Mercurial > repos > bgruening > sklearn_generalized_linear
comparison generalized_linear.xml @ 35:602edec75e1d draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
author | bgruening |
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date | Tue, 13 Apr 2021 17:25:00 +0000 |
parents | a8c7b9fa426c |
children | fe181d613429 |
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34:40f4447733b2 | 35:602edec75e1d |
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1 <tool id="sklearn_generalized_linear" name="Generalized linear models" version="@VERSION@"> | 1 <tool id="sklearn_generalized_linear" name="Generalized linear models" version="@VERSION@" profile="20.05"> |
2 <description>for classification and regression</description> | 2 <description>for classification and regression</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><![CDATA[ | 9 <command><![CDATA[ |
10 python "$glm_script" '$inputs' | 10 python "$glm_script" '$inputs' |
11 ]]> | 11 ]]> |
12 </command> | 12 </command> |
13 <configfiles> | 13 <configfiles> |
14 <inputs name="inputs"/> | 14 <inputs name="inputs" /> |
15 <configfile name="glm_script"> | 15 <configfile name="glm_script"><![CDATA[ |
16 <![CDATA[ | |
17 import sys | 16 import sys |
18 import json | 17 import json |
19 import numpy as np | 18 import numpy as np |
20 import sklearn.linear_model | 19 import sklearn.linear_model |
21 import pandas | 20 import pandas |
67 <option value="LogisticRegression">Logistic Regression</option> | 66 <option value="LogisticRegression">Logistic Regression</option> |
68 <option value="LogisticRegressionCV">Logitic Regression with Cross Validation</option> | 67 <option value="LogisticRegressionCV">Logitic Regression with Cross Validation</option> |
69 <option value="Perceptron">Perceptron</option> | 68 <option value="Perceptron">Perceptron</option> |
70 </param> | 69 </param> |
71 <when value="SGDClassifier"> | 70 <when value="SGDClassifier"> |
72 <expand macro="sl_mixed_input"/> | 71 <expand macro="sl_mixed_input" /> |
73 <section name="options" title="Advanced Options" expanded="False"> | 72 <section name="options" title="Advanced Options" expanded="False"> |
74 <expand macro="loss"> | 73 <expand macro="loss"> |
75 <option value="hinge" selected="true">hinge</option> | 74 <option value="hinge" selected="true">hinge</option> |
76 <option value="log">log</option> | 75 <option value="log">log</option> |
77 <option value="modified_huber">modified huber</option> | 76 <option value="modified_huber">modified huber</option> |
78 <option value="squared_hinge">squared hinge</option> | 77 <option value="squared_hinge">squared hinge</option> |
79 <option value="perceptron">perceptron</option> | 78 <option value="perceptron">perceptron</option> |
80 </expand> | 79 </expand> |
81 <expand macro="penalty"/> | 80 <expand macro="penalty" /> |
82 <expand macro="alpha"/> | 81 <expand macro="alpha" /> |
83 <expand macro="l1_ratio"/> | 82 <expand macro="l1_ratio" /> |
84 <expand macro="fit_intercept"/> | 83 <expand macro="fit_intercept" /> |
85 <expand macro="n_iter_no_change" /> | 84 <expand macro="n_iter_no_change" /> |
86 <expand macro="shuffle"/> | 85 <expand macro="shuffle" /> |
87 <expand macro="epsilon"/> | 86 <expand macro="epsilon" /> |
88 <expand macro="learning_rate_s" selected1="true"/> | 87 <expand macro="learning_rate_s" selected1="true" /> |
89 <expand macro="eta0"/> | 88 <expand macro="eta0" /> |
90 <expand macro="power_t"/> | 89 <expand macro="power_t" /> |
91 <!--class_weight--> | 90 <!--class_weight--> |
92 <expand macro="warm_start" checked="false"/> | 91 <expand macro="warm_start" checked="false" /> |
93 <expand macro="random_state"/> | 92 <expand macro="random_state" /> |
94 <!--average--> | 93 <!--average--> |
95 </section> | 94 </section> |
96 </when> | 95 </when> |
97 <when value="SGDRegressor"> | 96 <when value="SGDRegressor"> |
98 <expand macro="sl_mixed_input"/> | 97 <expand macro="sl_mixed_input" /> |
99 <section name="options" title="Advanced Options" expanded="False"> | 98 <section name="options" title="Advanced Options" expanded="False"> |
100 <expand macro="loss" select="true"/> | 99 <expand macro="loss" select="true" /> |
