Mercurial > repos > bgruening > sklearn_clf_metrics

comparison clf_metrics.xml @ 35:388f6ec0f3b3 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 19:05:25 +0000
parents c89a3bfb3b1d
children a7067bbf1e58
comparison
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34:adc6137e7c73 35:388f6ec0f3b3
1 <tool id="sklearn_clf_metrics" name="Calculate metrics" version="@VERSION@"> 1 <tool id="sklearn_clf_metrics" name="Calculate metrics" version="@VERSION@" profile="20.05">
2 <description>for classification performance</description> 2 <description>for classification performance</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 "$clf_metrics_script" '$inputs' 11 python "$clf_metrics_script" '$inputs'
12 ]]> 12 ]]>
92 <option value="log_loss">Log loss (aka logistic loss or cross-entropy loss)</option> 92 <option value="log_loss">Log loss (aka logistic loss or cross-entropy loss)</option>
93 <option value="average_precision_score">Average precision (AP) from prediction scores</option> 93 <option value="average_precision_score">Average precision (AP) from prediction scores</option>
94 <option value="roc_auc_score">Area Under the Curve (AUC) from prediction scores</option> 94 <option value="roc_auc_score">Area Under the Curve (AUC) from prediction scores</option>
95 </param> 95 </param>
96 <when value="accuracy_score"> 96 <when value="accuracy_score">
97 <expand macro="clf_inputs"/> 97 <expand macro="clf_inputs" />
98 <section name="options" title="Advanced Options" expanded="False"> 98 <section name="options" title="Advanced Options" expanded="False">
99 <!--sample_weight--> 99 <!--sample_weight-->
100 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" 100 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the number of correctly classified samples. Otherwise, returns the fraction of correctly classified samples. " />
101 label="Normalize" help="If false, returns the number of correctly classified samples. Otherwise, returns the fraction of correctly classified samples. "/>
102 </section> 101 </section>
103 </when> 102 </when>
104 <when value="classification_report"> 103 <when value="classification_report">
105 <expand macro="clf_inputs"/> 104 <expand macro="clf_inputs" />
106 <section name="options" title="Advanced Options" expanded="False"> 105 <section name="options" title="Advanced Options" expanded="False">
107 <!--labels--> 106 <!--labels-->
108 <!--target_names--> 107 <!--target_names-->
109 <!--sample_weight--> 108 <!--sample_weight-->
110 <param argument="digits" type="integer" value="2" label="Number of digits for formatting output floating point values" help=""/> 109 <param argument="digits" type="integer" value="2" label="Number of digits for formatting output floating point values" help="" />
111 </section> 110 </section>
112 </when> 111 </when>
113 <when value="f1_score"> 112 <when value="f1_score">
114 <expand macro="clf_inputs"/> 113 <expand macro="clf_inputs" />
115 <section name="options" title="Advanced Options" expanded="False"> 114 <section name="options" title="Advanced Options" expanded="False">
116 <!--labels--> 115 <!--labels-->
117 <!--sample_weight--> 116 <!--sample_weight-->
118 <expand macro="pos_label" default_value="1"/> 117 <expand macro="pos_label" default_value="1" />
119 <expand macro="average"> 118 <expand macro="average">
120 <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option> 119 <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option>
121 </expand> 120 </expand>
122 </section> 121 </section>
123 </when> 122 </when>
124 <when value="fbeta_score"> 123 <when value="fbeta_score">
125 <expand macro="clf_inputs"/> 124 <expand macro="clf_inputs" />
126 <section name="options" title="Advanced Options" expanded="False"> 125 <section name="options" title="Advanced Options" expanded="False">
127 <expand macro="beta"/> 126 <expand macro="beta" />
128 <!--labels--> 127 <!--labels-->
129 <!--sample_weight--> 128 <!--sample_weight-->
130 <expand macro="pos_label" default_value="1"/> 129 <expand macro="pos_label" default_value="1" />
131 <expand macro="average"> 130 <expand macro="average">
132 <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option> 131 <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option>
