Mercurial > repos > bgruening > sklearn_pca
comparison main_macros.xml @ 0:2d7016b3ae92 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
| author | bgruening |
|---|---|
| date | Fri, 02 Oct 2020 08:45:21 +0000 |
| parents | |
| children | 132805688fa3 |
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| -1:000000000000 | 0:2d7016b3ae92 |
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| 1 <macros> | |
| 2 <token name="@VERSION@">1.0.8.2</token> | |
| 3 | |
| 4 <xml name="python_requirements"> | |
| 5 <requirements> | |
| 6 <requirement type="package" version="3.6">python</requirement> | |
| 7 <requirement type="package" version="0.8.1">Galaxy-ML</requirement> | |
| 8 <yield/> | |
| 9 </requirements> | |
| 10 </xml> | |
| 11 | |
| 12 <xml name="macro_stdio"> | |
| 13 <stdio> | |
| 14 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/> | |
| 15 </stdio> | |
| 16 </xml> | |
| 17 | |
| 18 | |
| 19 <!--Generic interface--> | |
| 20 | |
| 21 <xml name="sl_Conditional" token_train="tabular" token_data="tabular" token_model="txt"> | |
| 22 <conditional name="selected_tasks"> | |
| 23 <param name="selected_task" type="select" label="Select a Classification Task"> | |
| 24 <option value="train" selected="true">Train a model</option> | |
| 25 <option value="load">Load a model and predict</option> | |
| 26 </param> | |
| 27 <when value="load"> | |
| 28 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/> | |
| 29 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/> | |
| 30 <param name="header" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
| 31 <conditional name="prediction_options"> | |
| 32 <param name="prediction_option" type="select" label="Select the type of prediction"> | |
| 33 <option value="predict">Predict class labels</option> | |
| 34 <option value="advanced">Include advanced options</option> | |
| 35 </param> | |
| 36 <when value="predict"> | |
| 37 </when> | |
| 38 <when value="advanced"> | |
| 39 </when> | |
| 40 </conditional> | |
| 41 </when> | |
| 42 <when value="train"> | |
| 43 <conditional name="selected_algorithms"> | |
| 44 <yield /> | |
| 45 </conditional> | |
| 46 </when> | |
| 47 </conditional> | |
| 48 </xml> | |
| 49 | |
| 50 <xml name="advanced_section"> | |
| 51 <section name="options" title="Advanced Options" expanded="False"> | |
| 52 <yield /> | |
| 53 </section> | |
| 54 </xml> | |
| 55 | |
| 56 | |
| 57 <!--Generalized Linear Models--> | |
| 58 <xml name="loss" token_help=" " token_select="false"> | |
| 59 <param argument="loss" type="select" label="Loss function" help="@HELP@"> | |
| 60 <option value="squared_loss" selected="@SELECT@">squared loss</option> | |
| 61 <option value="huber">huber</option> | |
| 62 <option value="epsilon_insensitive">epsilon insensitive</option> | |
| 63 <option value="squared_epsilon_insensitive">squared epsilon insensitive</option> | |
| 64 <yield/> | |
| 65 </param> | |
| 66 </xml> | |
| 67 | |
| 68 <xml name="penalty" token_help=" "> | |
| 69 <param argument="penalty" type="select" label="Penalty (regularization term)" help="@HELP@"> | |
| 70 <option value="l2" selected="true">l2</option> | |
| 71 <option value="l1">l1</option> | |
| 72 <option value="elasticnet">elastic net</option> | |
| 73 <option value="none">none</option> | |
| 74 <yield/> | |
| 75 </param> | |
| 76 </xml> | |
| 77 | |
| 78 <xml name="l1_ratio" token_default_value="0.15" token_help=" "> | |
| 79 <param argument="l1_ratio" type="float" value="@DEFAULT_VALUE@" label="Elastic Net mixing parameter" help="@HELP@"/> | |
| 80 </xml> | |
| 81 | |
| 82 <xml name="epsilon" token_default_value="0.1" token_help="Used if loss is ‘huber’, ‘epsilon_insensitive’, or ‘squared_epsilon_insensitive’. "> | |
| 83 <param argument="epsilon" type="float" value="@DEFAULT_VALUE@" label="Epsilon (epsilon-sensitive loss functions only)" help="@HELP@"/> | |
| 84 </xml> | |
| 85 | |
| 86 <xml name="learning_rate_s" token_help=" " token_selected1="false" token_selected2="false"> | |
| 87 <param argument="learning_rate" type="select" optional="true" label="Learning rate schedule" help="@HELP@"> | |
| 88 <option value="optimal" selected="@SELECTED1@">optimal</option> | |
| 89 <option value="constant">constant</option> | |
| 90 <option value="invscaling" selected="@SELECTED2@">inverse scaling</option> | |
| 91 <yield/> | |
| 92 </param> | |
| 93 </xml> | |
| 94 | |
| 95 <xml name="eta0" token_default_value="0.0" token_help="Used with ‘constant’ or ‘invscaling’ schedules. "> | |
| 96 <param argument="eta0" type="float" value="@DEFAULT_VALUE@" label="Initial learning rate" help="@HELP@"/> | |
| 97 </xml> | |
| 98 | |
| 99 <xml name="power_t" token_default_value="0.5" token_help=" "> | |
| 100 <param argument="power_t" type="float" value="@DEFAULT_VALUE@" label="Exponent for inverse scaling learning rate" help="@HELP@"/> | |
| 101 </xml> | |
| 102 | |
| 103 <xml name="normalize" token_checked="false" token_help=" "> | |
| 104 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Normalize samples before training" help=" "/> | |
| 105 </xml> | |
| 106 | |
| 107 <xml name="copy_X" token_checked="true" token_help=" "> | |
| 108 <param argument="copy_X" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use a copy of samples" help="If false, samples would be overwritten. "/> | |
| 109 </xml> | |
| 110 | |
| 111 <xml name="ridge_params"> | |
| 112 <expand macro="normalize"/> | |
| 113 <expand macro="alpha" default_value="1.0"/> | |
| 114 <expand macro="fit_intercept"/> | |
| 115 <expand macro="max_iter" default_value=""/> | |
| 116 <expand macro="tol" default_value="0.001" help_text="Precision of the solution. "/> | |
| 117 <!--class_weight--> | |
| 118 <expand macro="copy_X"/> | |
| 119 <param argument="solver" type="select" value="" label="Solver to use in the computational routines" help=" "> | |
| 120 <option value="auto" selected="true">auto</option> | |
| 121 <option value="svd">svd</option> | |
| 122 <option value="cholesky">cholesky</option> | |
| 123 <option value="lsqr">lsqr</option> | |
| 124 <option value="sparse_cg">sparse_cg</option> | |
| 125 <option value="sag">sag</option> | |
| 126 </param> | |
| 127 <expand macro="random_state"/> | |
| 128 </xml> | |
| 129 | |
| 130 <!--Ensemble methods--> | |
| 131 <xml name="n_estimators" token_default_value="10" token_help=" "> | |
| 132 <param argument="n_estimators" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of trees in the forest" help="@HELP@"/> | |
| 133 </xml> | |
| 134 | |
| 135 <xml name="max_depth" token_default_value="" token_help=" "> | |
| 136 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/> | |
| 137 </xml> | |
| 138 | |
| 139 <xml name="min_samples_split" token_type="integer" token_default_value="2" token_help=" "> | |
| 140 <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@"/> | |
| 141 </xml> | |
| 142 | |
| 143 <xml name="min_samples_leaf" token_type="integer" token_default_value="1" token_label="Minimum number of samples in newly created leaves" token_help=" "> | |
| 144 <param argument="min_samples_leaf" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP@"/> | |
| 145 </xml> | |
| 146 | |
| 147 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" "> | |
| 148 <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@"/> | |
| 149 </xml> | |
| 150 | |
| 151 <xml name="max_leaf_nodes" token_default_value="" token_help=" "> | |
| 152 <param argument="max_leaf_nodes" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum number of leaf nodes in best-first method" help="@HELP@"/> | |
| 153 </xml> | |
| 154 | |
| 155 <xml name="min_impurity_decrease" token_default_value="0" token_help=" "> | |
| 156 <param argument="min_impurity_decrease" type="float" value="@DEFAULT_VALUE@" optional="true" label="The threshold value of impurity for stopping node splitting" help="@HELP@"/> | |
| 157 </xml> | |
| 158 | |
| 159 <xml name="bootstrap" token_checked="true" token_help=" "> | |
| 160 <param argument="bootstrap" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Use bootstrap samples for building trees." help="@HELP@"/> | |
| 161 </xml> | |
| 162 | |
| 163 <xml name="criterion" token_help=" "> | |
| 164 <param argument="criterion" type="select" label="Function to measure the quality of a split" help=" "> | |
| 165 <option value="gini" selected="true">Gini impurity</option> | |
| 166 <option value="entropy">Information gain</option> | |
| 167 <yield/> | |
| 168 </param> | |
| 169 </xml> | |
| 170 | |
| 171 <xml name="criterion2" token_help=""> | |
| 172 <param argument="criterion" type="select" label="Function to measure the quality of a split" > | |
| 173 <option value="mse">mse - mean squared error</option> | |
| 174 <option value="mae">mae - mean absolute error</option> | |
| 175 <yield/> | |
| 176 </param> | |
| 177 </xml> | |
| 178 | |
| 179 <xml name="oob_score" token_checked="false" token_help=" "> | |
| 180 <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@"/> | |
| 181 </xml> | |
| 182 | |
| 183 <xml name="max_features"> | |
| 184 <conditional name="select_max_features"> | |
| 185 <param argument="max_features" type="select" label="max_features"> | |
| 186 <option value="auto" selected="true">auto - max_features=n_features</option> | |
| 187 <option value="sqrt">sqrt - max_features=sqrt(n_features)</option> | |
| 188 <option value="log2">log2 - max_features=log2(n_features)</option> | |
| 189 <option value="number_input">I want to type the number in or input None type</option> | |
| 190 </param> | |
| 191 <when value="auto"> | |
| 192 </when> | |
| 193 <when value="sqrt"> | |
| 194 </when> | |
| 195 <when value="log2"> | |
| 196 </when> | |
| 197 <when value="number_input"> | |
| 198 <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."/> | |
| 199 </when> | |
| 200 </conditional> | |
| 201 </xml> | |
| 202 | |
| 203 <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."> | |
| 204 <param argument="verbose" type="integer" value="@DEFAULT_VALUE@" optional="true" label="Enable verbose output" help="@HELP@"/> | |
| 205 </xml> | |
| 206 | |
| 207 <xml name="learning_rate" token_default_value="1.0" token_help=" "> | |
| 208 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/> | |
| 209 </xml> | |
| 210 | |
| 211 <xml name="subsample" token_help=" "> | |
| 212 <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@"/> | |
| 213 </xml> | |
| 214 | |
| 215 <xml name="presort"> | |
| 216 <param argument="presort" type="select" label="Whether to presort the data to speed up the finding of best splits in fitting" > | |
| 217 <option value="auto" selected="true">auto</option> | |
| 218 <option value="true">true</option> | |
| 219 <option value="false">false</option> | |
| 220 </param> | |
| 221 </xml> | |
| 222 | |
| 223 <!-- LightGBM --> | |
| 224 <xml name="feature_fraction" token_help="LightGBM will randomly select part of the features for each iteration (tree) if feature_fraction is smaller than 1.0. For example, if you set it to 0.8, LightGBM will select 80% of features before training each tree."> | |
| 225 <param argument="feature_fraction" type="float" value="1.0" label="Proportion of features to train each tree" help="@HELP@"/> | |
| 226 </xml> | |
| 227 | |
| 228 <xml name="lambda_l1" token_help=" "> | |
| 229 <param argument="lambda_l1" type="float" value="0.0" label="L1 regularization" help="@HELP@"/> | |
| 230 </xml> | |
| 231 | |
| 232 <xml name="lambda_l2" token_help=" "> | |
| 233 <param argument="lambda_l2" type="float" value="0.0" label="L1 regularization" help="@HELP@"/> | |
| 234 </xml> | |
| 235 | |
| 236 <xml name="min_gain_to_split" token_help=" "> | |
| 237 <param argument="min_gain_to_split" type="float" value="0.0" label="Minimal gain to perform split" help="@HELP@"/> | |
| 238 </xml> | |
| 239 | |
| 240 <xml name="min_child_weight" token_help="Minimal sum hessian in one leaf. It can be used to deal with over-fitting."> | |
| 241 <param argument="min_child_weight" type="float" value="0.0" label="Minimal sum hessian in one leaf" help="@HELP@"/> | |
| 242 </xml> | |
| 243 | |
| 244 | |
| 245 <!--Parameters--> | |
| 246 <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."> | |
| 247 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/> | |
| 248 </xml> | |
| 249 | |
| 250 <xml name="n_clusters" token_default_value="8"> | |
| 251 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/> | |
| 252 </xml> | |
| 253 | |
| 254 <xml name="fit_intercept" token_checked="true"> | |
| 255 <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."/> | |
| 256 </xml> | |
| 257 | |
| 258 <xml name="n_iter_no_change" token_default_value="5" token_help_text="Number of iterations with no improvement to wait before early stopping. "> | |
| 259 <param argument="n_iter_no_change" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/> | |