101 <expand macro="penalty"/> | 100 <expand macro="penalty" /> |
102 <expand macro="alpha"/> | 101 <expand macro="alpha" /> |
103 <expand macro="l1_ratio"/> | 102 <expand macro="l1_ratio" /> |
104 <expand macro="fit_intercept"/> | 103 <expand macro="fit_intercept" /> |
105 <expand macro="n_iter_no_change" /> | 104 <expand macro="n_iter_no_change" /> |
106 <expand macro="shuffle"/> | 105 <expand macro="shuffle" /> |
107 <expand macro="epsilon"/> | 106 <expand macro="epsilon" /> |
108 <expand macro="learning_rate_s" selected2="true"/> | 107 <expand macro="learning_rate_s" selected2="true" /> |
109 <expand macro="eta0" default_value="0.01"/> | 108 <expand macro="eta0" default_value="0.01" /> |
110 <expand macro="power_t" default_value="0.25"/> | 109 <expand macro="power_t" default_value="0.25" /> |
111 <expand macro="warm_start" checked="false"/> | 110 <expand macro="warm_start" checked="false" /> |
112 <expand macro="random_state"/> | 111 <expand macro="random_state" /> |
113 <!--average--> | 112 <!--average--> |
114 </section> | 113 </section> |
115 </when> | 114 </when> |
116 <when value="LinearRegression"> | 115 <when value="LinearRegression"> |
117 <expand macro="sl_mixed_input"/> | 116 <expand macro="sl_mixed_input" /> |
118 <section name="options" title="Advanced Options" expanded="False"> | 117 <section name="options" title="Advanced Options" expanded="False"> |
119 <expand macro="fit_intercept"/> | 118 <expand macro="fit_intercept" /> |
120 <expand macro="normalize"/> | 119 <expand macro="normalize" /> |
121 <expand macro="copy_X"/> | 120 <expand macro="copy_X" /> |
122 </section> | 121 </section> |
123 </when> | 122 </when> |
124 <when value="RidgeClassifier"> | 123 <when value="RidgeClassifier"> |
125 <expand macro="sl_mixed_input"/> | 124 <expand macro="sl_mixed_input" /> |
126 <section name="options" title="Advanced Options" expanded="False"> | 125 <section name="options" title="Advanced Options" expanded="False"> |
127 <expand macro="ridge_params"/> | 126 <expand macro="ridge_params" /> |
128 </section> | 127 </section> |
129 </when> | 128 </when> |
130 <when value="Ridge"> | 129 <when value="Ridge"> |
131 <expand macro="sl_mixed_input"/> | 130 <expand macro="sl_mixed_input" /> |
132 <section name="options" title="Advanced Options" expanded="False"> | 131 <section name="options" title="Advanced Options" expanded="False"> |
133 <expand macro="ridge_params"/> | 132 <expand macro="ridge_params" /> |
134 </section> | 133 </section> |
135 </when> | 134 </when> |
136 <when value="LogisticRegression"> | 135 <when value="LogisticRegression"> |
137 <expand macro="sl_mixed_input"/> | 136 <expand macro="sl_mixed_input" /> |
138 <section name="options" title="Advanced Options" expanded="False"> | 137 <section name="options" title="Advanced Options" expanded="False"> |
139 <expand macro="penalty"/> | 138 <expand macro="penalty" /> |
140 <param argument="dual" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Use dual formulation" help=" "/> | 139 <param argument="dual" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Use dual formulation" help=" " /> |
141 <expand macro="tol" default_value="0.0001" help_text="Tolerance for stopping criteria. "/> | 140 <expand macro="tol" default_value="0.0001" help_text="Tolerance for stopping criteria. " /> |
142 <expand macro="C"/> | 141 <expand macro="C" /> |
143 <expand macro="fit_intercept"/> | 142 <expand macro="fit_intercept" /> |
144 <expand macro="max_iter" default_value="100"/> | 143 <expand macro="max_iter" default_value="100" /> |
145 <expand macro="warm_start" checked="false"/> | 144 <expand macro="warm_start" checked="false" /> |
146 <param argument="solver" type="select" label="Optimization algorithm" help=" "> | 145 <param argument="solver" type="select" label="Optimization algorithm" help=" "> |
147 <option value="liblinear" selected="true">liblinear</option> | 146 <option value="liblinear" selected="true">liblinear</option> |
148 <option value="sag">sag</option> | 147 <option value="sag">sag</option> |
149 <option value="lbfgs">lbfgs</option> | 148 <option value="lbfgs">lbfgs</option> |