133 </expand> 132 </expand>
134 </section> 133 </section>
135 </when> 134 </when>
136 <when value="hamming_loss"> 135 <when value="hamming_loss">
137 <expand macro="clf_inputs"/> 136 <expand macro="clf_inputs" />
138 <!--section name="options" title="Advanced Options" expanded="False"> 137 <!--section name="options" title="Advanced Options" expanded="False">
139 <!- -classes- -> 138 <!- -classes- ->
140 </section--> 139 </section-->
141 </when> 140 </when>
142 <when value="jaccard_similarity_score"> 141 <when value="jaccard_similarity_score">
143 <expand macro="clf_inputs"/> 142 <expand macro="clf_inputs" />
144 <section name="options" title="Advanced Options" expanded="False"> 143 <section name="options" title="Advanced Options" expanded="False">
145 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the sum of the Jaccard similarity coefficient over the sample set. Otherwise, returns the average of Jaccard similarity coefficient. "/> 144 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the sum of the Jaccard similarity coefficient over the sample set. Otherwise, returns the average of Jaccard similarity coefficient. " />
146 </section> 145 </section>
147 </when> 146 </when>
148 <when value="precision_recall_fscore_support"> 147 <when value="precision_recall_fscore_support">
149 <expand macro="clf_inputs"/> 148 <expand macro="clf_inputs" />
150 <section name="options" title="Advanced Options" expanded="False"> 149 <section name="options" title="Advanced Options" expanded="False">
151 <expand macro="beta"/> 150 <expand macro="beta" />
152 <!--labels--> 151 <!--labels-->
153 <!--sample_weight--> 152 <!--sample_weight-->
154 <!--warn_for--> 153 <!--warn_for-->
155 <expand macro="pos_label" default_value="1"/> 154 <expand macro="pos_label" default_value="1" />
156 <expand macro="average"> 155 <expand macro="average">
157 <option value="binary" selected="true">Only report results for the class specified by pos_label. Applicable only on binary classification. (binary)</option> 156 <option value="binary" selected="true">Only report results for the class specified by pos_label. Applicable only on binary classification. (binary)</option>
158 </expand> 157 </expand>
159 </section> 158 </section>
160 </when> 159 </when>
161 <when value="precision_score"> 160 <when value="precision_score">
162 <expand macro="clf_inputs"/> 161 <expand macro="clf_inputs" />
163 <section name="options" title="Advanced Options" expanded="False"> 162 <section name="options" title="Advanced Options" expanded="False">
164 <!--labels--> 163 <!--labels-->
165 <!--sample_weight--> 164 <!--sample_weight-->
166 <expand macro="pos_label" default_value="1"/> 165 <expand macro="pos_label" default_value="1" />
167 <expand macro="average"> 166 <expand macro="average">
168 <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option> 167 <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option>
169 </expand> 168 </expand>
170 </section> 169 </section>
171 </when> 170 </when>
172 <when value="recall_score"> 171 <when value="recall_score">
173 <expand macro="clf_inputs"/> 172 <expand macro="clf_inputs" />
174 <section name="options" title="Advanced Options" expanded="False"> 173 <section name="options" title="Advanced Options" expanded="False">
175 <!--labels--> 174 <!--labels-->
176 <!--sample_weight--> 175 <!--sample_weight-->
177 <expand macro="pos_label" default_value="1"/> 176 <expand macro="pos_label" default_value="1" />
178 <expand macro="average"> 177 <expand macro="average">
179 <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option> 178 <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option>
180 </expand> 179 </expand>
181 </section> 180 </section>
182 </when> 181 </when>
183 <when value="zero_one_loss"> 182 <when value="zero_one_loss">
184 <expand macro="clf_inputs"/> 183 <expand macro="clf_inputs" />
185 <section name="options" title="Advanced Options" expanded="False"> 184 <section name="options" title="Advanced Options" expanded="False">
186 <!--sample_weight--> 185 <!--sample_weight-->