| 260 </xml> | |
| 261 | |
| 262 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration"> | |
| 263 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/> | |
| 264 </xml> | |
| 265 | |
| 266 <xml name="random_state" token_default_value="" token_help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data. A fixed seed allows reproducible results. default=None."> | |
| 267 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/> | |
| 268 </xml> | |
| 269 | |
| 270 <xml name="warm_start" token_checked="true" token_help_text="When set to True, reuse the solution of the previous call to fit as initialization,otherwise, just erase the previous solution."> | |
| 271 <param argument="warm_start" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Perform warm start" help="@HELP_TEXT@"/> | |
| 272 </xml> | |
| 273 | |
| 274 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term."> | |
| 275 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/> | |
| 276 </xml> | |
| 277 | |
| 278 <!--xml name="class_weight" token_default_value="" token_help_text=""> | |
| 279 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/> | |
| 280 </xml--> | |
| 281 | |
| 282 <xml name="alpha" token_default_value="0.0001" token_help_text="Constant that multiplies the regularization term if regularization is used. "> | |
| 283 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/> | |
| 284 </xml> | |
| 285 | |
| 286 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters."> | |
| 287 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/> | |
| 288 </xml> | |
| 289 | |
| 290 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample."> | |
| 291 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/> | |
| 292 </xml> | |
| 293 | |
| 294 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. "> | |
| 295 <param argument="noise" type="float" optional="true" value="@DEFAULT_VALUE@" label="Standard deviation of the Gaussian noise added to the data" help="@HELP_TEXT@"/> | |
| 296 </xml> | |
| 297 | |
| 298 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. "> | |
| 299 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/> | |
| 300 </xml> | |
| 301 | |
| 302 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" "> | |
| 303 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/> | |
| 304 </xml> | |
| 305 | |
| 306 <xml name="n_init" token_default_value="10" > | |
| 307 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/> | |
| 308 </xml> | |
| 309 | |
| 310 <xml name="init"> | |
| 311 <param argument="init" type="select" label="Centroid initialization method" help="''k-means++'' selects initial cluster centers that speed up convergence. ''random'' chooses k observations (rows) at random from data as initial centroids."> | |
| 312 <option value="k-means++">k-means++</option> | |
| 313 <option value="random">random</option> | |
| 314 </param> | |
| 315 </xml> | |
| 316 | |
| 317 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" "> | |
| 318 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/> | |
| 319 </xml> | |
| 320 | |
| 321 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" "> | |
| 322 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/> | |
| 323 </xml> | |
| 324 | |
| 325 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" "> | |
| 326 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/> | |
| 327 </xml> | |
| 328 | |
| 329 <xml name="pos_label" token_default_value=""> | |
| 330 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/> | |
| 331 </xml> | |
| 332 | |
| 333 <xml name="average"> | |
| 334 <param argument="average" type="select" optional="true" label="Averaging type" help=" "> | |
| 335 <option value="micro">Calculate metrics globally by counting the total true positives, false negatives and false positives. (micro)</option> | |
| 336 <option value="samples">Calculate metrics for each instance, and find their average. Only meaningful for multilabel. (samples)</option> | |
| 337 <option value="macro">Calculate metrics for each label, and find their unweighted mean. This does not take label imbalance into account. (macro)</option> | |
| 338 <option value="weighted">Calculate metrics for each label, and find their average, weighted by support (the number of true instances for each label). This alters ‘macro’ to account for label imbalance; it can result in an F-score that is not between precision and recall. (weighted)</option> | |
| 339 <option value="None">None</option> | |
| 340 <yield/> | |
| 341 </param> | |
| 342 </xml> | |
| 343 | |
| 344 <xml name="beta"> | |
| 345 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/> | |
| 346 </xml> | |
| 347 | |
| 348 | |
| 349 <!--Data interface--> | |
| 350 | |
| 351 <xml name="samples_tabular" token_label1="Training samples dataset:" token_multiple1="false" token_multiple2="false"> | |
| 352 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/> | |
| 353 <param name="header1" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
| 354 <conditional name="column_selector_options_1"> | |
| 355 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/> | |
| 356 </conditional> | |
| 357 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels or target values:"/> | |
| 358 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
| 359 <conditional name="column_selector_options_2"> | |
| 360 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE2@" infile="infile2"/> | |
| 361 </conditional> | |
| 362 <yield/> | |
| 363 </xml> | |
| 364 | |
| 365 <xml name="samples_column_selector_options" token_column_option="selected_column_selector_option" token_col_name="col1" token_multiple="False" token_infile="infile1"> | |
| 366 <param name="@COLUMN_OPTION@" type="select" label="Choose how to select data by column:"> | |
| 367 <option value="by_index_number" selected="true">Select columns by column index number(s)</option> | |
| 368 <option value="all_but_by_index_number">All columns EXCLUDING some by column index number(s)</option> | |
| 369 <option value="by_header_name">Select columns by column header name(s)</option> | |
| 370 <option value="all_but_by_header_name">All columns EXCLUDING some by column header name(s)</option> | |
| 371 <option value="all_columns">All columns</option> | |
| 372 </param> | |
| 373 <when value="by_index_number"> | |
| 374 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" use_header_names="true" data_ref="@INFILE@" label="Select target column(s):"/> | |
| 375 </when> | |
| 376 <when value="all_but_by_index_number"> | |
| 377 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" use_header_names="true" data_ref="@INFILE@" label="Select target column(s):"/> | |
| 378 </when> | |
| 379 <when value="by_header_name"> | |
| 380 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2"/> | |
| 381 </when> | |
| 382 <when value="all_but_by_header_name"> | |
| 383 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2"/> | |
| 384 </when> | |
| 385 <when value="all_columns"> | |
| 386 </when> | |
| 387 </xml> | |
| 388 | |
| 389 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False"> | |
| 390 <conditional name="true_columns"> | |
| 391 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:"> | |
| 392 <option value="tabular" selected="true">Tabular</option> | |
| 393 <option value="sparse">Sparse</option> | |
| 394 </param> | |
| 395 <when value="tabular"> | |
| 396 <param name="infile1" type="data" label="@LABEL1@"/> | |
| 397 <param name="col1" type="data_column" data_ref="infile1" label="Select the target column:"/> | |
| 398 </when> | |
| 399 <when value="sparse"> | |
| 400 <param name="infile1" type="data" format="txt" label="@LABEL1@"/> | |
| 401 </when> | |
| 402 </conditional> | |
| 403 <conditional name="predicted_columns"> | |
| 404 <param name="selected_input2" type="select" label="Select the input type of predicted labels dataset:"> | |
| 405 <option value="tabular" selected="true">Tabular</option> | |
| 406 <option value="sparse">Sparse</option> | |
| 407 </param> | |
| 408 <when value="tabular"> | |
| 409 <param name="infile2" type="data" label="@LABEL2@"/> | |
| 410 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/> | |
| 411 </when> | |
| 412 <when value="sparse"> | |
| 413 <param name="infile2" type="data" format="txt" label="@LABEL1@"/> | |
| 414 </when> | |
| 415 </conditional> | |
| 416 </xml> | |
| 417 | |
| 418 <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False"> | |
| 419 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/> | |
| 420 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
| 421 <conditional name="column_selector_options_1"> | |
| 422 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/> | |
| 423 </conditional> | |
| 424 <param name="infile2" type="data" format="tabular" label="@LABEL2@"/> | |
| 425 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
| 426 <conditional name="column_selector_options_2"> | |
| 427 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE@" infile="infile2"/> | |
| 428 </conditional> | |
| 429 </xml> | |
| 430 | |
| 431 <xml name="multiple_input" token_name="input_files" token_max_num="10" token_format="txt" token_label="Sparse matrix file (.mtx, .txt)" token_help_text="Specify a sparse matrix file in .txt format."> | |
| 432 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):"> | |
| 433 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/> | |
| 434 </repeat> | |
| 435 </xml> | |
| 436 | |
| 437 <xml name="sparse_target" token_label1="Select a sparse matrix:" token_label2="Select the tabular containing true labels:" token_multiple="False" token_format1="txt" token_format2="tabular" token_help1="" token_help2=""> | |
| 438 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/> | |
| 439 <expand macro="input_tabular_target"/> | |
| 440 </xml> | |
| 441 | |
| 442 <xml name="sl_mixed_input"> | |
| 443 <conditional name="input_options"> | |
| 444 <expand macro="data_input_options"/> | |
| 445 <expand macro="data_input_whens"/> | |
| 446 </conditional> | |
| 447 </xml> | |
| 448 | |
| 449 <xml name="sl_mixed_input_plus_sequence"> | |
| 450 <conditional name="input_options"> | |
| 451 <expand macro="data_input_options"> | |
| 452 <option value="seq_fasta">sequnences in a fasta file</option> | |
| 453 <option value="refseq_and_interval">reference genome and intervals</option> | |
| 454 </expand> | |
| 455 <expand macro="data_input_whens"> | |
| 456 <when value="seq_fasta"> | |
| 457 <expand macro="inputs_seq_fasta"/> | |
| 458 </when> | |
| 459 <when value="refseq_and_interval"> | |
| 460 <expand macro="inputs_refseq_and_interval"/> | |
| 461 </when> | |
| 462 </expand> | |
| 463 </conditional> | |
| 464 </xml> | |
| 465 | |
| 466 <xml name="data_input_options"> | |
| 467 <param name="selected_input" type="select" label="Select input type:"> | |
| 468 <option value="tabular" selected="true">tabular data</option> | |
| 469 <option value="sparse">sparse matrix</option> | |
| 470 <yield/> | |
| 471 </param> | |
| 472 </xml> | |
| 473 | |
| 474 <xml name="data_input_whens"> | |
| 475 <when value="tabular"> | |
| 476 <expand macro="samples_tabular" multiple1="true" multiple2="false"/> | |
| 477 </when> | |
| 478 <when value="sparse"> | |
| 479 <expand macro="sparse_target"/> | |
| 480 </when> | |
| 481 <yield/> | |
| 482 </xml> | |
| 483 | |
| 484 <xml name="input_tabular_target"> | |
| 485 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels or target values:"/> | |
| 486 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" /> | |
| 487 <conditional name="column_selector_options_2"> | |
| 488 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="false" infile="infile2"/> | |
| 489 </conditional> | |
| 490 </xml> | |
| 491 | |
| 492 <xml name="inputs_seq_fasta"> | |
| 493 <param name="fasta_path" type="data" format="fasta" label="Dataset containing fasta genomic/protein sequences" help="Sequences will be one-hot encoded to arrays."/> | |
| 494 <expand macro="input_tabular_target"/> | |
| 495 </xml> | |
| 496 | |
| 497 <xml name="inputs_refseq_and_interval"> | |
| 498 <param name="ref_genome_file" type="data" format="fasta" label="Dataset containing reference genomic sequence"/> | |
| 499 <param name="interval_file" type="data" format="interval" label="Dataset containing sequence intervals for training" help="interval. Sequences will be retrieved from the reference genome and one-hot encoded to training arrays."/> | |
| 500 <param name="target_file" type="data" format="bed" label="Dataset containing positions and features for target values." help="bed. The file will be compressed with `bgzip` and then indexed using `tabix`."/> | |
| 501 <param name="infile2" type="data" format="tabular" label="Dataset containing the feature list for prediction"/> | |