150 <option value="newton-cg">newton-cg</option> | 149 <option value="newton-cg">newton-cg</option> |
151 </param> | 150 </param> |
152 <param argument="intercept_scaling" type="float" value="1" label="Intercept scaling factor" help="Useful only if solver is liblinear. "/> | 151 <param argument="intercept_scaling" type="float" value="1" label="Intercept scaling factor" help="Useful only if solver is liblinear. " /> |
153 <param argument="multi_class" type="select" label="Multiclass option" help="Works only for lbfgs solver. "> | 152 <param argument="multi_class" type="select" label="Multiclass option" help="Works only for lbfgs solver. "> |
154 <option value="ovr" selected="true">ovr</option> | 153 <option value="ovr" selected="true">ovr</option> |
155 <option value="multinomial">multinomial</option> | 154 <option value="multinomial">multinomial</option> |
156 </param> | 155 </param> |
157 <!--class_weight--> | 156 <!--class_weight--> |
158 <expand macro="random_state"/> | 157 <expand macro="random_state" /> |
159 </section> | 158 </section> |
160 </when> | 159 </when> |
161 <when value="LogisticRegressionCV"> | 160 <when value="LogisticRegressionCV"> |
162 <expand macro="sl_mixed_input"/> | 161 <expand macro="sl_mixed_input" /> |
163 <section name="options" title="Advanced Options" expanded="False"> | 162 <section name="options" title="Advanced Options" expanded="False"> |
164 <param argument="Cs" type="integer" value="10" label="Inverse of regularization strength" help="A grid of Cs values are chosen in a logarithmic scale between 1e-4 and 1e4. Like in support vector machines, smaller values specify stronger regularization. "/> | 163 <param argument="Cs" type="integer" value="10" label="Inverse of regularization strength" help="A grid of Cs values are chosen in a logarithmic scale between 1e-4 and 1e4. Like in support vector machines, smaller values specify stronger regularization. " /> |
165 <param argument="dual" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Use dual formulation" help=" "/> | 164 <param argument="dual" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Use dual formulation" help=" " /> |
166 <param argument="cv" type="integer" optional="true" value="" label="Number of folds used in cross validation" help="If not set, the default cross-validation generator (Stratified K-Folds) is used. "/> | 165 <param argument="cv" type="integer" optional="true" value="" label="Number of folds used in cross validation" help="If not set, the default cross-validation generator (Stratified K-Folds) is used. " /> |
167 <expand macro="penalty"/> | 166 <expand macro="penalty" /> |
168 <expand macro="tol" default_value="0.0001" help_text="Tolerance for stopping criteria. "/> | 167 <expand macro="tol" default_value="0.0001" help_text="Tolerance for stopping criteria. " /> |
169 <expand macro="fit_intercept"/> | 168 <expand macro="fit_intercept" /> |
170 <expand macro="max_iter" default_value="100"/> | 169 <expand macro="max_iter" default_value="100" /> |
171 <param argument="solver" type="select" label="Optimization algorithm" help=" "> | 170 <param argument="solver" type="select" label="Optimization algorithm" help=" "> |
172 <option value="liblinear" selected="true">liblinear</option> | 171 <option value="liblinear" selected="true">liblinear</option> |
173 <option value="sag">sag</option> | 172 <option value="sag">sag</option> |
174 <option value="lbfgs">lbfgs</option> | 173 <option value="lbfgs">lbfgs</option> |
175 <option value="newton-cg">newton-cg</option> | 174 <option value="newton-cg">newton-cg</option> |
176 </param> | 175 </param> |
177 <param argument="intercept_scaling" type="float" value="1" label="Intercept scaling factor" help="Useful only if solver is liblinear. "/> | 176 <param argument="intercept_scaling" type="float" value="1" label="Intercept scaling factor" help="Useful only if solver is liblinear. " /> |
178 <param argument="multi_class" type="select" label="Multiclass option" help="Works only for lbfgs solver. "> | 177 <param argument="multi_class" type="select" label="Multiclass option" help="Works only for lbfgs solver. "> |
179 <option value="ovr" selected="true">ovr</option> | 178 <option value="ovr" selected="true">ovr</option> |