187 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the number of misclassifications. Otherwise, returns the fraction of misclassifications. "/> 186 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the number of misclassifications. Otherwise, returns the fraction of misclassifications. " />
188 </section> 187 </section>
189 </when> 188 </when>
190 <when value="auc"> 189 <when value="auc">
191 <expand macro="clf_inputs"/> 190 <expand macro="clf_inputs" />
192 <section name="options" title="Advanced Options" expanded="False"> 191 <section name="options" title="Advanced Options" expanded="False">
193 <param argument="reorder" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Assume an ascending curve in the case of ties" help="If the curve is non-ascending, the result will be wrong. "/> 192 <param argument="reorder" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Assume an ascending curve in the case of ties" help="If the curve is non-ascending, the result will be wrong. " />
194 </section> 193 </section>
195 </when> 194 </when>
196 <when value="brier_score_loss"> 195 <when value="brier_score_loss">
197 <expand macro="clf_inputs"/> 196 <expand macro="clf_inputs" />
198 <section name="options" title="Advanced Options" expanded="False"> 197 <section name="options" title="Advanced Options" expanded="False">
199 <!--weights--> 198 <!--weights-->
200 <expand macro="pos_label"/> 199 <expand macro="pos_label" />
201 </section> 200 </section>
202 </when> 201 </when>
203 <when value="matthews_corrcoef"> 202 <when value="matthews_corrcoef">
204 <expand macro="clf_inputs"/> 203 <expand macro="clf_inputs" />
205 <!--section name="options" title="Advanced Options" expanded="False"> 204 <!--section name="options" title="Advanced Options" expanded="False">
206 </section--> 205 </section-->
207 </when> 206 </when>
208 <when value="confusion_matrix"> 207 <when value="confusion_matrix">
209 <expand macro="clf_inputs"/> 208 <expand macro="clf_inputs" />
210 <!--section name="options" title="Advanced Options" expanded="False"> 209 <!--section name="options" title="Advanced Options" expanded="False">
211 <!- -labels- -> 210 <!- -labels- ->
212 </section--> 211 </section-->
213 </when> 212 </when>
214 <when value="precision_recall_curve"> 213 <when value="precision_recall_curve">
215 <expand macro="clf_inputs"/> 214 <expand macro="clf_inputs" />
216 <section name="options" title="Advanced Options" expanded="False"> 215 <section name="options" title="Advanced Options" expanded="False">
217 <expand macro="pos_label"/> 216 <expand macro="pos_label" />
218 <!--sample_weight--> 217 <!--sample_weight-->
219 </section> 218 </section>
220 </when> 219 </when>
221 <when value="roc_curve"> 220 <when value="roc_curve">
222 <expand macro="clf_inputs"/> 221 <expand macro="clf_inputs" />
223 <section name="options" title="Advanced Options" expanded="False"> 222 <section name="options" title="Advanced Options" expanded="False">
224 <!--sample_weight--> 223 <!--sample_weight-->
225 <expand macro="pos_label"/> 224 <expand macro="pos_label" />
226 <param argument="drop_intermediate" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label=" Drop suboptimal thresholds" help="This is useful in order to create lighter ROC curves. "/> 225 <param argument="drop_intermediate" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label=" Drop suboptimal thresholds" help="This is useful in order to create lighter ROC curves. " />
227 </section> 226 </section>
228 </when> 227 </when>
229 <when value="hinge_loss"> 228 <when value="hinge_loss">
230 <expand macro="clf_inputs" multiple="true"/> 229 <expand macro="clf_inputs" multiple="true" />
231 <!--section name="options" title="Advanced Options" expanded="False"> 230 <!--section name="options" title="Advanced Options" expanded="False">
232 <!- -labels- -> 231 <!- -labels- ->
233 <!- -sample_weight- -> 232 <!- -sample_weight- ->
234 </section--> 233 </section-->
235 </when> 234 </when>
236 <when value="log_loss"> 235 <when value="log_loss">
237 <expand macro="clf_inputs" multiple="true"/> 236 <expand macro="clf_inputs" multiple="true" />
238 <section name="options" title="Advanced Options" expanded="False"> 237 <section name="options" title="Advanced Options" expanded="False">
