectFdr" />
222 <param name="alpha" value="0.05"/> 222 <param name="alpha" value="0.05" />
223 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> 223 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
224 <param name="header1" value="True"/> 224 <param name="header1" value="True" />
225 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> 225 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
226 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> 226 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
227 <param name="col2" value="1"/> 227 <param name="col2" value="1" />
228 <param name="header2" value="True"/> 228 <param name="header2" value="True" />
229 <output name="outfile" file="feature_selection_result06"/> 229 <output name="outfile" file="feature_selection_result06" />
230 </test> 230 </test>
231 <test> 231 <test>
232 <param name="selected_algorithm" value="SelectFwe"/> 232 <param name="selected_algorithm" value="SelectFwe" />
233 <param name="alpha" value="0.05"/> 233 <param name="alpha" value="0.05" />
234 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> 234 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
235 <param name="header1" value="True"/> 235 <param name="header1" value="True" />
236 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> 236 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
237 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> 237 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
238 <param name="col2" value="1"/> 238 <param name="col2" value="1" />
239 <param name="header2" value="True"/> 239 <param name="header2" value="True" />
240 <output name="outfile" file="feature_selection_result07"/> 240 <output name="outfile" file="feature_selection_result07" />
241 </test> 241 </test>
242 <test> 242 <test>
243 <param name="selected_algorithm" value="RFE"/> 243 <param name="selected_algorithm" value="RFE" />
244 <param name="input_mode" value="new"/> 244 <param name="input_mode" value="new" />
245 <param name="selected_module" value="ensemble"/> 245 <param name="selected_module" value="ensemble" />
246 <param name="selected_estimator" value="RandomForestRegressor"/> 246 <param name="selected_estimator" value="RandomForestRegressor" />
247 <param name="text_params" value="n_estimators=10, random_state=10"/> 247 <param name="text_params" value="n_estimators=10, random_state=10" />
248 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> 248 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
249 <param name="header1" value="false"/> 249 <param name="header1" value="false" />
250 <param name="col1" value="1,2,3,4,5"/> 250 <param name="col1" value="1,2,3,4,5" />
251 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> 251 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
252 <param name="col2" value="6"/> 252 <param name="col2" value="6" />
253 <param name="header2" value="false"/> 253 <param name="header2" value="false" />
254 <output name="outfile" file="feature_selection_result08"/> 254 <output name="outfile" file="feature_selection_result08" />
255 </test> 255 </test>
256 <test> 256 <test>
257 <param name="selected_algorithm" value="RFECV"/> 257 <param name="selected_algorithm" value="RFECV" />
258 <param name="input_mode" value="new"/> 258 <param name="input_mode" value="new" />
259 <param name="selected_module" value="ensemble"/> 259 <param name="selected_module" value="ensemble" />
260 <param name="selected_estimator" value="RandomForestRegressor"/> 260 <param name="selected_estimator" value="RandomForestRegressor" />
261 <param name="text_params" value="n_estimators=10, random_state=10"/> 261 <param name="text_params" value="n_estimators=10, random_state=10" />
262 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> 262 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
263 <param name="header1" value="false"/> 263 <param name="header1" value="false" />
264 <param name="col1" value="1,2,3,4,5"/> 264 <param name="col1" value="1,2,3,4,5" />
265 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> 265 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
266 <param name="col2" value="6"/> 266 <param name="col2" value="6" />
267 <param name="header2" value="false"/> 267 <param name="header2" value="false" />
268 <output name="outfile" file="feature_selection_result09"/> 268 <output name="outfile" file="feature_selection_result09" />
269 </test> 269 </test>
270 <test> 270 <test>
271 <param name="selected_algorithm" value="VarianceThreshold"/> 271 <param name="selected_algorithm" value="VarianceThreshold" />
272 <param name="threshold" value="0.1"/> 272 <param name="threshold" value="0.1" />
273 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> 273 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
274 <param name="header1" value="True"/> 274 <param name="header1" value="True" />
275 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> 275 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
276 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> 276 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
277 <param name="col2" value="1"/> 277 <param name="col2" value="1" />
278 <param name="header2" value="True"/> 278 <param name="header2" value="True" />