| 502 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" /> | |
| 503 <conditional name="column_selector_options_2"> | |
| 504 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="true" infile="infile2"/> | |
| 505 </conditional> | |
| 506 </xml> | |
| 507 | |
| 508 <!--Advanced options--> | |
| 509 <xml name="nn_advanced_options"> | |
| 510 <section name="options" title="Advanced Options" expanded="False"> | |
| 511 <yield/> | |
| 512 <param argument="weights" type="select" label="Weight function" help="Used in prediction."> | |
| 513 <option value="uniform" selected="true">Uniform weights. All points in each neighborhood are weighted equally. (Uniform)</option> | |
| 514 <option value="distance">Weight points by the inverse of their distance. (Distance)</option> | |
| 515 </param> | |
| 516 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" "> | |
| 517 <option value="auto" selected="true">Auto</option> | |
| 518 <option value="ball_tree">BallTree</option> | |
| 519 <option value="kd_tree">KDTree</option> | |
| 520 <option value="brute">Brute-force</option> | |
| 521 </param> | |
| 522 <param argument="leaf_size" type="integer" value="30" label="Leaf size" help="Used with BallTree and KDTree. Affects the time and memory usage of the constructed tree."/> | |
| 523 <!--param name="metric"--> | |
| 524 <!--param name="p"--> | |
| 525 <!--param name="metric_params"--> | |
| 526 </section> | |
| 527 </xml> | |
| 528 | |
| 529 <xml name="svc_advanced_options"> | |
| 530 <section name="options" title="Advanced Options" expanded="False"> | |
| 531 <yield/> | |
| 532 <param argument="kernel" type="select" optional="true" label="Kernel type" help="Kernel type to be used in the algorithm. If none is given, ‘rbf’ will be used."> | |
| 533 <option value="rbf" selected="true">rbf</option> | |
| 534 <option value="linear">linear</option> | |
| 535 <option value="poly">poly</option> | |
| 536 <option value="sigmoid">sigmoid</option> | |
| 537 <option value="precomputed">precomputed</option> | |
| 538 </param> | |
| 539 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/> | |
| 540 <!--TODO: param argument="gamma" float, optional (default=’auto’) --> | |
| 541 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)" | |
| 542 help="Independent term in kernel function. dafault: 0.0 "/> | |
| 543 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | |
| 544 label="Use the shrinking heuristic" help=" "/> | |
| 545 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" | |
| 546 label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/> | |
| 547 <!-- param argument="cache_size"--> | |
| 548 <!--expand macro="class_weight"/--> | |
| 549 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/> | |
| 550 <expand macro="max_iter" default_value="-1" label="Solver maximum number of iterations" help_text="Hard limit on iterations within solver, or -1 for no limit."/> | |
| 551 <!--param argument="decision_function_shape"--> | |
| 552 <expand macro="random_state" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data for probability estimation. A fixed seed allows reproducible results."/> | |
| 553 </section> | |
| 554 </xml> | |
| 555 | |
| 556 <xml name="spectral_clustering_advanced_options"> | |
| 557 <section name="options" title="Advanced Options" expanded="False"> | |
| 558 <expand macro="n_clusters"/> | |
| 559 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use."> | |
| 560 <option value="arpack" selected="true">arpack</option> | |
| 561 <option value="lobpcg">lobpcg</option> | |
| 562 <option value="amg">amg</option> | |
| 563 <!--None--> | |
| 564 </param> | |
| 565 <expand macro="random_state"/> | |
| 566 <expand macro="n_init"/> | |
| 567 <param argument="gamma" type="float" optional="true" value="1.0" label="Kernel scaling factor" help="Scaling factor of RBF, polynomial, exponential chi^2 and sigmoid affinity kernel. Ignored for affinity=''nearest_neighbors''."/> | |
| 568 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. "> | |
| 569 <option value="rbf" selected="true">RBF</option> | |
| 570 <option value="precomputed">precomputed</option> | |
| 571 <option value="nearest_neighbors">Nearset neighbors</option> | |
| 572 </param> | |
| 573 <param argument="n_neighbors" type="integer" optional="true" value="10" label="Number of neighbors" help="Number of neighbors to use when constructing the affinity matrix using the nearest neighbors method. Ignored for affinity=''rbf''"/> | |
| 574 <!--param argument="eigen_tol"--> | |
| 575 <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space."> | |
| 576 <option value="kmeans" selected="true">kmeans</option> | |
| 577 <option value="discretize">discretize</option> | |
| 578 </param> | |
| 579 <param argument="degree" type="integer" optional="true" value="3" | |
| 580 label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/> | |
| 581 <param argument="coef0" type="integer" optional="true" value="1" | |
| 582 label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/> | |
| 583 <!--param argument="kernel_params"--> | |
| 584 </section> | |
| 585 </xml> | |
| 586 | |
| 587 <xml name="minibatch_kmeans_advanced_options"> | |
| 588 <section name="options" title="Advanced Options" expanded="False"> | |
| 589 <expand macro="n_clusters"/> | |
| 590 <expand macro="init"/> | |
| 591 <expand macro="n_init" default_value="3"/> | |
| 592 <expand macro="max_iter" default_value="100"/> | |
| 593 <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ."/> | |
| 594 <expand macro="random_state"/> | |
| 595 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/> | |
| 596 <!--param argument="compute_labels"--> | |
| 597 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help=" | |
| 598 Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia). | |
| 599 To disable, set max_no_improvement to None. "/> | |
| 600 <param argument="init_size" type="integer" optional="true" value="" label="Number of random initialization samples" help="Number of samples to randomly sample for speeding up the initialization . ( default: 3 * batch_size )"/> | |
| 601 <param argument="reassignment_ratio" type="float" optional="true" value="0.01" label="Re-assignment ratio" help="Controls the fraction of the maximum number of counts for a center to be reassigned. Higher values yield better clustering results."/> | |
| 602 </section> | |
| 603 </xml> | |
| 604 | |
| 605 <xml name="kmeans_advanced_options"> | |
| 606 <section name="options" title="Advanced Options" expanded="False"> | |
| 607 <expand macro="n_clusters"/> | |
| 608 <expand macro="init"/> | |
| 609 <expand macro="n_init"/> | |
| 610 <expand macro="max_iter"/> | |
| 611 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence."/> | |
| 612 <!--param argument="precompute_distances"/--> | |
| 613 <expand macro="random_state"/> | |
| 614 <param argument="copy_x" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Use a copy of data for precomputing distances" help="Mofifying the original data introduces small numerical differences caused by subtracting and then adding the data mean."/> | |
| 615 <expand macro="kmeans_algorithm"/> | |
| 616 </section> | |
| 617 </xml> | |
| 618 | |
| 619 <xml name="kmeans_algorithm"> | |
| 620 <param argument="algorithm" type="select" label="K-means algorithm to use:"> | |
| 621 <option value="auto" selected="true">auto</option> | |
| 622 <option value="full">full</option> | |
| 623 <option value="elkan">elkan</option> | |
| 624 </param> | |
| 625 </xml> | |
| 626 | |
| 627 <xml name="birch_advanced_options"> | |
| 628 <section name="options" title="Advanced Options" expanded="False"> | |
| 629 <param argument="threshold" type="float" optional="true" value="0.5" label="Subcluster radius threshold" help="The radius of the subcluster obtained by merging a new sample; the closest subcluster should be less than the threshold to avoid a new subcluster."/> | |
| 630 <param argument="branching_factor" type="integer" optional="true" value="50" label="Maximum number of subclusters per branch" help="Maximum number of CF subclusters in each node."/> | |
| 631 <expand macro="n_clusters" default_value="3"/> | |
| 632 <!--param argument="compute_labels"/--> | |
| 633 </section> | |
| 634 </xml> | |
| 635 | |
| 636 <xml name="dbscan_advanced_options"> | |
| 637 <section name="options" title="Advanced Options" expanded="False"> | |
| 638 <param argument="eps" type="float" optional="true" value="0.5" label="Maximum neighborhood distance" help="The maximum distance between two samples for them to be considered as in the same neighborhood."/> | |
| 639 <param argument="min_samples" type="integer" optional="true" value="5" label="Minimal core point density" help="The number of samples (or total weight) in a neighborhood for a point (including the point itself) to be considered as a core point."/> | |
| 640 <param argument="metric" type="text" optional="true" value="euclidean" label="Metric" help="The metric to use when calculating distance between instances in a feature array."/> | |
| 641 <param argument="algorithm" type="select" label="Pointwise distance computation algorithm" help="The algorithm to be used by the NearestNeighbors module to compute pointwise distances and find nearest neighbors."> | |
| 642 <option value="auto" selected="true">auto</option> | |
| 643 <option value="ball_tree">ball_tree</option> | |
| 644 <option value="kd_tree">kd_tree</option> | |
| 645 <option value="brute">brute</option> | |
| 646 </param> | |
| 647 <param argument="leaf_size" type="integer" optional="true" value="30" label="Leaf size" help="Leaf size passed to BallTree or cKDTree. Memory and time efficieny factor in tree constrution and querying."/> | |
| 648 </section> | |
| 649 </xml> | |
| 650 | |
| 651 <xml name="clustering_algorithms_options"> | |
| 652 <conditional name="algorithm_options"> | |
| 653 <param name="selected_algorithm" type="select" label="Clustering Algorithm"> | |
| 654 <option value="KMeans" selected="true">KMeans</option> | |
| 655 <option value="SpectralClustering">Spectral Clustering</option> | |
| 656 <option value="MiniBatchKMeans">Mini Batch KMeans</option> | |
| 657 <option value="DBSCAN">DBSCAN</option> | |
| 658 <option value="Birch">Birch</option> | |
| 659 </param> | |
| 660 <when value="KMeans"> | |
| 661 <expand macro="kmeans_advanced_options"/> | |
| 662 </when> | |
| 663 <when value="DBSCAN"> | |
| 664 <expand macro="dbscan_advanced_options"/> | |
| 665 </when> | |
| 666 <when value="Birch"> | |
| 667 <expand macro="birch_advanced_options"/> | |
| 668 </when> | |
| 669 <when value="SpectralClustering"> | |
| 670 <expand macro="spectral_clustering_advanced_options"/> | |
| 671 </when> | |
| 672 <when value="MiniBatchKMeans"> | |
| 673 <expand macro="minibatch_kmeans_advanced_options"/> | |
| 674 </when> | |
| 675 </conditional> | |
| 676 </xml> | |
| 677 | |
| 678 <xml name="distance_metrics"> | |
| 679 <param argument="metric" type="select" label="Distance metric" help=" "> | |
| 680 <option value="euclidean" selected="true">euclidean</option> | |
| 681 <option value="cityblock">cityblock</option> | |
| 682 <option value="cosine">cosine</option> | |
| 683 <option value="l1">l1</option> | |
| 684 <option value="l2">l2</option> | |
| 685 <option value="manhattan">manhattan</option> | |
| 686 <yield/> | |
| 687 </param> | |
| 688 </xml> | |
| 689 | |
| 690 <xml name="distance_nonsparse_metrics"> | |
| 691 <option value="braycurtis">braycurtis</option> | |
| 692 <option value="canberra">canberra</option> | |
| 693 <option value="chebyshev">chebyshev</option> | |
| 694 <option value="correlation">correlation</option> | |
| 695 <option value="dice">dice</option> | |
| 696 <option value="hamming">hamming</option> | |
| 697 <option value="jaccard">jaccard</option> | |
| 698 <option value="kulsinski">kulsinski</option> | |
| 699 <option value="mahalanobis">mahalanobis</option> | |
| 700 <option value="matching">matching</option> | |
| 701 <option value="minkowski">minkowski</option> | |
| 702 <option value="rogerstanimoto">rogerstanimoto</option> | |
| 703 <option value="russellrao">russellrao</option> | |
| 704 <option value="seuclidean">seuclidean</option> | |
| 705 <option value="sokalmichener">sokalmichener</option> | |
| 706 <option value="sokalsneath">sokalsneath</option> | |
| 707 <option value="sqeuclidean">sqeuclidean</option> | |
| 708 <option value="yule">yule</option> | |
| 709 </xml> | |
| 710 | |
| 711 <xml name="pairwise_kernel_metrics"> | |
| 712 <param argument="metric" type="select" label="Pirwise Kernel metric" help=" "> | |
| 713 <option value="rbf" selected="true">rbf</option> | |
| 714 <option value="sigmoid">sigmoid</option> | |
| 715 <option value="polynomial">polynomial</option> | |