180 <option value="multinomial">multinomial</option> | 179 <option value="multinomial">multinomial</option> |
181 </param> | 180 </param> |
182 <param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Average scores across all folds" help=" "/> | 181 <param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Average scores across all folds" help=" " /> |
183 <expand macro="random_state"/> | 182 <expand macro="random_state" /> |
184 <!--scoring=None> | 183 <!--scoring=None> <class_weight=None--> |
185 <class_weight=None--> | |
186 </section> | 184 </section> |
187 </when> | 185 </when> |
188 <when value="Perceptron"> | 186 <when value="Perceptron"> |
189 <expand macro="sl_mixed_input"/> | 187 <expand macro="sl_mixed_input" /> |
190 <section name="options" title="Advanced Options" expanded="False"> | 188 <section name="options" title="Advanced Options" expanded="False"> |
191 <expand macro="penalty" default_value="none"/> | 189 <expand macro="penalty" default_value="none" /> |
192 <expand macro="alpha"/> | 190 <expand macro="alpha" /> |
193 <expand macro="fit_intercept"/> | 191 <expand macro="fit_intercept" /> |
194 <expand macro="n_iter_no_change" /> | 192 <expand macro="n_iter_no_change" /> |
195 <expand macro="shuffle"/> | 193 <expand macro="shuffle" /> |
196 <expand macro="eta0" default_value="1"/> | 194 <expand macro="eta0" default_value="1" /> |
197 <expand macro="warm_start" checked="false"/> | 195 <expand macro="warm_start" checked="false" /> |
198 <expand macro="random_state" default_value="0"/> | 196 <expand macro="random_state" default_value="0" /> |
199 <!--class_weight=None--> | 197 <!--class_weight=None--> |
200 </section> | 198 </section> |
201 </when> | 199 </when> |
202 </expand> | 200 </expand> |
203 </inputs> | 201 </inputs> |
204 <expand macro="output"/> | 202 <expand macro="output" /> |
205 <tests> | 203 <tests> |
206 <test> | 204 <test> |
207 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> | 205 <param name="infile1" value="regression_train.tabular" ftype="tabular" /> |
208 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> | 206 <param name="infile2" value="regression_train.tabular" ftype="tabular" /> |
209 <param name="selected_column_selector_option" value="all_but_by_index_number"/> | 207 <param name="selected_column_selector_option" value="all_but_by_index_number" /> |
210 <param name="col1" value="6"/> | 208 <param name="col1" value="6" /> |
211 <param name="col2" value="6"/> | 209 <param name="col2" value="6" /> |
212 <param name="selected_task" value="train"/> | 210 <param name="selected_task" value="train" /> |
213 <param name="selected_algorithm" value="SGDRegressor"/> | 211 <param name="selected_algorithm" value="SGDRegressor" /> |
214 <param name="random_state" value="10"/> | 212 <param name="random_state" value="10" /> |
215 <output name="outfile_fit" file="glm_model01" compare="sim_size" delta="5"/> | 213 <output name="outfile_fit" file="glm_model01" compare="sim_size" delta="5" /> |
216 </test> | 214 </test> |
217 <test> | 215 <test> |
218 <param name="infile_model" value="glm_model01" ftype="zip"/> | 216 <param name="infile_model" value="glm_model01" ftype="zip" /> |
219 <param name="infile_data" value="regression_test.tabular" ftype="tabular"/> | 217 <param name="infile_data" value="regression_test.tabular" ftype="tabular" /> |
220 <param name="selected_task" value="load"/> | 218 <param name="selected_task" value="load" /> |
221 <output name="outfile_predict" file="glm_result01" lines_diff="4"/> | 219 <output name="outfile_predict" file="glm_result01" lines_diff="4" /> |
222 </test> | 220 </test> |
223 <test> | 221 <test> |
224 <param name="infile1" value="train.tabular" ftype="tabular"/> | 222 <param name="infile1" value="train.tabular" ftype="tabular" /> |
225 <param name="infile2" value="train.tabular" ftype="tabular"/> | 223 <param name="infile2" value="train.tabular" ftype="tabular" /> |
226 <param name="col1" value="1,2,3,4"/> | 224 <param name="col1" value="1,2,3,4" /> |
227 <param name="col2" value="5"/> | 225 <param name="col2" value="5" /> |
228 <param name="selected_task" value="train"/> | 226 <param name="selected_task" value="train" /> |
