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comparison main_macros.xml @ 5:16ec53208a69 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
author bgruening
date Tue, 10 Apr 2018 15:19:06 -0400
parents 9177ec66e11b
children 9967cad18b02
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4:9177ec66e11b 5:16ec53208a69
64 <option value="load">Load a model and predict</option> 64 <option value="load">Load a model and predict</option>
65 </param> 65 </param>
66 <when value="load"> 66 <when value="load">
67 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/> 67 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
68 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/> 68 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
69 <param name="header" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
69 <conditional name="prediction_options"> 70 <conditional name="prediction_options">
70 <param name="prediction_option" type="select" label="Select the type of prediction"> 71 <param name="prediction_option" type="select" label="Select the type of prediction">
71 <option value="predict">Predict class labels</option> 72 <option value="predict">Predict class labels</option>
72 <option value="advanced">Include advanced options</option> 73 <option value="advanced">Include advanced options</option>
73 </param> 74 </param>
172 173
173 <xml name="max_depth" token_default_value="" token_help=" "> 174 <xml name="max_depth" token_default_value="" token_help=" ">
174 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/> 175 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/>
175 </xml> 176 </xml>
176 177
177 <xml name="min_samples_split" token_default_value="2" token_help=" "> 178 <xml name="min_samples_split" token_type="integer" token_default_value="2" token_help=" ">
178 <param argument="min_samples_split" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples required to split an internal node" help="@HELP@"/> 179 <param argument="min_samples_split" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples required to split an internal node" help="@HELP@"/>
179 </xml> 180 </xml>
180 181
181 <xml name="min_samples_leaf" token_default_value="1" token_help=" "> 182 <xml name="min_samples_leaf" token_type="integer" token_default_value="1" token_label="Minimum number of samples in newly created leaves" token_help=" ">
182 <param argument="min_samples_leaf" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples in newly created leaves" help="@HELP@"/> 183 <param argument="min_samples_leaf" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP@"/>
183 </xml> 184 </xml>
184 185
185 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" "> 186 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" ">
186 <param argument="min_weight_fraction_leaf" type="float" optional="true" value="@DEFAULT_VALUE@" label="Minimum weighted fraction of the input samples required to be at a leaf node" help="@HELP@"/> 187 <param argument="min_weight_fraction_leaf" type="float" optional="true" value="@DEFAULT_VALUE@" label="Minimum weighted fraction of the input samples required to be at a leaf node" help="@HELP@"/>
187 </xml> 188 </xml>
188 189
189 <xml name="max_leaf_nodes" token_default_value="" token_help=" "> 190 <xml name="max_leaf_nodes" token_default_value="" token_help=" ">
190 <param argument="max_leaf_nodes" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum number of leaf nodes in best-first method" help="@HELP@"/> 191 <param argument="max_leaf_nodes" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum number of leaf nodes in best-first method" help="@HELP@"/>
192 </xml>
193
194 <xml name="min_impurity_decrease" token_default_value="0" token_help=" ">
195 <param argument="min_impurity_decrease" type="float" value="@DEFAULT_VALUE@" optional="true" label="The threshold value of impurity for stopping node splitting" help="@HELP@"/>
191 </xml> 196 </xml>
192 197
193 <xml name="bootstrap" token_checked="true" token_help=" "> 198 <xml name="bootstrap" token_checked="true" token_help=" ">
194 <param argument="bootstrap" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Use bootstrap samples for building trees." help="@HELP@"/> 199 <param argument="bootstrap" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Use bootstrap samples for building trees." help="@HELP@"/>
195 </xml> 200 </xml>
200 <option value="entropy">Information gain</option> 205 <option value="entropy">Information gain</option>
201 <yield/> 206 <yield/>
202 </param> 207 </param>
203 </xml> 208 </xml>
204 209
210 <xml name="criterion2" token_help="">
211 <param argument="criterion" type="select" label="Function to measure the quality of a split" >
212 <option value="mse">mse - mean squared error</option>
213 <option value="mae">mae - mean absolute error</option>
214 <yield/>