| 716 <option value="linear" selected="true">linear</option> | |
| 717 <option value="chi2">chi2</option> | |
| 718 <option value="additive_chi2">additive_chi2</option> | |
| 719 </param> | |
| 720 </xml> | |
| 721 | |
| 722 <xml name="sparse_pairwise_metric_functions"> | |
| 723 <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:"> | |
| 724 <option value="euclidean_distances" selected="true">Euclidean distance matrix</option> | |
| 725 <option value="pairwise_distances">Distance matrix</option> | |
| 726 <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option> | |
| 727 <yield/> | |
| 728 </param> | |
| 729 </xml> | |
| 730 | |
| 731 <xml name="pairwise_metric_functions"> | |
| 732 <option value="additive_chi2_kernel" >Additive chi-squared kernel</option> | |
| 733 <option value="chi2_kernel">Exponential chi-squared kernel</option> | |
| 734 <option value="linear_kernel">Linear kernel</option> | |
| 735 <option value="manhattan_distances">L1 distances</option> | |
| 736 <option value="pairwise_kernels">Kernel</option> | |
| 737 <option value="polynomial_kernel">Polynomial kernel</option> | |
| 738 <option value="rbf_kernel">Gaussian (rbf) kernel</option> | |
| 739 <option value="laplacian_kernel">Laplacian kernel</option> | |
| 740 </xml> | |
| 741 | |
| 742 <xml name="sparse_pairwise_condition"> | |
| 743 <when value="pairwise_distances"> | |
| 744 <section name="options" title="Advanced Options" expanded="False"> | |
| 745 <expand macro="distance_metrics"> | |
| 746 <yield/> | |
| 747 </expand> | |
| 748 </section> | |
| 749 </when> | |
| 750 <when value="euclidean_distances"> | |
| 751 <section name="options" title="Advanced Options" expanded="False"> | |
| 752 <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" | |
| 753 label="Return squared Euclidean distances" help=" "/> | |
| 754 </section> | |
| 755 </when> | |
| 756 </xml> | |
| 757 | |
| 758 <xml name="argmin_distance_condition"> | |
| 759 <when value="pairwise_distances_argmin"> | |
| 760 <section name="options" title="Advanced Options" expanded="False"> | |
| 761 <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed."/> | |
| 762 <expand macro="distance_metrics"> | |
| 763 <yield/> | |
| 764 </expand> | |
| 765 <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run."/> | |
| 766 </section> | |
| 767 </when> | |
| 768 </xml> | |
| 769 | |
| 770 <xml name="sparse_preprocessors"> | |
| 771 <param name="selected_pre_processor" type="select" label="Select a preprocessor:"> | |
| 772 <option value="StandardScaler" selected="true">Standard Scaler (Standardizes features by removing the mean and scaling to unit variance)</option> | |
| 773 <option value="Binarizer">Binarizer (Binarizes data)</option> | |
| 774 <option value="MaxAbsScaler">Max Abs Scaler (Scales features by their maximum absolute value)</option> | |
| 775 <option value="Normalizer">Normalizer (Normalizes samples individually to unit norm)</option> | |
| 776 <yield/> | |
| 777 </param> | |
| 778 </xml> | |
| 779 | |
| 780 <xml name="sparse_preprocessors_ext"> | |
| 781 <expand macro="sparse_preprocessors"> | |
| 782 <option value="KernelCenterer">Kernel Centerer (Centers a kernel matrix)</option> | |
| 783 <option value="MinMaxScaler">Minmax Scaler (Scales features to a range)</option> | |
| 784 <option value="PolynomialFeatures">Polynomial Features (Generates polynomial and interaction features)</option> | |
| 785 <option value="RobustScaler">Robust Scaler (Scales features using outlier-invariance statistics)</option> | |
| 786 <option value="QuantileTransformer">QuantileTransformer (Transform features using quantiles information)</option> | |
| 787 <option value="PowerTransformer">PowerTransformer (Apply a power transform featurewise to make data more Gaussian-like)</option> | |
| 788 <option value="KBinsDiscretizer">KBinsDiscretizer (Bin continuous data into intervals.)</option> | |
| 789 </expand> | |
| 790 </xml> | |
| 791 | |
| 792 <xml name="sparse_preprocessor_options"> | |
| 793 <when value="Binarizer"> | |
| 794 <section name="options" title="Advanced Options" expanded="False"> | |
| 795 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | |
| 796 label="Use a copy of data for precomputing binarization" help=" "/> | |
| 797 <param argument="threshold" type="float" optional="true" value="0.0" | |
| 798 label="Threshold" | |
| 799 help="Feature values below or equal to this are replaced by 0, above it by 1. Threshold may not be less than 0 for operations on sparse matrices. "/> | |
| 800 </section> | |
| 801 </when> | |
| 802 <when value="StandardScaler"> | |
| 803 <section name="options" title="Advanced Options" expanded="False"> | |
| 804 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | |
| 805 label="Use a copy of data for performing inplace scaling" help=" "/> | |
| 806 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | |
| 807 label="Center the data before scaling" help=" "/> | |
| 808 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | |
| 809 label="Scale the data to unit variance (or unit standard deviation)" help=" "/> | |
| 810 </section> | |
| 811 </when> | |
| 812 <when value="MaxAbsScaler"> | |
| 813 <section name="options" title="Advanced Options" expanded="False"> | |
| 814 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | |
| 815 label="Use a copy of data for precomputing scaling" help=" "/> | |
| 816 </section> | |
| 817 </when> | |
| 818 <when value="Normalizer"> | |
| 819 <section name="options" title="Advanced Options" expanded="False"> | |
| 820 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" "> | |
| 821 <option value="l1" selected="true">l1</option> | |
| 822 <option value="l2">l2</option> | |
| 823 <option value="max">max</option> | |
| 824 </param> | |
| 825 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | |
| 826 label="Use a copy of data for precomputing row normalization" help=" "/> | |
| 827 </section> | |
| 828 </when> | |
| 829 <yield/> | |
| 830 </xml> | |
| 831 | |
| 832 <xml name="sparse_preprocessor_options_ext"> | |
| 833 <expand macro="sparse_preprocessor_options"> | |
| 834 <when value="KernelCenterer"> | |
| 835 <section name="options" title="Advanced Options" expanded="False"> | |
| 836 </section> | |
| 837 </when> | |
| 838 <when value="MinMaxScaler"> | |
| 839 <section name="options" title="Advanced Options" expanded="False"> | |
| 840 <param argument="feature_range" type="text" value="(0, 1)" optional="true" help="Desired range of transformed data. None or tuple (min, max). None equals to (0, 1)"/> | |
| 841 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" | |
| 842 label="Use a copy of data for precomputing normalization" help=" "/> | |
| 843 </section> | |
| 844 </when> | |
| 845 <when value="PolynomialFeatures"> | |
| 846 <section name="options" title="Advanced Options" expanded="False"> | |
| 847 <param argument="degree" type="integer" optional="true" value="2" label="The degree of the polynomial features " help=""/> | |
| 848 <param argument="interaction_only" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Produce interaction features only" help="(Features that are products of at most degree distinct input features) "/> | |
| 849 <param argument="include_bias" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Include a bias column" help="Feature in which all polynomial powers are zero "/> | |
| 850 </section> | |
| 851 </when> | |
| 852 <when value="RobustScaler"> | |
| 853 <section name="options" title="Advanced Options" expanded="False"> | |
| 854 <!--=True, =True, copy=True--> | |
| 855 <param argument="with_centering" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" | |
| 856 label="Center the data before scaling" help=" "/> | |
| 857 <param argument="with_scaling" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" | |
| 858 label="Scale the data to interquartile range" help=" "/> | |
| 859 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" | |
| 860 label="Use a copy of data for inplace scaling" help=" "/> | |
| 861 </section> | |
| 862 </when> | |
| 863 <when value="QuantileTransformer"> | |
| 864 <section name="options" title="Advanced Options" expanded="False"> | |
| 865 <param name="n_quantiles" type="integer" value="1000" min="0" label="Number of quantiles to be computed" /> | |
| 866 <param name="output_distribution" type="select" label="Marginal distribution for the transformed data"> | |
| 867 <option value="uniform" selected="true">uniform</option> | |
| 868 <option value="normal">normal</option> | |
| 869 </param> | |
| 870 <param name="ignore_implicit_zeros" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to discard sparse entries" help="Only applies to sparse matrices. If False, sparse entries are treated as zeros"/> | |
| 871 <param name="subsample" type="integer" value="100000" label="Maximum number of samples used to estimate the quantiles for computational efficiency" help="Note that the subsampling procedure may differ for value-identical sparse and dense matrices."/> | |
| 872 <expand macro="random_state" help_text="This is used by subsampling and smoothing noise"/> | |
| 873 </section> | |
| 874 </when> | |
| 875 <when value="PowerTransformer"> | |
| 876 <section name="options" title="Advanced Options" expanded="False"> | |
| 877 <param name="method" type="select" label="The power transform method"> | |
| 878 <option value="yeo-johnson" selected="true">yeo-johnson (works with positive and negative values)</option> | |
| 879 <option value="box-cox">box-cox (might perform better, but only works with strictly positive values)</option> | |
| 880 </param> | |
| 881 <param name="standardize" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Whether to apply zero-mean, unit-variance normalization to the transformed output."/> | |
| 882 </section> | |
| 883 </when> | |
| 884 <when value="KBinsDiscretizer"> | |
| 885 <section name="options" title="Advanced Options" expanded="False"> | |
| 886 <param name="n_bins" type="integer" value="5" min="2" label="The number of bins to produce"/> | |
| 887 <param name="encode" type="select" label="Method used to encode the transformed result"> | |
| 888 <option value="onehot" selected="true">onehot (encode the transformed result with one-hot encoding and return a sparse matrix)</option> | |
| 889 <option value="onehot-dense">onehot-dense (encode the transformed result with one-hot encoding and return a dense array)</option> | |
| 890 <option value="ordinal">ordinal (return the bin identifier encoded as an integer value)</option> | |
| 891 </param> | |
| 892 <param name="strategy" type="select" label="Strategy used to define the widths of the bins"> | |
| 893 <option value="uniform">uniform (all bins in each feature have identical widths)</option> | |
| 894 <option value="quantile" selected="true">quantile (all bins in each feature have the same number of points)</option> | |
| 895 <option value="kmeans">kmeans (values in each bin have the same nearest center of a 1D k-means cluster)</option> | |
| 896 </param> | |
| 897 </section> | |
| 898 </when> | |
| 899 </expand> | |
| 900 </xml> | |
| 901 | |
| 902 <xml name="cv_splitter"> | |
| 903 <option value="default" selected="true">default splitter</option> | |
| 904 <option value="KFold">KFold</option> | |
| 905 <option value="StratifiedKFold">StratifiedKFold</option> | |
| 906 <option value="LeaveOneOut">LeaveOneOut</option> | |
| 907 <option value="LeavePOut">LeavePOut</option> | |
| 908 <option value="RepeatedKFold">RepeatedKFold</option> | |
| 909 <option value="RepeatedStratifiedKFold">RepeatedStratifiedKFold</option> | |
| 910 <option value="ShuffleSplit">ShuffleSplit</option> | |
| 911 <option value="StratifiedShuffleSplit">StratifiedShuffleSplit</option> | |
| 912 <option value="TimeSeriesSplit">TimeSeriesSplit</option> | |
| 913 <option value="PredefinedSplit">PredefinedSplit</option> | |
| 914 <option value="OrderedKFold">OrderedKFold</option> | |
| 915 <option value="RepeatedOrderedKFold">RepeatedOrderedKFold</option> | |
| 916 <yield/> | |
| 917 </xml> | |
| 918 | |
| 919 <xml name="cv_splitter_options"> | |
| 920 <when value="default"> | |
| 921 <expand macro="cv_n_splits"/> | |
| 922 </when> | |
| 923 <when value="KFold"> | |
| 924 <expand macro="cv_n_splits"/> | |
| 925 <expand macro="cv_shuffle"/> | |
| 926 <expand macro="random_state"/> | |
| 927 </when> | |
| 928 <when value="StratifiedKFold"> | |
| 929 <expand macro="cv_n_splits"/> | |
| 930 <expand macro="cv_shuffle"/> | |
| 931 <expand macro="random_state"/> | |
| 932 </when> | |
| 933 <when value="LeaveOneOut"> | |
| 934 </when> | |
| 935 <when value="LeavePOut"> | |
| 936 <param argument="p" type="integer" value="" label="p" help="Integer. Size of the test sets."/> | |