229 <param name="selected_algorithm" value="SGDClassifier"/> | 227 <param name="selected_algorithm" value="SGDClassifier" /> |
230 <param name="random_state" value="10"/> | 228 <param name="random_state" value="10" /> |
231 <output name="outfile_fit" file="glm_model02" compare="sim_size" delta="5"/> | 229 <output name="outfile_fit" file="glm_model02" compare="sim_size" delta="5" /> |
232 </test> | 230 </test> |
233 <test> | 231 <test> |
234 <param name="infile_model" value="glm_model02" ftype="zip"/> | 232 <param name="infile_model" value="glm_model02" ftype="zip" /> |
235 <param name="infile_data" value="test.tabular" ftype="tabular"/> | 233 <param name="infile_data" value="test.tabular" ftype="tabular" /> |
236 <param name="selected_task" value="load"/> | 234 <param name="selected_task" value="load" /> |
237 <output name="outfile_predict" file="glm_result02"/> | 235 <output name="outfile_predict" file="glm_result02" /> |
238 </test> | 236 </test> |
239 <test> | 237 <test> |
240 <param name="infile1" value="train.tabular" ftype="tabular"/> | 238 <param name="infile1" value="train.tabular" ftype="tabular" /> |
241 <param name="infile2" value="train.tabular" ftype="tabular"/> | 239 <param name="infile2" value="train.tabular" ftype="tabular" /> |
242 <param name="col1" value="1,2,3,4"/> | 240 <param name="col1" value="1,2,3,4" /> |
243 <param name="col2" value="5"/> | 241 <param name="col2" value="5" /> |
244 <param name="selected_task" value="train"/> | 242 <param name="selected_task" value="train" /> |
245 <param name="selected_algorithm" value="RidgeClassifier"/> | 243 <param name="selected_algorithm" value="RidgeClassifier" /> |
246 <param name="random_state" value="10"/> | 244 <param name="random_state" value="10" /> |
247 <output name="outfile_fit" file="glm_model03" compare="sim_size" delta="5"/> | 245 <output name="outfile_fit" file="glm_model03" compare="sim_size" delta="5" /> |
248 </test> | 246 </test> |
249 <test> | 247 <test> |
250 <param name="infile_model" value="glm_model03" ftype="zip"/> | 248 <param name="infile_model" value="glm_model03" ftype="zip" /> |
251 <param name="infile_data" value="test.tabular" ftype="tabular"/> | 249 <param name="infile_data" value="test.tabular" ftype="tabular" /> |
252 <param name="selected_task" value="load"/> | 250 <param name="selected_task" value="load" /> |
253 <output name="outfile_predict" file="glm_result03"/> | 251 <output name="outfile_predict" file="glm_result03" /> |
254 </test> | 252 </test> |
255 <test> | 253 <test> |
256 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> | 254 <param name="infile1" value="regression_train.tabular" ftype="tabular" /> |
257 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> | 255 <param name="infile2" value="regression_train.tabular" ftype="tabular" /> |
258 <param name="col1" value="1,2,3,4,5"/> | 256 <param name="col1" value="1,2,3,4,5" /> |
259 <param name="col2" value="6"/> | 257 <param name="col2" value="6" /> |
260 <param name="selected_task" value="train"/> | 258 <param name="selected_task" value="train" /> |
261 <param name="selected_algorithm" value="LinearRegression"/> | 259 <param name="selected_algorithm" value="LinearRegression" /> |
262 <output name="outfile_fit" file="glm_model04" compare="sim_size" delta="5"/> | 260 <output name="outfile_fit" file="glm_model04" compare="sim_size" delta="5" /> |
263 </test> | 261 </test> |
264 <test> | 262 <test> |
265 <param name="infile_model" value="glm_model04" ftype="zip"/> | 263 <param name="infile_model" value="glm_model04" ftype="zip" /> |
266 <param name="infile_data" value="regression_test.tabular" ftype="tabular"/> | 264 <param name="infile_data" value="regression_test.tabular" ftype="tabular" /> |
267 <param name="selected_task" value="load"/> | 265 <param name="selected_task" value="load" /> |
268 <output name="outfile_predict" file="glm_result04" lines_diff="8"/> | 266 <output name="outfile_predict" file="glm_result04" lines_diff="8" /> |
269 </test> | 267 </test> |
270 <test> | 268 <test> |
271 <param name="infile1" value="train.tabular" ftype="tabular"/> | 269 <param name="infile1" value="train.tabular" ftype="tabular" /> |