279 <output name="outfile" file="feature_selection_result10"/> 279 <output name="outfile" file="feature_selection_result10" />
280 </test> 280 </test>
281 <test> 281 <test>
282 <param name="selected_algorithm" value="SelectKBest"/> 282 <param name="selected_algorithm" value="SelectKBest" />
283 <param name="k" value="3"/> 283 <param name="k" value="3" />
284 <param name="infile1" value="test3.tabular" ftype="tabular"/> 284 <param name="infile1" value="test3.tabular" ftype="tabular" />
285 <param name="header1" value="True"/> 285 <param name="header1" value="True" />
286 <param name="selected_column_selector_option" value="all_but_by_header_name"/> 286 <param name="selected_column_selector_option" value="all_but_by_header_name" />
287 <param name="col1" value="target"/> 287 <param name="col1" value="target" />
288 <param name="infile2" value="test3.tabular" ftype="tabular"/> 288 <param name="infile2" value="test3.tabular" ftype="tabular" />
289 <param name="header2" value="True"/> 289 <param name="header2" value="True" />
290 <param name="selected_column_selector_option2" value="by_header_name"/> 290 <param name="selected_column_selector_option2" value="by_header_name" />
291 <param name="col2" value="target"/> 291 <param name="col2" value="target" />
292 <output name="outfile" file="feature_selection_result11"/> 292 <output name="outfile" file="feature_selection_result11" />
293 </test> 293 </test>
294 <test> 294 <test>
295 <param name="selected_algorithm" value="SelectFromModel"/> 295 <param name="selected_algorithm" value="SelectFromModel" />
296 <param name="input_mode" value="prefitted"/> 296 <param name="input_mode" value="prefitted" />
297 <param name="fitted_estimator" value="rfr_model01" ftype="zip"/> 297 <param name="fitted_estimator" value="rfr_model01" ftype="zip" />
298 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> 298 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
299 <param name="header1" value="false"/> 299 <param name="header1" value="false" />
300 <param name="col1" value="1,2,3,4,5"/> 300 <param name="col1" value="1,2,3,4,5" />
301 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> 301 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
302 <param name="col2" value="1"/> 302 <param name="col2" value="1" />
303 <param name="header2" value="false"/> 303 <param name="header2" value="false" />
304 <output name="outfile" file="feature_selection_result12"/> 304 <output name="outfile" file="feature_selection_result12" />
305 </test> 305 </test>
306 <test> 306 <test>
307 <param name="selected_algorithm" value="RFECV"/> 307 <param name="selected_algorithm" value="RFECV" />
308 <param name="input_mode" value="new"/> 308 <param name="input_mode" value="new" />
309 <param name="selected_module" value="ensemble"/> 309 <param name="selected_module" value="ensemble" />
310 <param name="selected_estimator" value="RandomForestRegressor"/> 310 <param name="selected_estimator" value="RandomForestRegressor" />
311 <param name="text_params" value="n_estimators=10, random_state=10"/> 311 <param name="text_params" value="n_estimators=10, random_state=10" />
312 <section name="groups_selector"> 312 <section name="groups_selector">
313 <param name="infile_groups" value="regression_y.tabular" ftype="tabular"/> 313 <param name="infile_groups" value="regression_y.tabular" ftype="tabular" />
314 <param name="header_g" value="true"/> 314 <param name="header_g" value="true" />
315 <param name="selected_column_selector_option_g" value="by_index_number"/> 315 <param name="selected_column_selector_option_g" value="by_index_number" />
316 <param name="col_g" value="1"/> 316 <param name="col_g" value="1" />
317 </section> 317 </section>
318 <param name="selected_cv" value="GroupShuffleSplit"/> 318 <param name="selected_cv" value="GroupShuffleSplit" />
319 <param name="random_state" value="0"/> 319 <param name="random_state" value="0" />
320 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> 320 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
321 <param name="header1" value="true"/> 321 <param name="header1" value="true" />
322 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> 322 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
323 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> 323 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
324 <param name="col2" value="1"/> 324 <param name="col2" value="1" />
325 <param name="header2" value="true"/> 325 <param name="header2" value="true" />
326 <output name="outfile" file="feature_selection_result13"/> 326 <output name="outfile" file="feature_selection_result13" />
327 </test> 327 </test>
328 </tests> 328 </tests>
329 <help> 329 <help>
330 <![CDATA[ 330 <![CDATA[
331 **What it does** 331 **What it does**
335 335
336 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics 336 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
337 ]]> 337 ]]>
338 </help> 338 </help>
339 <expand macro="sklearn_citation"> 339 <expand macro="sklearn_citation">
340 <expand macro="skrebate_citation"/> 340 <expand macro="skrebate_citation" />
341 <expand macro="xgboost_citation"/> 341 <expand macro="xgboost_citation" />
342 </expand> 342 </expand>
343 </tool> 343 </tool>