| 937 </when> | |
| 938 <when value="RepeatedKFold"> | |
| 939 <expand macro="cv_n_splits" value="5"/> | |
| 940 <param argument="n_repeats" type="integer" value="10" label="n_repeats" help="Number of times cross-validator needs to be repeated." /> | |
| 941 <expand macro="random_state" /> | |
| 942 </when> | |
| 943 <when value="RepeatedStratifiedKFold"> | |
| 944 <expand macro="cv_n_splits" value="5"/> | |
| 945 <param argument="n_repeats" type="integer" value="10" label="n_repeats" help="Number of times cross-validator needs to be repeated." /> | |
| 946 <expand macro="random_state" /> | |
| 947 </when> | |
| 948 <when value="ShuffleSplit"> | |
| 949 <expand macro="cv_n_splits" value="10" help="Number of re-shuffling and splitting iterations."/> | |
| 950 <expand macro="cv_test_size" value="0.1" /> | |
| 951 <expand macro="random_state"/> | |
| 952 </when> | |
| 953 <when value="StratifiedShuffleSplit"> | |
| 954 <expand macro="cv_n_splits" value="10" help="Number of re-shuffling and splitting iterations."/> | |
| 955 <expand macro="cv_test_size" value="0.1" /> | |
| 956 <expand macro="random_state"/> | |
| 957 </when> | |
| 958 <when value="TimeSeriesSplit"> | |
| 959 <expand macro="cv_n_splits"/> | |
| 960 <param argument="max_train_size" type="integer" value="" optional="true" label="Maximum size of the training set" help="Maximum size for a single training set." /> | |
| 961 </when> | |
| 962 <when value="PredefinedSplit"> | |
| 963 <param argument="test_fold" type="text" value="" area="true" label="test_fold" help="List, e.g., [0, 1, -1, 1], represents two test sets, [X[0]] and [X[1], X[3]], X[2] is excluded from any test set due to '-1'."/> | |
| 964 </when> | |
| 965 <when value="OrderedKFold"> | |
| 966 <expand macro="cv_n_splits"/> | |
| 967 <expand macro="cv_shuffle"/> | |
| 968 <expand macro="random_state"/> | |
| 969 </when> | |
| 970 <when value="RepeatedOrderedKFold"> | |
| 971 <expand macro="cv_n_splits"/> | |
| 972 <param argument="n_repeats" type="integer" value="5"/> | |
| 973 <expand macro="random_state"/> | |
| 974 </when> | |
| 975 <yield/> | |
| 976 </xml> | |
| 977 | |
| 978 <xml name="cv"> | |
| 979 <conditional name="cv_selector"> | |
| 980 <param name="selected_cv" type="select" label="Select the cv splitter:"> | |
| 981 <expand macro="cv_splitter"> | |
| 982 <option value="GroupKFold">GroupKFold</option> | |
| 983 <option value="GroupShuffleSplit">GroupShuffleSplit</option> | |
| 984 <option value="LeaveOneGroupOut">LeaveOneGroupOut</option> | |
| 985 <option value="LeavePGroupsOut">LeavePGroupsOut</option> | |
| 986 </expand> | |
| 987 </param> | |
| 988 <expand macro="cv_splitter_options"> | |
| 989 <when value="GroupKFold"> | |
| 990 <expand macro="cv_n_splits"/> | |
| 991 <expand macro="cv_groups" /> | |
| 992 </when> | |
| 993 <when value="GroupShuffleSplit"> | |
| 994 <expand macro="cv_n_splits" value="5"/> | |
| 995 <expand macro="cv_test_size"/> | |
| 996 <expand macro="random_state"/> | |
| 997 <expand macro="cv_groups"/> | |
| 998 </when> | |
| 999 <when value="LeaveOneGroupOut"> | |
| 1000 <expand macro="cv_groups"/> | |
| 1001 </when> | |
| 1002 <when value="LeavePGroupsOut"> | |
| 1003 <param argument="n_groups" type="integer" value="" label="n_groups" help="Number of groups (p) to leave out in the test split." /> | |
| 1004 <expand macro="cv_groups"/> | |
| 1005 </when> | |
| 1006 </expand> | |
| 1007 </conditional> | |
| 1008 </xml> | |
| 1009 | |
| 1010 <xml name="cv_reduced" token_label="Select the cv splitter"> | |
| 1011 <conditional name="cv_selector"> | |
| 1012 <param name="selected_cv" type="select" label="@LABEL@"> | |
| 1013 <expand macro="cv_splitter"/> | |
| 1014 </param> | |
| 1015 <expand macro="cv_splitter_options"/> | |
| 1016 </conditional> | |
| 1017 </xml> | |
| 1018 | |
| 1019 <xml name="cv_n_splits" token_value="3" token_help="Number of folds. Must be at least 2."> | |
| 1020 <param argument="n_splits" type="integer" value="@VALUE@" min="1" label="n_splits" help="@HELP@"/> | |
| 1021 </xml> | |
| 1022 | |
| 1023 <xml name="cv_shuffle"> | |
| 1024 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to shuffle data before splitting" /> | |
| 1025 </xml> | |
| 1026 | |
| 1027 <xml name="cv_test_size" token_value="0.2"> | |
| 1028 <param argument="test_size" type="float" value="@VALUE@" min="0.0" label="Portion or number of the test set" help="0.0-1.0, proportion of the dataset to include in the test split; >1, integer only, the absolute number of test samples "/> | |
| 1029 </xml> | |
| 1030 | |
| 1031 <xml name="cv_groups" > | |
| 1032 <section name="groups_selector" title="Groups column selector" expanded="true"> | |
| 1033 <param name="infile_g" type="data" format="tabular" label="Choose dataset containing groups info:"/> | |
| 1034 <param name="header_g" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
| 1035 <conditional name="column_selector_options_g"> | |
| 1036 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option_g" col_name="col_g" multiple="False" infile="infile_g"/> | |
| 1037 </conditional> | |
| 1038 </section> | |
| 1039 </xml> | |
| 1040 | |
| 1041 <xml name="train_test_split_params"> | |
| 1042 <conditional name="split_algos"> | |
| 1043 <param name="shuffle" type="select" label="Select the splitting method"> | |
| 1044 <option value="None">No shuffle</option> | |
| 1045 <option value="simple" selected="true">ShuffleSplit</option> | |
| 1046 <option value="stratified">StratifiedShuffleSplit -- target values serve as class labels</option> | |
| 1047 <option value="group">GroupShuffleSplit or split by group names</option> | |
| 1048 </param> | |
| 1049 <when value="None"> | |
| 1050 <expand macro="train_test_split_test_size"/> | |
| 1051 </when> | |
| 1052 <when value="simple"> | |
| 1053 <expand macro="train_test_split_test_size"/> | |
| 1054 <expand macro="random_state"/> | |
| 1055 </when> | |
| 1056 <when value="stratified"> | |
| 1057 <expand macro="train_test_split_test_size"/> | |
| 1058 <expand macro="random_state"/> | |
| 1059 </when> | |
| 1060 <when value="group"> | |
| 1061 <expand macro="train_test_split_test_size" optional="true"/> | |
| 1062 <expand macro="random_state"/> | |
| 1063 <param argument="group_names" type="text" value="" optional="true" label="Type in group names instead" | |
| 1064 help="For example: chr6, chr7. This parameter is optional. If used, it will override the holdout size and random seed."/> | |
| 1065 <yield/> | |
| 1066 </when> | |
| 1067 </conditional> | |
| 1068 <!--param argument="train_size" type="float" optional="True" value="" label="Train size:"/>--> | |
| 1069 </xml> | |
| 1070 | |
| 1071 <xml name="train_test_split_test_size" token_optional="false"> | |
| 1072 <param name="test_size" type="float" value="0.2" optional="@OPTIONAL@" label="Holdout size" help="Leass than 1, for preportion; greater than 1 (integer), for number of samples."/> | |
| 1073 </xml> | |
| 1074 | |
| 1075 <xml name="feature_selection_algorithms"> | |
| 1076 <option value="SelectKBest" selected="true">SelectKBest - Select features according to the k highest scores</option> | |
| 1077 <option value="GenericUnivariateSelect">GenericUnivariateSelect - Univariate feature selector with configurable strategy</option> | |
| 1078 <option value="SelectPercentile">SelectPercentile - Select features according to a percentile of the highest scores</option> | |
| 1079 <option value="SelectFpr">SelectFpr - Filter: Select the p-values below alpha based on a FPR test</option> | |
| 1080 <option value="SelectFdr">SelectFdr - Filter: Select the p-values for an estimated false discovery rate</option> | |
| 1081 <option value="SelectFwe">SelectFwe - Filter: Select the p-values corresponding to Family-wise error rate</option> | |
| 1082 <option value="VarianceThreshold">VarianceThreshold - Feature selector that removes all low-variance features</option> | |
| 1083 <option value="SelectFromModel">SelectFromModel - Meta-transformer for selecting features based on importance weights</option> | |
| 1084 <option value="RFE">RFE - Feature ranking with recursive feature elimination</option> | |
| 1085 <option value="RFECV">RFECV - Feature ranking with recursive feature elimination and cross-validated selection of the best number of features</option> | |
| 1086 <yield/> | |
| 1087 </xml> | |
| 1088 | |
| 1089 <xml name="feature_selection_algorithm_details"> | |
| 1090 <when value="GenericUnivariateSelect"> | |
| 1091 <expand macro="feature_selection_score_function" /> | |
| 1092 <section name="options" title="Advanced Options" expanded="False"> | |
| 1093 <param argument="mode" type="select" label="Feature selection mode"> | |
| 1094 <option value="percentile">percentile</option> | |
| 1095 <option value="k_best">k_best</option> | |
| 1096 <option value="fpr">fpr</option> | |
| 1097 <option value="fdr">fdr</option> | |
| 1098 <option value="fwe">fwe</option> | |
| 1099 </param> | |
| 1100 <param argument="param" type="float" value="" optional="true" label="Parameter of the corresponding mode" help="float or int depending on the feature selection mode" /> | |
| 1101 </section> | |
| 1102 </when> | |
| 1103 <when value="SelectPercentile"> | |
| 1104 <expand macro="feature_selection_score_function" /> | |
| 1105 <section name="options" title="Advanced Options" expanded="False"> | |
| 1106 <param argument="percentile" type="integer" value="10" optional="True" label="Percent of features to keep" /> | |
| 1107 </section> | |
| 1108 </when> | |
| 1109 <when value="SelectKBest"> | |
| 1110 <expand macro="feature_selection_score_function" /> | |
| 1111 <section name="options" title="Advanced Options" expanded="False"> | |
| 1112 <param argument="k" type="integer" value="10" optional="True" label="Number of top features to select" help="No 'all' option is supported." /> | |
| 1113 </section> | |
| 1114 </when> | |
| 1115 <when value="SelectFpr"> | |
| 1116 <expand macro="feature_selection_score_function" /> | |
| 1117 <section name="options" title="Advanced Options" expanded="False"> | |
| 1118 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest p-value for features to be kept."/> | |
| 1119 </section> | |
| 1120 </when> | |
| 1121 <when value="SelectFdr"> | |
| 1122 <expand macro="feature_selection_score_function" /> | |
| 1123 <section name="options" title="Advanced Options" expanded="False"> | |
| 1124 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/> | |
| 1125 </section> | |
| 1126 </when> | |
| 1127 <when value="SelectFwe"> | |
| 1128 <expand macro="feature_selection_score_function" /> | |
| 1129 <section name="options" title="Advanced Options" expanded="False"> | |
| 1130 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/> | |
| 1131 </section> | |
| 1132 </when> | |
| 1133 <when value="VarianceThreshold"> | |
| 1134 <section name="options" title="Options" expanded="False"> | |
| 1135 <param argument="threshold" type="float" value="0.0" optional="True" label="Threshold" help="Features with a training-set variance lower than this threshold will be removed."/> | |
| 1136 </section> | |
| 1137 </when> | |
| 1138 </xml> | |
| 1139 | |
| 1140 <xml name="feature_selection_SelectFromModel"> | |
| 1141 <when value="SelectFromModel"> | |
| 1142 <conditional name="model_inputter"> | |
| 1143 <param name="input_mode" type="select" label="Construct a new estimator from a selection list?" > | |
| 1144 <option value="new" selected="true">Yes</option> | |
| 1145 <option value="prefitted">No. Load a prefitted estimator</option> | |
| 1146 </param> | |
| 1147 <when value="new"> | |
| 1148 <expand macro="estimator_selector_fs"/> | |
| 1149 </when> | |
| 1150 <when value="prefitted"> | |
| 1151 <param name="fitted_estimator" type="data" format='zip' label="Load a prefitted estimator" /> | |
| 1152 </when> | |
| 1153 </conditional> | |
| 1154 <expand macro="feature_selection_SelectFromModel_options"/> | |
| 1155 </when> | |
| 1156 </xml> | |
| 1157 | |
| 1158 <xml name="feature_selection_SelectFromModel_no_prefitted"> | |
| 1159 <when value="SelectFromModel"> | |
| 1160 <conditional name="model_inputter"> | |
| 1161 <param name="input_mode" type="select" label="Construct a new estimator from a selection list?" > | |
| 1162 <option value="new" selected="true">Yes</option> | |
| 1163 </param> | |
| 1164 <when value="new"> | |
| 1165 <expand macro="estimator_selector_all"/> | |
| 1166 </when> | |
| 1167 </conditional> | |
| 1168 <expand macro="feature_selection_SelectFromModel_options"/> | |
| 1169 </when> | |
| 1170 </xml> | |
| 1171 | |
| 1172 <xml name="feature_selection_SelectFromModel_options"> | |
| 1173 <section name="options" title="Advanced Options" expanded="False"> | |