272 <param name="infile2" value="train.tabular" ftype="tabular"/> | 270 <param name="infile2" value="train.tabular" ftype="tabular" /> |
273 <param name="col1" value="1,2,3,4"/> | 271 <param name="col1" value="1,2,3,4" /> |
274 <param name="col2" value="5"/> | 272 <param name="col2" value="5" /> |
275 <param name="selected_task" value="train"/> | 273 <param name="selected_task" value="train" /> |
276 <param name="selected_algorithm" value="LogisticRegression"/> | 274 <param name="selected_algorithm" value="LogisticRegression" /> |
277 <param name="random_state" value="10"/> | 275 <param name="random_state" value="10" /> |
278 <output name="outfile_fit" file="glm_model05" compare="sim_size" delta="5"/> | 276 <output name="outfile_fit" file="glm_model05" compare="sim_size" delta="5" /> |
279 </test> | 277 </test> |
280 <test> | 278 <test> |
281 <param name="infile_model" value="glm_model05" ftype="zip"/> | 279 <param name="infile_model" value="glm_model05" ftype="zip" /> |
282 <param name="infile_data" value="test.tabular" ftype="tabular"/> | 280 <param name="infile_data" value="test.tabular" ftype="tabular" /> |
283 <param name="selected_task" value="load"/> | 281 <param name="selected_task" value="load" /> |
284 <output name="outfile_predict" file="glm_result05"/> | 282 <output name="outfile_predict" file="glm_result05" /> |
285 </test> | 283 </test> |
286 <test> | 284 <test> |
287 <param name="infile1" value="train.tabular" ftype="tabular"/> | 285 <param name="infile1" value="train.tabular" ftype="tabular" /> |
288 <param name="infile2" value="train.tabular" ftype="tabular"/> | 286 <param name="infile2" value="train.tabular" ftype="tabular" /> |
289 <param name="col1" value="1,2,3,4"/> | 287 <param name="col1" value="1,2,3,4" /> |
290 <param name="col2" value="5"/> | 288 <param name="col2" value="5" /> |
291 <param name="selected_task" value="train"/> | 289 <param name="selected_task" value="train" /> |
292 <param name="selected_algorithm" value="LogisticRegressionCV"/> | 290 <param name="selected_algorithm" value="LogisticRegressionCV" /> |
293 <param name="random_state" value="10"/> | 291 <param name="random_state" value="10" /> |
294 <output name="outfile_fit" file="glm_model06" compare="sim_size" delta="5"/> | 292 <output name="outfile_fit" file="glm_model06" compare="sim_size" delta="5" /> |
295 </test> | 293 </test> |
296 <test> | 294 <test> |
297 <param name="infile_model" value="glm_model06" ftype="zip"/> | 295 <param name="infile_model" value="glm_model06" ftype="zip" /> |
298 <param name="infile_data" value="test.tabular" ftype="tabular"/> | 296 <param name="infile_data" value="test.tabular" ftype="tabular" /> |
299 <param name="selected_task" value="load"/> | 297 <param name="selected_task" value="load" /> |
300 <output name="outfile_predict" file="glm_result06"/> | 298 <output name="outfile_predict" file="glm_result06" /> |
301 </test> | 299 </test> |
302 <test> | 300 <test> |
303 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> | 301 <param name="infile1" value="regression_train.tabular" ftype="tabular" /> |
304 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> | 302 <param name="infile2" value="regression_train.tabular" ftype="tabular" /> |
305 <param name="col1" value="1,2,3,4,5"/> | 303 <param name="col1" value="1,2,3,4,5" /> |
306 <param name="col2" value="6"/> | 304 <param name="col2" value="6" /> |
307 <param name="selected_task" value="train"/> | 305 <param name="selected_task" value="train" /> |
308 <param name="selected_algorithm" value="Ridge"/> | 306 <param name="selected_algorithm" value="Ridge" /> |
309 <param name="random_state" value="10"/> | 307 <param name="random_state" value="10" /> |
310 <output name="outfile_fit" file="glm_model07" compare="sim_size" delta="5"/> | 308 <output name="outfile_fit" file="glm_model07" compare="sim_size" delta="5" /> |
311 </test> | 309 </test> |
312 <test> | 310 <test> |
313 <param name="infile_model" value="glm_model07" ftype="zip"/> | 311 <param name="infile_model" value="glm_model07" ftype="zip" /> |
