Mercurial > repos > bgruening > sklearn_clf_metrics
comparison main_macros.xml @ 5:d093d6091216 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
| author | bgruening |
|---|---|
| date | Tue, 10 Apr 2018 15:19:27 -0400 |
| parents | 7e7573de4c92 |
| children | 961e9696f3d8 |
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| 4:7e7573de4c92 | 5:d093d6091216 |
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| 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> |