215 </param>
216 </xml>
217
205 <xml name="oob_score" token_checked="false" token_help=" "> 218 <xml name="oob_score" token_checked="false" token_help=" ">
206 <param argument="oob_score" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use out-of-bag samples to estimate the generalization error" help="@HELP@"/> 219 <param argument="oob_score" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use out-of-bag samples to estimate the generalization error" help="@HELP@"/>
207 </xml> 220 </xml>
208 221
209 <xml name="max_features" token_default_value="auto" token_help="This could be an integer, float, string, or None. For more information please refer to help. "> 222 <xml name="max_features">
210 <param argument="max_features" type="text" optional="true" value="@DEFAULT_VALUE@" label="Number of features for finding the best split" help="@HELP@"/> 223 <conditional name="select_max_features">
224 <param argument="max_features" type="select" label="max_features">
225 <option value="auto" selected="true">auto - max_features=n_features</option>
226 <option value="sqrt">sqrt - max_features=sqrt(n_features)</option>
227 <option value="log2">log2 - max_features=log2(n_features)</option>
228 <option value="number_input">I want to type the number in or input None type</option>
229 </param>
230 <when value="auto">
231 </when>
232 <when value="sqrt">
233 </when>
234 <when value="log2">
235 </when>
236 <when value="number_input">
237 <param name="num_max_features" type="float" value="" optional="true" label="Input max_features number:" help="If int, consider the number of features at each split; If float, then max_features is a percentage and int(max_features * n_features) features are considered at each split."/>
238 </when>
239 </conditional>
240 </xml>
241
242 <xml name="verbose" token_default_value="0" token_help="If 1 then it prints progress and performance once in a while. If greater than 1 then it prints progress and performance for every tree.">
243 <param argument="verbose" type="integer" value="@DEFAULT_VALUE@" optional="true" label="Enable verbose output" help="@HELP@"/>
211 </xml> 244 </xml>
212 245
213 <xml name="learning_rate" token_default_value="1.0" token_help=" "> 246 <xml name="learning_rate" token_default_value="1.0" token_help=" ">
214 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/> 247 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/>
215 </xml> 248 </xml>
216 249
250 <xml name="subsample" token_help=" ">
251 <param argument="subsample" type="float" value="1.0" optional="true" label="The fraction of samples to be used for fitting the individual base learners" help="@HELP@"/>
252 </xml>
253
254 <xml name="presort">
255 <param argument="presort" type="select" label="Whether to presort the data to speed up the finding of best splits in fitting" >
256 <option value="auto" selected="true">auto</option>
257 <option value="true">true</option>
258 <option value="false">false</option>
259 </param>
260 </xml>
217 261
218 <!--Parameters--> 262 <!--Parameters-->
219 <xml name="tol" token_default_value="0.0" token_help_text="Early stopping heuristics based on the relative center changes. Set to default (0.0) to disable this convergence detection."> 263 <xml name="tol" token_default_value="0.0" token_help_text="Early stopping heuristics based on the relative center changes. Set to default (0.0) to disable this convergence detection.">
220 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/> 264 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/>
221 </xml> 265 </xml>
224 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/> 268 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/>
225 </xml> 269 </xml>
226 270
227 <xml name="fit_intercept" token_checked="true"> 271 <xml name="fit_intercept" token_checked="true">
228 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Estimate the intercept" help="If false, the data is assumed to be already centered."/> 272 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Estimate the intercept" help="If false, the data is assumed to be already centered."/>
273 </xml>
274
275 <xml name="n_jobs" token_default_value="1" token_label="The number of jobs to run in parallel for both fit and predict">
276 <param argument="n_jobs" type="integer" value="@DEFAULT_VALUE@" optional="true" label="@LABEL@" help="If -1, then the number of jobs is set to the number of cores"/>
229 </xml> 277 </xml>
230 278
231 <xml name="n_iter" token_default_value="5" token_help_text="The number of passes over the training data (aka epochs). "> 279 <xml name="n_iter" token_default_value="5" token_help_text="The number of passes over the training data (aka epochs). ">
232 <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/> 280 <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
233 </xml> 281 </xml>