239 <!--sample_weight--> 238 <!--sample_weight-->
240 <param argument="eps" type="float" value="1e-15" label="Clipping factor" 239 <param argument="eps" type="float" value="1e-15" label="Clipping factor" help="Log loss is undefined for p=0 or p=1, so probabilities are clipped to max(eps, min(1 - eps, p)). " />
241 help="Log loss is undefined for p=0 or p=1, so probabilities are clipped to max(eps, min(1 - eps, p)). "/> 240 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If true, returns the mean loss per sample. Otherwise, returns the sum of the per-sample losses. " />
242 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
243 label="Normalize" help="If true, returns the mean loss per sample. Otherwise, returns the sum of the per-sample losses. "/>
244 </section> 241 </section>
245 </when> 242 </when>
246 <when value="average_precision_score"> 243 <when value="average_precision_score">
247 <expand macro="clf_inputs" multiple1="true" multiple="true"/> 244 <expand macro="clf_inputs" multiple1="true" multiple="true" />
248 <!-- section name="options" title="Advanced Options" expanded="False"> 245 <!-- section name="options" title="Advanced Options" expanded="False">
249 <!- -average='macro', sample_weight=None- -> 246 <!- -average='macro', sample_weight=None- ->
250 </section--> 247 </section-->
251 </when> 248 </when>
252 <when value="roc_auc_score"> 249 <when value="roc_auc_score">
253 <expand macro="clf_inputs" multiple1="true" multiple="true"/> 250 <expand macro="clf_inputs" multiple1="true" multiple="true" />
254 <section name="options" title="Advanced Options" expanded="False"> 251 <section name="options" title="Advanced Options" expanded="False">
255 <expand macro="average"> 252 <expand macro="average">
256 <option value="macro" selected="true">Calculate metrics for each label, and find their unweighted mean. (macro)</option> 253 <option value="macro" selected="true">Calculate metrics for each label, and find their unweighted mean. (macro)</option>
257 </expand> 254 </expand>
258 </section> 255 </section>
259 </when> 256 </when>
260 </conditional> 257 </conditional>
261 </inputs> 258 </inputs>
262 <outputs> 259 <outputs>
263 <data format="txt" name="outfile"/> 260 <data format="txt" name="outfile" />
264 </outputs> 261 </outputs>
265 <tests> 262 <tests>
266 <test> 263 <test>
267 <param name="selected_metric" value="accuracy_score"/> 264 <param name="selected_metric" value="accuracy_score" />
268 <param name="infile1" value="y.tabular" ftype="tabular"/> 265 <param name="infile1" value="y.tabular" ftype="tabular" />
269 <param name="col1" value="1"/> 266 <param name="col1" value="1" />
270 <param name="infile2" value="y.tabular" ftype="tabular"/> 267 <param name="infile2" value="y.tabular" ftype="tabular" />
271 <param name="col2" value="2"/> 268 <param name="col2" value="2" />
272 <output name="outfile" file="accuracy_score.txt"/> 269 <output name="outfile" file="accuracy_score.txt" />
273 </test> 270 </test>
274 <test> 271 <test>
275 <param name="selected_metric" value="classification_report"/> 272 <param name="selected_metric" value="classification_report" />
276 <param name="infile1" value="y.tabular" ftype="tabular"/> 273 <param name="infile1" value="y.tabular" ftype="tabular" />
277 <param name="col1" value="1"/> 274 <param name="col1" value="1" />
278 <param name="infile2" value="y.tabular" ftype="tabular"/> 275 <param name="infile2" value="y.tabular" ftype="tabular" />
279 <param name="col2" value="2"/> 276 <param name="col2" value="2" />
280 <output name="outfile" file="classification_report.txt"/> 277 <output name="outfile" file="classification_report.txt" />
281 </test> 278 </test>
282 <test> 279 <test>
283 <param name="selected_metric" value="f1_score"/> 280 <param name="selected_metric" value="f1_score" />
284 <param name="infile1" value="y.tabular" ftype="tabular"/> 281 <param name="infile1" value="y.tabular" ftype="tabular" />
285 <param name="col1" value="1"/> 282 <param name="col1" value="1" />
286 <param name="infile2" value="y.tabular" ftype="tabular"/> 283 <param name="infile2" value="y.tabular" ftype="tabular" />
287 <param name="col2" value="2"/> 284 <param name="col2" value="2" />