| 1174 <param argument="threshold" type="text" value="" optional="true" label="threshold" help="The threshold value to use for feature selection. e.g. 'mean', 'median', '1.25*mean'." /> | |
| 1175 <param argument="norm_order" type="integer" value="1" label="norm_order" help="Order of the norm used to filter the vectors of coefficients below threshold in the case where the coef_ attribute of the estimator is of dimension 2. " /> | |
| 1176 <param argument="max_features" type="integer" value="" optional="true" label="The maximum number of features selected scoring above threshold" help="To disable threshold and only select based on max_features, set threshold=-np.inf."/> | |
| 1177 </section> | |
| 1178 </xml> | |
| 1179 | |
| 1180 <xml name="feature_selection_RFE"> | |
| 1181 <when value="RFE"> | |
| 1182 <yield/> | |
| 1183 <section name="options" title="Advanced Options" expanded="False"> | |
| 1184 <param argument="n_features_to_select" type="integer" value="" optional="true" label="n_features_to_select" help="The number of features to select. If None, half of the features are selected." /> | |
| 1185 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " /> | |
| 1186 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> | |
| 1187 </section> | |
| 1188 </when> | |
| 1189 </xml> | |
| 1190 | |
| 1191 <xml name="feature_selection_RFECV_fs"> | |
| 1192 <when value="RFECV"> | |
| 1193 <yield/> | |
| 1194 <section name="options" title="Advanced Options" expanded="False"> | |
| 1195 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " /> | |
| 1196 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/> | |
| 1197 <expand macro="cv"/> | |
| 1198 <expand macro="scoring_selection"/> | |
| 1199 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> | |
| 1200 </section> | |
| 1201 </when> | |
| 1202 </xml> | |
| 1203 | |
| 1204 <xml name="feature_selection_RFECV_pipeline"> | |
| 1205 <when value="RFECV"> | |
| 1206 <yield/> | |
| 1207 <section name="options" title="Advanced Options" expanded="False"> | |
| 1208 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " /> | |
| 1209 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/> | |
| 1210 <expand macro="cv_reduced"/> | |
| 1211 <!-- TODO: group splitter support--> | |
| 1212 <expand macro="scoring_selection"/> | |
| 1213 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> | |
| 1214 </section> | |
| 1215 </when> | |
| 1216 </xml> | |
| 1217 | |
| 1218 <xml name="feature_selection_DyRFECV_fs"> | |
| 1219 <when value="DyRFECV"> | |
| 1220 <yield/> | |
| 1221 <section name="options" title="Advanced Options" expanded="False"> | |
| 1222 <param argument="step" type="text" size="30" value="1" label="step" optional="true" help="Default = 1. Support float, int and list." > | |
| 1223 <sanitizer> | |
| 1224 <valid initial="default"> | |
| 1225 <add value="["/> | |
| 1226 <add value="]"/> | |
| 1227 </valid> | |
| 1228 </sanitizer> | |
| 1229 </param> | |
| 1230 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/> | |
| 1231 <expand macro="cv"/> | |
| 1232 <expand macro="scoring_selection"/> | |
| 1233 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> | |
| 1234 </section> | |
| 1235 </when> | |
| 1236 </xml> | |
| 1237 | |
| 1238 <xml name="feature_selection_pipeline"> | |
| 1239 <!--compare to `feature_selection_fs`, no fitted estimator for SelectFromModel and no custom estimator for RFE and RFECV--> | |
| 1240 <conditional name="fs_algorithm_selector"> | |
| 1241 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm"> | |
| 1242 <expand macro="feature_selection_algorithms"/> | |
| 1243 </param> | |
| 1244 <expand macro="feature_selection_algorithm_details"/> | |
| 1245 <expand macro="feature_selection_SelectFromModel_no_prefitted"/> | |
| 1246 <expand macro="feature_selection_RFE"> | |
| 1247 <expand macro="estimator_selector_all"/> | |
| 1248 </expand> | |
| 1249 <expand macro="feature_selection_RFECV_pipeline"> | |
| 1250 <expand macro="estimator_selector_all"/> | |
| 1251 </expand> | |
| 1252 <!-- TODO: add DyRFECV to pipeline--> | |
| 1253 </conditional> | |
| 1254 </xml> | |
| 1255 | |
| 1256 <xml name="feature_selection_fs"> | |
| 1257 <conditional name="fs_algorithm_selector"> | |
| 1258 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm"> | |
| 1259 <expand macro="feature_selection_algorithms"> | |
| 1260 <option value="DyRFECV">DyRFECV - Extended RFECV with changeable steps</option> | |
| 1261 </expand> | |
| 1262 </param> | |
| 1263 <expand macro="feature_selection_algorithm_details"/> | |
| 1264 <expand macro="feature_selection_SelectFromModel"/> | |
| 1265 <expand macro="feature_selection_RFE"> | |
| 1266 <expand macro="estimator_selector_fs"/> | |
| 1267 </expand> | |
| 1268 <expand macro="feature_selection_RFECV_fs"> | |
| 1269 <expand macro="estimator_selector_fs"/> | |
| 1270 </expand> | |
| 1271 <expand macro="feature_selection_DyRFECV_fs"> | |
| 1272 <expand macro="estimator_selector_fs"/> | |
| 1273 </expand> | |
| 1274 </conditional> | |
| 1275 </xml> | |
| 1276 | |
| 1277 <xml name="feature_selection_score_function"> | |
| 1278 <param argument="score_func" type="select" label="Select a score function"> | |
| 1279 <option value="chi2">chi2 - Compute chi-squared stats between each non-negative feature and class</option> | |
| 1280 <option value="f_classif">f_classif - Compute the ANOVA F-value for the provided sample</option> | |
| 1281 <option value="f_regression">f_regression - Univariate linear regression tests</option> | |
| 1282 <option value="mutual_info_classif">mutual_info_classif - Estimate mutual information for a discrete target variable</option> | |
| 1283 <option value="mutual_info_regression">mutual_info_regression - Estimate mutual information for a continuous target variable</option> | |
| 1284 </param> | |
| 1285 </xml> | |
| 1286 | |
| 1287 <xml name="model_validation_common_options"> | |
| 1288 <expand macro="cv"/> | |
| 1289 <expand macro="verbose"/> | |
| 1290 <yield/> | |
| 1291 </xml> | |
| 1292 | |
| 1293 <xml name="scoring_selection"> | |
| 1294 <conditional name="scoring"> | |
| 1295 <param name="primary_scoring" type="select" multiple="false" label="Select the primary metric (scoring):" help="Metric to refit the best estimator."> | |
| 1296 <option value="default" selected="true">default with estimator</option> | |
| 1297 <option value="accuracy">Classification -- 'accuracy'</option> | |
| 1298 <option value="balanced_accuracy">Classification -- 'balanced_accuracy'</option> | |
| 1299 <option value="average_precision">Classification -- 'average_precision'</option> | |
| 1300 <option value="f1">Classification -- 'f1'</option> | |
| 1301 <option value="f1_micro">Classification -- 'f1_micro'</option> | |
| 1302 <option value="f1_macro">Classification -- 'f1_macro'</option> | |
| 1303 <option value="f1_weighted">Classification -- 'f1_weighted'</option> | |
| 1304 <option value="f1_samples">Classification -- 'f1_samples'</option> | |
| 1305 <option value="neg_log_loss">Classification -- 'neg_log_loss'</option> | |
| 1306 <option value="precision">Classification -- 'precision'</option> | |
| 1307 <option value="precision_micro">Classification -- 'precision_micro'</option> | |
| 1308 <option value="precision_macro">Classification -- 'precision_macro'</option> | |
| 1309 <option value="precision_wighted">Classification -- 'precision_wighted'</option> | |
| 1310 <option value="precision_samples">Classification -- 'precision_samples'</option> | |
| 1311 <option value="recall">Classification -- 'recall'</option> | |
| 1312 <option value="recall_micro">Classification -- 'recall_micro'</option> | |
| 1313 <option value="recall_macro">Classification -- 'recall_macro'</option> | |
| 1314 <option value="recall_wighted">Classification -- 'recall_wighted'</option> | |
| 1315 <option value="recall_samples">Classification -- 'recall_samples'</option> | |
| 1316 <option value="roc_auc">Classification -- 'roc_auc'</option> | |
| 1317 <option value="explained_variance">Regression -- 'explained_variance'</option> | |
| 1318 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option> | |
| 1319 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option> | |
| 1320 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option> | |
| 1321 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option> | |
| 1322 <option value="r2">Regression -- 'r2'</option> | |
| 1323 <option value="max_error">Regression -- 'max_error'</option> | |
| 1324 <option value="binarize_auc_scorer">anomaly detection -- binarize_auc_scorer</option> | |
| 1325 <option value="binarize_average_precision_scorer">anomaly detection -- binarize_average_precision_scorer</option> | |
| 1326 </param> | |
| 1327 <when value="default"/> | |
| 1328 <when value="accuracy"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1329 <when value="balanced_accuracy"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1330 <when value="average_precision"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1331 <when value="f1"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1332 <when value="f1_micro"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1333 <when value="f1_macro"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1334 <when value="f1_weighted"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1335 <when value="f1_samples"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1336 <when value="neg_log_loss"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1337 <when value="precision"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1338 <when value="precision_micro"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1339 <when value="precision_macro"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1340 <when value="precision_wighted"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1341 <when value="precision_samples"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1342 <when value="recall"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1343 <when value="recall_micro"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1344 <when value="recall_macro"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1345 <when value="recall_wighted"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1346 <when value="recall_samples"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1347 <when value="roc_auc"><expand macro="secondary_scoring_selection_classification"/></when> | |
| 1348 <when value="explained_variance"><expand macro="secondary_scoring_selection_regression"/></when> | |
| 1349 <when value="neg_mean_absolute_error"><expand macro="secondary_scoring_selection_regression"/></when> | |
| 1350 <when value="neg_mean_squared_error"><expand macro="secondary_scoring_selection_regression"/></when> | |
| 1351 <when value="neg_mean_squared_log_error"><expand macro="secondary_scoring_selection_regression"/></when> | |
| 1352 <when value="neg_median_absolute_error"><expand macro="secondary_scoring_selection_regression"/></when> | |
| 1353 <when value="r2"><expand macro="secondary_scoring_selection_regression"/></when> | |
| 1354 <when value="max_error"><expand macro="secondary_scoring_selection_regression"/></when> | |
| 1355 <when value="binarize_auc_scorer"><expand macro="secondary_scoring_selection_anormaly"/></when> | |
| 1356 <when value="binarize_average_precision_scorer"><expand macro="secondary_scoring_selection_anormaly"/></when> | |
| 1357 </conditional> | |
| 1358 </xml> | |
| 1359 | |
| 1360 <xml name="secondary_scoring_selection_classification"> | |
| 1361 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored."> | |
| 1362 <option value="accuracy">Classification -- 'accuracy'</option> | |
| 1363 <option value="balanced_accuracy">Classification -- 'balanced_accuracy'</option> | |
| 1364 <option value="average_precision">Classification -- 'average_precision'</option> | |
| 1365 <option value="f1">Classification -- 'f1'</option> | |
| 1366 <option value="f1_micro">Classification -- 'f1_micro'</option> | |
| 1367 <option value="f1_macro">Classification -- 'f1_macro'</option> | |
| 1368 <option value="f1_weighted">Classification -- 'f1_weighted'</option> | |
| 1369 <option value="f1_samples">Classification -- 'f1_samples'</option> | |
| 1370 <option value="neg_log_loss">Classification -- 'neg_log_loss'</option> | |
| 1371 <option value="precision">Classification -- 'precision'</option> | |
| 1372 <option value="precision_micro">Classification -- 'precision_micro'</option> | |
| 1373 <option value="precision_macro">Classification -- 'precision_macro'</option> | |
| 1374 <option value="precision_wighted">Classification -- 'precision_wighted'</option> | |
| 1375 <option value="precision_samples">Classification -- 'precision_samples'</option> | |
| 1376 <option value="recall">Classification -- 'recall'</option> | |