314 <param name="infile_data" value="regression_test.tabular" ftype="tabular"/> | 312 <param name="infile_data" value="regression_test.tabular" ftype="tabular" /> |
315 <param name="selected_task" value="load"/> | 313 <param name="selected_task" value="load" /> |
316 <output name="outfile_predict" file="glm_result07"/> | 314 <output name="outfile_predict"> |
317 </test> | 315 <assert_contents> |
318 <test> | 316 <has_n_columns n="6" /> |
319 <param name="infile1" value="train.tabular" ftype="tabular"/> | 317 <has_text text="86.9702122735000" /> |
320 <param name="infile2" value="train.tabular" ftype="tabular"/> | 318 <has_text text="-1.0173960197" /> |
321 <param name="col1" value="1,2,3,4"/> | 319 <has_text text="0.64184687433" /> |
322 <param name="col2" value="5"/> | 320 <has_text text="-0.621522971207000" /> |
323 <param name="selected_task" value="train"/> | 321 <has_text text="0.39001218449" /> |
324 <param name="selected_algorithm" value="Perceptron"/> | 322 <has_text text="0.596382816494397" /> |
325 <param name="random_state" value="10"/> | 323 <has_text text="-47.4101632272" /> |
326 <output name="outfile_fit" file="glm_model08" compare="sim_size" delta="5"/> | 324 <has_text text="-0.732777468453000" /> |
327 </test> | 325 <has_text text="-1.0610977011" /> |
328 <test> | 326 <has_text text="-1.099948005770000" /> |
329 <param name="infile_model" value="glm_model08" ftype="zip"/> | 327 <has_text text="0.58565796301" /> |
330 <param name="infile_data" value="test.tabular" ftype="tabular"/> | 328 <has_text text="0.262144044202223" /> |
331 <param name="selected_task" value="load"/> | 329 <has_text text="-206.99829512" /> |
332 <output name="outfile_predict" file="glm_result08"/> | 330 <has_text text="0.7057412304" /> |
331 <has_text text="-1.332209237379999" /> | |
332 </assert_contents> | |
333 </output> | |
334 </test> | |
335 <test> | |
336 <param name="infile1" value="train.tabular" ftype="tabular" /> | |
337 <param name="infile2" value="train.tabular" ftype="tabular" /> | |
338 <param name="col1" value="1,2,3,4" /> | |
339 <param name="col2" value="5" /> | |
340 <param name="selected_task" value="train" /> | |
341 <param name="selected_algorithm" value="Perceptron" /> | |
342 <param name="random_state" value="10" /> | |
343 <output name="outfile_fit" file="glm_model08" compare="sim_size" delta="5" /> | |
344 </test> | |
345 <test> | |
346 <param name="infile_model" value="glm_model08" ftype="zip" /> | |
347 <param name="infile_data" value="test.tabular" ftype="tabular" /> | |
348 <param name="selected_task" value="load" /> | |
349 <output name="outfile_predict" file="glm_result08" /> | |
333 </test> | 350 </test> |
334 </tests> | 351 </tests> |
335 <help><![CDATA[ | 352 <help><![CDATA[ |
336 ***What it does*** | 353 ***What it does*** |
337 This module implements a set of linear models for classification and regression such as: SGD classification and regression, Linear and Ridge regression and classification. This wrapper is using sklearn.linear_model module at its core. For information about linear models and their parameter settings please refer to `Scikit-learn generalized linear models`_. | 354 This module implements a set of linear models for classification and regression such as: SGD classification and regression, Linear and Ridge regression and classification. This wrapper is using sklearn.linear_model module at its core. For information about linear models and their parameter settings please refer to `Scikit-learn generalized linear models`_. |
394 | 411 |
395 | 412 |
396 **3 - Prediction output** | 413 **3 - Prediction output** |
397 The tool predicts the class labels for new samples and adds them as the last column to the prediction dataset. The new dataset then is output as a tabular file. The prediction output format should look like the training dataset. | 414 The tool predicts the class labels for new samples and adds them as the last column to the prediction dataset. The new dataset then is output as a tabular file. The prediction output format should look like the training dataset. |
398 | 415 |
399 ]]></help> | 416 ]]> </help> |
400 <expand macro="sklearn_citation"/> | 417 <expand macro="sklearn_citation" /> |
401 </tool> | 418 </tool> |