288 <param name="average" value="micro"/> 285 <param name="average" value="micro" />
289 <output name="outfile" file="f1_score.txt"/> 286 <output name="outfile" file="f1_score.txt" />
290 </test> 287 </test>
291 <test> 288 <test>
292 <param name="selected_metric" value="fbeta_score"/> 289 <param name="selected_metric" value="fbeta_score" />
293 <param name="infile1" value="y.tabular" ftype="tabular"/> 290 <param name="infile1" value="y.tabular" ftype="tabular" />
294 <param name="col1" value="1"/> 291 <param name="col1" value="1" />
295 <param name="infile2" value="y.tabular" ftype="tabular"/> 292 <param name="infile2" value="y.tabular" ftype="tabular" />
296 <param name="col2" value="2"/> 293 <param name="col2" value="2" />
297 <param name="average" value="micro"/> 294 <param name="average" value="micro" />
298 <output name="outfile" file="fbeta_score.txt"/> 295 <output name="outfile" file="fbeta_score.txt" />
299 </test> 296 </test>
300 <test> 297 <test>
301 <param name="selected_metric" value="hamming_loss"/> 298 <param name="selected_metric" value="hamming_loss" />
302 <param name="infile1" value="y.tabular" ftype="tabular"/> 299 <param name="infile1" value="y.tabular" ftype="tabular" />
303 <param name="col1" value="1"/> 300 <param name="col1" value="1" />
304 <param name="infile2" value="y.tabular" ftype="tabular"/> 301 <param name="infile2" value="y.tabular" ftype="tabular" />
305 <param name="col2" value="2"/> 302 <param name="col2" value="2" />
306 <output name="outfile" file="hamming_loss.txt"/> 303 <output name="outfile" file="hamming_loss.txt" />
307 </test> 304 </test>
308 <test> 305 <test>
309 <param name="selected_metric" value="jaccard_similarity_score"/> 306 <param name="selected_metric" value="jaccard_similarity_score" />
310 <param name="infile1" value="y.tabular" ftype="tabular"/> 307 <param name="infile1" value="y.tabular" ftype="tabular" />
311 <param name="col1" value="1"/> 308 <param name="col1" value="1" />
312 <param name="infile2" value="y.tabular" ftype="tabular"/> 309 <param name="infile2" value="y.tabular" ftype="tabular" />
313 <param name="col2" value="2"/> 310 <param name="col2" value="2" />
314 <output name="outfile" file="jaccard_similarity_score.txt"/> 311 <output name="outfile" file="jaccard_similarity_score.txt" />
315 </test> 312 </test>
316 <test> 313 <test>
317 <param name="selected_metric" value="precision_recall_fscore_support"/> 314 <param name="selected_metric" value="precision_recall_fscore_support" />
318 <param name="infile1" value="y.tabular" ftype="tabular"/> 315 <param name="infile1" value="y.tabular" ftype="tabular" />
319 <param name="col1" value="1"/> 316 <param name="col1" value="1" />
320 <param name="infile2" value="y.tabular" ftype="tabular"/> 317 <param name="infile2" value="y.tabular" ftype="tabular" />
321 <param name="col2" value="2"/> 318 <param name="col2" value="2" />
322 <param name="average" value="micro"/> 319 <param name="average" value="micro" />
323 <output name="outfile" file="precision_recall_fscore_support.txt"/> 320 <output name="outfile" file="precision_recall_fscore_support.txt" />
324 </test> 321 </test>
325 <test> 322 <test>
326 <param name="selected_metric" value="precision_score"/> 323 <param name="selected_metric" value="precision_score" />
327 <param name="infile1" value="y.tabular" ftype="tabular"/> 324 <param name="infile1" value="y.tabular" ftype="tabular" />
328 <param name="col1" value="1"/> 325 <param name="col1" value="1" />
329 <param name="infile2" value="y.tabular" ftype="tabular"/> 326 <param name="infile2" value="y.tabular" ftype="tabular" />
330 <param name="col2" value="2"/> 327 <param name="col2" value="2" />
331 <param name="average" value="micro"/> 328 <param name="average" value="micro" />
332 <output name="outfile" file="precision_score.txt"/> 329 <output name="outfile" file="precision_score.txt" />
333 </test> 330 </test>
334 <test> 331 <test>
335 <param name="selected_metric" value="recall_score"/> 332 <param name="selected_metric" value="recall_score" />
336 <param name="infile1" value="y.tabular" ftype="tabular"/> 333 <param name="infile1" value="y.tabular" ftype="tabular" />