| 1377 <option value="recall_micro">Classification -- 'recall_micro'</option> | |
| 1378 <option value="recall_macro">Classification -- 'recall_macro'</option> | |
| 1379 <option value="recall_wighted">Classification -- 'recall_wighted'</option> | |
| 1380 <option value="recall_samples">Classification -- 'recall_samples'</option> | |
| 1381 <option value="roc_auc">Classification -- 'roc_auc'</option> | |
| 1382 </param> | |
| 1383 </xml> | |
| 1384 | |
| 1385 <xml name="secondary_scoring_selection_regression"> | |
| 1386 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored."> | |
| 1387 <option value="explained_variance">Regression -- 'explained_variance'</option> | |
| 1388 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option> | |
| 1389 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option> | |
| 1390 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option> | |
| 1391 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option> | |
| 1392 <option value="r2">Regression -- 'r2'</option> | |
| 1393 <option value="max_error">Regression -- 'max_error'</option> | |
| 1394 </param> | |
| 1395 </xml> | |
| 1396 | |
| 1397 <xml name="secondary_scoring_selection_anormaly"> | |
| 1398 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored."> | |
| 1399 <option value="binarize_auc_scorer">anomaly detection -- binarize_auc_scorer</option> | |
| 1400 <option value="binarize_average_precision_scorer">anomaly detection -- binarize_average_precision_scorer</option> | |
| 1401 </param> | |
| 1402 </xml> | |
| 1403 | |
| 1404 <xml name="pre_dispatch" token_type="hidden" token_default_value="all" token_help="Number of predispatched jobs for parallel execution"> | |
| 1405 <param argument="pre_dispatch" type="@TYPE@" value="@DEFAULT_VALUE@" optional="true" label="pre_dispatch" help="@HELP@"/> | |
| 1406 </xml> | |
| 1407 | |
| 1408 <xml name="estimator_and_hyperparameter"> | |
| 1409 <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing pipeline/estimator object"/> | |
| 1410 <section name="hyperparams_swapping" title="Hyperparameter Swapping" expanded="false"> | |
| 1411 <param name="infile_params" type="data" format="tabular" optional="true" label="Choose the dataset containing hyperparameters for the pipeline/estimator above" help="This dataset could be the output of `get_params` in the `Estimator Attributes` tool."/> | |
| 1412 <repeat name="param_set" min="1" max="30" title="New hyperparameter setting"> | |
| 1413 <param name="sp_name" type="select" optional="true" label="Choose a parameter name (with current value)"> | |
| 1414 <options from_dataset="infile_params" startswith="@"> | |
| 1415 <column name="name" index="2"/> | |
| 1416 <column name="value" index="1"/> | |
| 1417 <filter type="unique_value" name="unique_param" column="1"/> | |
| 1418 </options> | |
| 1419 </param> | |
| 1420 <param name="sp_value" type="text" value="" optional="true" label="New value" help="Supports int, float, boolean, single quoted string, and selected object constructor. Similar to the `Parameter settings for search` section in `searchcv` tool except that only single value is expected here."> | |
| 1421 <sanitizer> | |
| 1422 <valid initial="default"> | |
| 1423 <add value="'"/> | |
| 1424 <add value="""/> | |
| 1425 </valid> | |
| 1426 </sanitizer> | |
| 1427 </param> | |
| 1428 </repeat> | |
| 1429 </section> | |
| 1430 </xml> | |
| 1431 | |
| 1432 <xml name="search_cv_options"> | |
| 1433 <expand macro="scoring_selection"/> | |
| 1434 <expand macro="model_validation_common_options"/> | |
| 1435 <!--expand macro="pre_dispatch" default_value="2*n_jobs" help="Controls the number of jobs that get dispatched during parallel execution"/--> | |
| 1436 <param argument="iid" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="iid" help="If True, data is identically distributed across the folds"/> | |
| 1437 <!--param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="refit" help="Refit an estimator using the best found parameters on the whole dataset. Be aware that `refit=True` invokes extra computation, but it's REQUIRED for outputting the best estimator!"/> --> | |
| 1438 <param argument="error_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Raise fit error:" help="If false, the metric score is assigned to NaN if an error occurs in estimator fitting and FitFailedWarning is raised."/> | |
| 1439 <param argument="return_train_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="return_train_score" help=""/> | |
| 1440 </xml> | |
| 1441 | |
| 1442 <xml name="estimator_module_options"> | |
| 1443 <option value="svm" selected="true">sklearn.svm</option> | |
| 1444 <option value="linear_model">sklearn.linear_model</option> | |
| 1445 <option value="ensemble">sklearn.ensemble</option> | |
| 1446 <option value="naive_bayes">sklearn.naive_bayes</option> | |
| 1447 <option value="tree">sklearn.tree</option> | |
| 1448 <option value="neighbors">sklearn.neighbors</option> | |
| 1449 <option value="xgboost">xgboost</option> | |
| 1450 <yield/> | |
| 1451 </xml> | |
| 1452 | |
| 1453 <xml name="estimator_suboptions"> | |
| 1454 <when value="svm"> | |
| 1455 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
| 1456 <option value="LinearSVC" selected="true">LinearSVC</option> | |
| 1457 <option value="LinearSVR">LinearSVR</option> | |
| 1458 <option value="NuSVC">NuSVC</option> | |
| 1459 <option value="NuSVR">NuSVR</option> | |
| 1460 <option value="OneClassSVM">OneClassSVM</option> | |
| 1461 <option value="SVC">SVC</option> | |
| 1462 <option value="SVR">SVR</option> | |
| 1463 </param> | |
| 1464 <expand macro="estimator_params_text"/> | |
| 1465 </when> | |
| 1466 <when value="linear_model"> | |
| 1467 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
| 1468 <option value="ARDRegression" selected="true">ARDRegression</option> | |
| 1469 <option value="BayesianRidge">BayesianRidge</option> | |
| 1470 <option value="ElasticNet">ElasticNet</option> | |
| 1471 <option value="ElasticNetCV">ElasticNetCV</option> | |
| 1472 <option value="HuberRegressor">HuberRegressor</option> | |
| 1473 <option value="Lars">Lars</option> | |
| 1474 <option value="LarsCV">LarsCV</option> | |
| 1475 <option value="Lasso">Lasso</option> | |
| 1476 <option value="LassoCV">LassoCV</option> | |
| 1477 <option value="LassoLars">LassoLars</option> | |
| 1478 <option value="LassoLarsCV">LassoLarsCV</option> | |
| 1479 <option value="LassoLarsIC">LassoLarsIC</option> | |
| 1480 <option value="LinearRegression">LinearRegression</option> | |
| 1481 <option value="LogisticRegression">LogisticRegression</option> | |
| 1482 <option value="LogisticRegressionCV">LogisticRegressionCV</option> | |
| 1483 <option value="MultiTaskLasso">MultiTaskLasso</option> | |
| 1484 <option value="MultiTaskElasticNet">MultiTaskElasticNet</option> | |
| 1485 <option value="MultiTaskLassoCV">MultiTaskLassoCV</option> | |
| 1486 <option value="MultiTaskElasticNetCV">MultiTaskElasticNetCV</option> | |
| 1487 <option value="OrthogonalMatchingPursuit">OrthogonalMatchingPursuit</option> | |
| 1488 <option value="OrthogonalMatchingPursuitCV">OrthogonalMatchingPursuitCV</option> | |
| 1489 <option value="PassiveAggressiveClassifier">PassiveAggressiveClassifier</option> | |
| 1490 <option value="PassiveAggressiveRegressor">PassiveAggressiveRegressor</option> | |
| 1491 <option value="Perceptron">Perceptron</option> | |
| 1492 <option value="RANSACRegressor">RANSACRegressor</option> | |
| 1493 <option value="Ridge">Ridge</option> | |
| 1494 <option value="RidgeClassifier">RidgeClassifier</option> | |
| 1495 <option value="RidgeClassifierCV">RidgeClassifierCV</option> | |
| 1496 <option value="RidgeCV">RidgeCV</option> | |
| 1497 <option value="SGDClassifier">SGDClassifier</option> | |
| 1498 <option value="SGDRegressor">SGDRegressor</option> | |
| 1499 <option value="TheilSenRegressor">TheilSenRegressor</option> | |
| 1500 </param> | |
| 1501 <expand macro="estimator_params_text"/> | |
| 1502 </when> | |
| 1503 <when value="ensemble"> | |
| 1504 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
| 1505 <option value="AdaBoostClassifier" selected="true">AdaBoostClassifier</option> | |
| 1506 <option value="AdaBoostRegressor">AdaBoostRegressor</option> | |
| 1507 <option value="BaggingClassifier">BaggingClassifier</option> | |
| 1508 <option value="BaggingRegressor">BaggingRegressor</option> | |
| 1509 <option value="ExtraTreesClassifier">ExtraTreesClassifier</option> | |
| 1510 <option value="ExtraTreesRegressor">ExtraTreesRegressor</option> | |
| 1511 <option value="GradientBoostingClassifier">GradientBoostingClassifier</option> | |
| 1512 <option value="GradientBoostingRegressor">GradientBoostingRegressor</option> | |
| 1513 <option value="IsolationForest">IsolationForest</option> | |
| 1514 <option value="HistGradientBoostingClassifier">HistGradientBoostingClassifier</option> | |
| 1515 <option value="HistGradientBoostingRegressor">HistGradientBoostingRegressor</option> | |
| 1516 <option value="RandomForestClassifier">RandomForestClassifier</option> | |
| 1517 <option value="RandomForestRegressor">RandomForestRegressor</option> | |
| 1518 <option value="RandomTreesEmbedding">RandomTreesEmbedding</option> | |
| 1519 <!--option value="VotingClassifier">VotingClassifier</option--> | |
| 1520 </param> | |
| 1521 <expand macro="estimator_params_text"/> | |
| 1522 </when> | |
| 1523 <when value="naive_bayes"> | |
| 1524 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
| 1525 <option value="BernoulliNB" selected="true">BernoulliNB</option> | |
| 1526 <option value="GaussianNB">GaussianNB</option> | |
| 1527 <option value="MultinomialNB">MultinomialNB</option> | |
| 1528 </param> | |
| 1529 <expand macro="estimator_params_text"/> | |
| 1530 </when> | |
| 1531 <when value="tree"> | |
| 1532 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
| 1533 <option value="DecisionTreeClassifier" selected="true">DecisionTreeClassifier</option> | |
| 1534 <option value="DecisionTreeRegressor">DecisionTreeRegressor</option> | |
| 1535 <option value="ExtraTreeClassifier">ExtraTreeClassifier</option> | |
| 1536 <option value="ExtraTreeRegressor">ExtraTreeRegressor</option> | |
| 1537 </param> | |
| 1538 <expand macro="estimator_params_text"/> | |
| 1539 </when> | |
| 1540 <when value="neighbors"> | |
| 1541 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
| 1542 <option value="KNeighborsClassifier" selected="true">KNeighborsClassifier</option> | |
| 1543 <option value="KNeighborsRegressor">KNeighborsRegressor</option> | |
| 1544 <!--option value="BallTree">BallTree</option--> | |
| 1545 <!--option value="KDTree">KDTree</option--> | |
| 1546 <option value="KernelDensity">KernelDensity</option> | |
| 1547 <option value="LocalOutlierFactor">LocalOutlierFactor</option> | |
| 1548 <option value="RadiusNeighborsClassifier">RadiusNeighborsClassifier</option> | |
| 1549 <option value="RadiusNeighborsRegressor">RadiusNeighborsRegressor</option> | |
| 1550 <option value="NearestCentroid">NearestCentroid</option> | |
| 1551 <option value="NearestNeighbors">NearestNeighbors</option> | |
| 1552 </param> | |
| 1553 <expand macro="estimator_params_text"/> | |
| 1554 </when> | |
| 1555 <when value="xgboost"> | |
| 1556 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
| 1557 <option value="XGBRegressor" selected="true">XGBRegressor</option> | |
| 1558 <option value="XGBClassifier">XGBClassifier</option> | |
| 1559 </param> | |
| 1560 <expand macro="estimator_params_text"/> | |
| 1561 </when> | |
| 1562 <yield/> | |
| 1563 </xml> | |
| 1564 | |
| 1565 <xml name="estimator_selector_all"> | |
| 1566 <conditional name="estimator_selector"> | |
| 1567 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" > | |
| 1568 <expand macro="estimator_module_options"/> | |
| 1569 </param> | |
| 1570 <expand macro="estimator_suboptions"/> | |
| 1571 </conditional> | |
| 1572 </xml> | |
| 1573 | |
| 1574 <xml name="estimator_selector_fs"> | |
| 1575 <conditional name="estimator_selector"> | |
| 1576 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" > | |
| 1577 <expand macro="estimator_module_options"> | |
| 1578 <option value="custom_estimator">Load a custom estimator</option> | |
| 1579 </expand> | |
| 1580 </param> | |
| 1581 <expand macro="estimator_suboptions"> | |
| 1582 <when value="custom_estimator"> | |
| 1583 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline:"/> | |
| 1584 </when> | |
| 1585 </expand> | |
| 1586 </conditional> | |
| 1587 </xml> | |
| 1588 | |
| 1589 <xml name="estimator_params_text" token_label="Type in parameter settings if different from default:" token_default_value='' | |
| 1590 token_help="Dictionary-capable, e.g., C=1, kernel='linear'. No double quotes. Leave this box blank for default estimator."> | |