337 <param name="col1" value="1"/> 334 <param name="col1" value="1" />
338 <param name="infile2" value="y.tabular" ftype="tabular"/> 335 <param name="infile2" value="y.tabular" ftype="tabular" />
339 <param name="col2" value="2"/> 336 <param name="col2" value="2" />
340 <param name="average" value="micro"/> 337 <param name="average" value="micro" />
341 <output name="outfile" file="recall_score.txt"/> 338 <output name="outfile" file="recall_score.txt" />
342 </test> 339 </test>
343 <test> 340 <test>
344 <param name="selected_metric" value="zero_one_loss"/> 341 <param name="selected_metric" value="zero_one_loss" />
345 <param name="infile1" value="y.tabular" ftype="tabular"/> 342 <param name="infile1" value="y.tabular" ftype="tabular" />
346 <param name="col1" value="1"/> 343 <param name="col1" value="1" />
347 <param name="infile2" value="y.tabular" ftype="tabular"/> 344 <param name="infile2" value="y.tabular" ftype="tabular" />
348 <param name="col2" value="2"/> 345 <param name="col2" value="2" />
349 <output name="outfile" file="zero_one_loss.txt"/> 346 <output name="outfile" file="zero_one_loss.txt" />
350 </test> 347 </test>
351 <test> 348 <test>
352 <param name="selected_metric" value="auc"/> 349 <param name="selected_metric" value="auc" />
353 <param name="infile1" value="y.tabular" ftype="tabular"/> 350 <param name="infile1" value="y.tabular" ftype="tabular" />
354 <param name="col1" value="1"/> 351 <param name="col1" value="1" />
355 <param name="infile2" value="y.tabular" ftype="tabular"/> 352 <param name="infile2" value="y.tabular" ftype="tabular" />
356 <param name="col2" value="2"/> 353 <param name="col2" value="2" />
357 <param name="reorder" value="true"/> 354 <param name="reorder" value="true" />
358 <output name="outfile" file="auc.txt"/> 355 <output name="outfile" file="auc.txt" />
359 </test> 356 </test>
360 <test> 357 <test>
361 <param name="selected_metric" value="brier_score_loss"/> 358 <param name="selected_metric" value="brier_score_loss" />
362 <param name="infile1" value="y.tabular" ftype="tabular"/> 359 <param name="infile1" value="y.tabular" ftype="tabular" />
363 <param name="col1" value="6"/> 360 <param name="col1" value="6" />
364 <param name="infile2" value="y.tabular" ftype="tabular"/> 361 <param name="infile2" value="y.tabular" ftype="tabular" />
365 <param name="col2" value="4"/> 362 <param name="col2" value="4" />
366 <output name="outfile" file="brier_score_loss.txt"/> 363 <output name="outfile" file="brier_score_loss.txt" />
367 </test> 364 </test>
368 <test> 365 <test>
369 <param name="selected_metric" value="matthews_corrcoef"/> 366 <param name="selected_metric" value="matthews_corrcoef" />
370 <param name="infile1" value="y.tabular"/> 367 <param name="infile1" value="y.tabular" />
371 <param name="col1" value="6"/> 368 <param name="col1" value="6" />
372 <param name="infile2" value="y.tabular"/> 369 <param name="infile2" value="y.tabular" />
373 <param name="col2" value="7"/> 370 <param name="col2" value="7" />
374 <output name="outfile" file="matthews_corrcoef.txt"/> 371 <output name="outfile" file="matthews_corrcoef.txt" />
375 </test> 372 </test>
376 <test> 373 <test>
377 <param name="selected_metric" value="confusion_matrix"/> 374 <param name="selected_metric" value="confusion_matrix" />
378 <param name="infile1" value="y.tabular" ftype="tabular"/> 375 <param name="infile1" value="y.tabular" ftype="tabular" />
379 <param name="col1" value="1"/> 376 <param name="col1" value="1" />
380 <param name="infile2" value="y.tabular" ftype="tabular"/> 377 <param name="infile2" value="y.tabular" ftype="tabular" />
381 <param name="col2" value="2"/> 378 <param name="col2" value="2" />
382 <output name="outfile" file="confusion_matrix.txt"/> 379 <output name="outfile" file="confusion_matrix.txt" />
383 </test> 380 </test>
384 <test> 381 <test>
385 <param name="selected_metric" value="precision_recall_curve"/> 382 <param name="selected_metric" value="precision_recall_curve" />
386 <param name="infile1" value="y.tabular" ftype="tabular"/> 383 <param name="infile1" value="y.tabular" ftype="tabular" />
387 <param name="col1" value="6"/> 384 <param name="col1" value="6" />
388 <param name="infile2" value="y.tabular" ftype="tabular"/> 385 <param name="infile2" value="y.tabular" ftype="tabular" />
389 <param name="col2" value="7"/> 386 <param name="col2" value="7" />
390 <output name="outfile" file="precision_recall_curve.txt"/> 387 <output name="outfile" file="precision_recall_curve.txt" />
391 </test> 388 </test>
392 <test> 389 <test>
393 <param name="selected_metric" value="roc_curve"/> 390 <param name="selected_metric" value="roc_curve" />
394 <param name="infile1" value="y.tabular" ftype="tabular"/> 391 <param name="infile1" value="y.tabular" ftype="tabular" />
395 <param name="col1" value="6"/> 392 <param name="col1" value="6" />
396 <param name="infile2" value="y.tabular" ftype="tabular"/> 393 <param name="infile2" value="y.tabular" ftype="tabular" />
397 <param name="col2" value="7"/> 394 <param name="col2" value="7" />
398 <output name="outfile" file="roc_curve.txt"/> 395 <output name="outfile" file="roc_curve.txt" />
399 </test> 396 </test>
400 <test> 397 <test>
401 <param name="selected_metric" value="hinge_loss"/> 398 <param name="selected_metric" value="hinge_loss" />
402 <param name="infile1" value="y.tabular" ftype="tabular"/> 399 <param name="infile1" value="y.tabular" ftype="tabular" />
403 <param name="col1" value="1"/> 400 <param name="col1" value="1" />
404 <param name="infile2" value="y.tabular" ftype="tabular"/> 401 <param name="infile2" value="y.tabular" ftype="tabular" />
405 <param name="col2" value="8,9,10"/> 402 <param name="col2" value="8,9,10" />
406 <output name="outfile" file="hinge_loss.txt"/> 403 <output name="outfile" file="hinge_loss.txt" />
407 </test> 404 </test>
408 <test> 405 <test>
409 <param name="selected_metric" value="log_loss"/> 406 <param name="selected_metric" value="log_loss" />
410 <param name="infile1" value="y.tabular" ftype="tabular"/> 407 <param name="infile1" value="y.tabular" ftype="tabular" />
411 <param name="col1" value="2"/> 408 <param name="col1" value="2" />
412 <param name="infile2" value="y.tabular" ftype="tabular"/> 409 <param name="infile2" value="y.tabular" ftype="tabular" />
413 <param name="col2" value="3,4,5"/> 410 <param name="col2" value="3,4,5" />
414 <output name="outfile" file="log_loss.txt"/> 411 <output name="outfile" file="log_loss.txt" />
415 </test> 412 </test>
416 <test> 413 <test>
417 <param name="selected_metric" value="average_precision_score"/> 414 <param name="selected_metric" value="average_precision_score" />
418 <param name="infile1" value="y.tabular" ftype="tabular"/> 415 <param name="infile1" value="y.tabular" ftype="tabular" />
419 <param name="col1" value="6"/> 416 <param name="col1" value="6" />
420 <param name="infile2" value="y.tabular" ftype="tabular"/> 417 <param name="infile2" value="y.tabular" ftype="tabular" />
421 <param name="col2" value="7"/> 418 <param name="col2" value="7" />
422 <output name="outfile" file="average_precision_score.txt"/> 419 <output name="outfile" file="average_precision_score.txt" />
423 </test> 420 </test>
424 <test> 421 <test>
425 <param name="selected_metric" value="roc_auc_score"/> 422 <param name="selected_metric" value="roc_auc_score" />
426 <param name="infile1" value="y.tabular" ftype="tabular"/> 423 <param name="infile1" value="y.tabular" ftype="tabular" />
427 <param name="col1" value="6"/> 424 <param name="col1" value="6" />
428 <param name="infile2" value="y.tabular" ftype="tabular"/> 425 <param name="infile2" value="y.tabular" ftype="tabular" />
429 <param name="col2" value="7"/> 426 <param name="col2" value="7" />
430 <output name="outfile" file="roc_auc_score.txt"/> 427 <output name="outfile" file="roc_auc_score.txt" />
431 </test> 428 </test>
432 </tests> 429 </tests>
433 <help> 430 <help>
434 <![CDATA[ 431 <![CDATA[
435 **What it does** 432 **What it does**
438 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_. 435 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
439 436
440 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics 437 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
441 ]]> 438 ]]>
442 </help> 439 </help>
443 <expand macro="sklearn_citation"/> 440 <expand macro="sklearn_citation" />
444 </tool> 441 </tool>