| 1591 <param name="text_params" type="text" value="@DEFAULT_VALUE@" optional="true" label="@LABEL@" help="@HELP@"> | |
| 1592 <sanitizer> | |
| 1593 <valid initial="default"> | |
| 1594 <add value="'"/> | |
| 1595 </valid> | |
| 1596 </sanitizer> | |
| 1597 </param> | |
| 1598 </xml> | |
| 1599 | |
| 1600 <xml name="kernel_approximation_all"> | |
| 1601 <conditional name="kernel_approximation_selector"> | |
| 1602 <param name="select_algorithm" type="select" label="Choose a kernel approximation algorithm:"> | |
| 1603 <option value="Nystroem" selected="true">Nystroem</option> | |
| 1604 <option value="RBFSampler">RBFSampler</option> | |
| 1605 <option value="AdditiveChi2Sampler">AdditiveChi2Sampler</option> | |
| 1606 <option value="SkewedChi2Sampler">SkewedChi2Sampler</option> | |
| 1607 </param> | |
| 1608 <when value="Nystroem"> | |
| 1609 <expand macro="estimator_params_text" | |
| 1610 help="Default(=blank): coef0=None, degree=None, gamma=None, kernel='rbf', kernel_params=None, n_components=100, random_state=None. No double quotes"/> | |
| 1611 </when> | |
| 1612 <when value="RBFSampler"> | |
| 1613 <expand macro="estimator_params_text" | |
| 1614 help="Default(=blank): gamma=1.0, n_components=100, random_state=None."/> | |
| 1615 </when> | |
| 1616 <when value="AdditiveChi2Sampler"> | |
| 1617 <expand macro="estimator_params_text" | |
| 1618 help="Default(=blank): sample_interval=None, sample_steps=2."/> | |
| 1619 </when> | |
| 1620 <when value="SkewedChi2Sampler"> | |
| 1621 <expand macro="estimator_params_text" | |
| 1622 help="Default(=blank): n_components=100, random_state=None, skewedness=1.0."/> | |
| 1623 </when> | |
| 1624 </conditional> | |
| 1625 </xml> | |
| 1626 | |
| 1627 <xml name="matrix_decomposition_all"> | |
| 1628 <conditional name="matrix_decomposition_selector"> | |
| 1629 <param name="select_algorithm" type="select" label="Choose a matrix decomposition algorithm:"> | |
| 1630 <option value="DictionaryLearning" selected="true">DictionaryLearning</option> | |
| 1631 <option value="FactorAnalysis">FactorAnalysis</option> | |
| 1632 <option value="FastICA">FastICA</option> | |
| 1633 <option value="IncrementalPCA">IncrementalPCA</option> | |
| 1634 <option value="KernelPCA">KernelPCA</option> | |
| 1635 <option value="LatentDirichletAllocation">LatentDirichletAllocation</option> | |
| 1636 <option value="MiniBatchDictionaryLearning">MiniBatchDictionaryLearning</option> | |
| 1637 <option value="MiniBatchSparsePCA">MiniBatchSparsePCA</option> | |
| 1638 <option value="NMF">NMF</option> | |
| 1639 <option value="PCA">PCA</option> | |
| 1640 <option value="SparsePCA">SparsePCA</option> | |
| 1641 <!--option value="SparseCoder">SparseCoder</option--> | |
| 1642 <option value="TruncatedSVD">TruncatedSVD</option> | |
| 1643 </param> | |
| 1644 <when value="DictionaryLearning"> | |
| 1645 <expand macro="estimator_params_text" | |
| 1646 help="Default(=blank): alpha=1, code_init=None, dict_init=None, fit_algorithm='lars', max_iter=1000, n_components=None, random_state=None, split_sign=False, tol=1e-08, transform_algorithm='omp', transform_alpha=None, transform_n_nonzero_coefs=None, verbose=False."/> | |
| 1647 </when> | |
| 1648 <when value="FactorAnalysis"> | |
| 1649 <expand macro="estimator_params_text" | |
| 1650 help="Default(=blank): copy=True, iterated_power=3, max_iter=1000, n_components=None, noise_variance_init=None, random_state=0, svd_method='randomized', tol=0.01."/> | |
| 1651 </when> | |
| 1652 <when value="FastICA"> | |
| 1653 <expand macro="estimator_params_text" | |
| 1654 help="Default(=blank): algorithm='parallel', fun='logcosh', fun_args=None, max_iter=200, n_components=None, random_state=None, tol=0.0001, w_init=None, whiten=True. No double quotes."/> | |
| 1655 </when> | |
| 1656 <when value="IncrementalPCA"> | |
| 1657 <expand macro="estimator_params_text" | |
| 1658 help="Default(=blank): batch_size=None, copy=True, n_components=None, whiten=False."/> | |
| 1659 </when> | |
| 1660 <when value="KernelPCA"> | |
| 1661 <expand macro="estimator_params_text" | |
| 1662 help="Default(=blank): alpha=1.0, coef0=1, copy_X=True, degree=3, eigen_solver='auto', fit_inverse_transform=False, gamma=None, kernel='linear', kernel_params=None, max_iter=None, n_components=None, random_state=None, remove_zero_eig=False, tol=0. No double quotes."/> | |
| 1663 </when> | |
| 1664 <when value="LatentDirichletAllocation"> | |
| 1665 <expand macro="estimator_params_text" | |
| 1666 help="Default(=blank): batch_size=128, doc_topic_prior=None, evaluate_every=-1, learning_decay=0.7, learning_method=None, learning_offset=10.0, max_doc_update_iter=100, max_iter=10, mean_change_tol=0.001, n_components=10, n_topics=None, perp_tol=0.1, random_state=None, topic_word_prior=None, total_samples=1000000.0, verbose=0."/> | |
| 1667 </when> | |
| 1668 <when value="MiniBatchDictionaryLearning"> | |
| 1669 <expand macro="estimator_params_text" | |
| 1670 help="Default(=blank): alpha=1, batch_size=3, dict_init=None, fit_algorithm='lars', n_components=None, n_iter=1000, random_state=None, shuffle=True, split_sign=False, transform_algorithm='omp', transform_alpha=None, transform_n_nonzero_coefs=None, verbose=False."/> | |
| 1671 </when> | |
| 1672 <when value="MiniBatchSparsePCA"> | |
| 1673 <expand macro="estimator_params_text" | |
| 1674 help="Default(=blank): alpha=1, batch_size=3, callback=None, method='lars', n_components=None, n_iter=100, random_state=None, ridge_alpha=0.01, shuffle=True, verbose=False."/> | |
| 1675 </when> | |
| 1676 <when value="NMF"> | |
| 1677 <expand macro="estimator_params_text" | |
| 1678 help="Default(=blank): alpha=0.0, beta_loss='frobenius', init=None, l1_ratio=0.0, max_iter=200, n_components=None, random_state=None, shuffle=False, solver='cd', tol=0.0001, verbose=0."/> | |
| 1679 </when> | |
| 1680 <when value="PCA"> | |
| 1681 <expand macro="estimator_params_text" | |
| 1682 help="Default(=blank): copy=True, iterated_power='auto', n_components=None, random_state=None, svd_solver='auto', tol=0.0, whiten=False."/> | |
| 1683 </when> | |
| 1684 <when value="SparsePCA"> | |
| 1685 <expand macro="estimator_params_text" | |
| 1686 help="Default(=blank): U_init=None, V_init=None, alpha=1, max_iter=1000, method='lars', n_components=None, random_state=None, ridge_alpha=0.01, tol=1e-08, verbose=False."/> | |
| 1687 </when> | |
| 1688 <when value="TruncatedSVD"> | |
| 1689 <expand macro="estimator_params_text" | |
| 1690 help="Default(=blank): algorithm='randomized', n_components=2, n_iter=5, random_state=None, tol=0.0."/> | |
| 1691 </when> | |
| 1692 </conditional> | |
| 1693 </xml> | |
| 1694 | |
| 1695 <xml name="FeatureAgglomeration"> | |
| 1696 <conditional name="FeatureAgglomeration_selector"> | |
| 1697 <param name="select_algorithm" type="select" label="Choose the algorithm:"> | |
| 1698 <option value="FeatureAgglomeration" selected="true">FeatureAgglomeration</option> | |
| 1699 </param> | |
| 1700 <when value="FeatureAgglomeration"> | |
| 1701 <expand macro="estimator_params_text" | |
| 1702 help="Default(=blank): affinity='euclidean', compute_full_tree='auto', connectivity=None, linkage='ward', memory=None, n_clusters=2, pooling_func=np.mean."/> | |
| 1703 </when> | |
| 1704 </conditional> | |
| 1705 </xml> | |
| 1706 | |
| 1707 <xml name="skrebate"> | |
| 1708 <conditional name="skrebate_selector"> | |
| 1709 <param name="select_algorithm" type="select" label="Choose the algorithm:"> | |
| 1710 <option value="ReliefF">ReliefF</option> | |
| 1711 <option value="SURF">SURF</option> | |
| 1712 <option value="SURFstar">SURFstar</option> | |
| 1713 <option value="MultiSURF">MultiSURF</option> | |
| 1714 <option value="MultiSURFstar">MultiSURFstar</option> | |
| 1715 <!--option value="TuRF">TuRF</option> --> | |
| 1716 </param> | |
| 1717 <when value="ReliefF"> | |
| 1718 <expand macro="estimator_params_text" | |
| 1719 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, n_neighbors=100, verbose=False."/> | |
| 1720 </when> | |
| 1721 <when value="SURF"> | |
| 1722 <expand macro="estimator_params_text" | |
| 1723 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False."/> | |
| 1724 </when> | |
| 1725 <when value="SURFstar"> | |
| 1726 <expand macro="estimator_params_text" | |
| 1727 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False."/> | |
| 1728 </when> | |
| 1729 <when value="MultiSURF"> | |
| 1730 <expand macro="estimator_params_text" | |
| 1731 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False."/> | |
| 1732 </when> | |
| 1733 <when value="MultiSURFstar"> | |
| 1734 <expand macro="estimator_params_text" | |
| 1735 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False."/> | |
| 1736 </when> | |
| 1737 <!--when value="TuRF"> | |
| 1738 <expand macro="estimator_params_text" | |
| 1739 help="Default(=blank): core_algorithm='ReliefF', discrete_threshold=10, n_features_to_select=10, n_neighbors=100, pct=0.5, verbose=False."/> | |
| 1740 </when> --> | |
| 1741 </conditional> | |
| 1742 </xml> | |
| 1743 | |
| 1744 <xml name="imbalanced_learn_sampling"> | |
| 1745 <conditional name="imblearn_selector"> | |
| 1746 <param name="select_algorithm" type="select" label="Choose the algorithm:"> | |
| 1747 <option value="under_sampling.ClusterCentroids" selected="true">under_sampling.ClusterCentroids</option> | |
| 1748 <option value="under_sampling.CondensedNearestNeighbour">under_sampling.CondensedNearestNeighbour</option> | |
| 1749 <option value="under_sampling.EditedNearestNeighbours">under_sampling.EditedNearestNeighbours</option> | |
| 1750 <option value="under_sampling.RepeatedEditedNearestNeighbours">under_sampling.RepeatedEditedNearestNeighbours</option> | |
| 1751 <option value="under_sampling.AllKNN">under_sampling.AllKNN</option> | |
| 1752 <option value="under_sampling.InstanceHardnessThreshold">under_sampling.InstanceHardnessThreshold</option> | |
| 1753 <option value="under_sampling.NearMiss">under_sampling.NearMiss</option> | |
| 1754 <option value="under_sampling.NeighbourhoodCleaningRule">under_sampling.NeighbourhoodCleaningRule</option> | |
| 1755 <option value="under_sampling.OneSidedSelection">under_sampling.OneSidedSelection</option> | |
| 1756 <option value="under_sampling.RandomUnderSampler">under_sampling.RandomUnderSampler</option> | |
| 1757 <option value="under_sampling.TomekLinks">under_sampling.TomekLinks</option> | |
| 1758 <option value="over_sampling.ADASYN">over_sampling.ADASYN</option> | |
| 1759 <option value="over_sampling.RandomOverSampler">over_sampling.RandomOverSampler</option> | |
| 1760 <option value="over_sampling.SMOTE">over_sampling.SMOTE</option> | |
| 1761 <option value="over_sampling.SVMSMOTE">over_sampling.SVMSMOTE</option> | |
| 1762 <option value="over_sampling.BorderlineSMOTE">over_sampling.BorderlineSMOTE</option> | |
| 1763 <option value="over_sampling.SMOTENC">over_sampling.SMOTENC</option> | |
| 1764 <option value="combine.SMOTEENN">combine.SMOTEENN</option> | |
| 1765 <option value="combine.SMOTETomek">combine.SMOTETomek</option> | |
| 1766 <option value="Z_RandomOverSampler">Z_RandomOverSampler - for regression</option> | |
| 1767 </param> | |
| 1768 <when value="under_sampling.ClusterCentroids"> | |
| 1769 <expand macro="estimator_params_text" | |
| 1770 help="Default(=blank): sampling_strategy='auto', random_state=None, estimator=None, voting='auto'."/> | |
| 1771 </when> | |
| 1772 <when value="under_sampling.CondensedNearestNeighbour"> | |
| 1773 <expand macro="estimator_params_text" | |
| 1774 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=None, n_seeds_S=1."/> | |
| 1775 </when> | |
| 1776 <when value="under_sampling.EditedNearestNeighbours"> | |
| 1777 <expand macro="estimator_params_text" | |
| 1778 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, max_iter=100, kind_sel='all'."/> | |
| 1779 </when> | |
| 1780 <when value="under_sampling.RepeatedEditedNearestNeighbours"> | |
| 1781 <expand macro="estimator_params_text" | |
| 1782 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, max_iter=100, kind_sel='all'."/> | |
| 1783 </when> | |
| 1784 <when value="under_sampling.AllKNN"> | |
| 1785 <expand macro="estimator_params_text" | |
| 1786 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, kind_sel='all', allow_minority=False."/> | |
| 1787 </when> | |
| 1788 <when value="under_sampling.InstanceHardnessThreshold"> | |
| 1789 <expand macro="estimator_params_text" | |
| 1790 help="Default(=blank): estimator=None, sampling_strategy='auto', random_state=None, cv=5."/> | |
| 1791 </when> | |
| 1792 <when value="under_sampling.NearMiss"> | |
| 1793 <expand macro="estimator_params_text" | |
| 1794 help="Default(=blank): sampling_strategy='auto', random_state=None, version=1, n_neighbors=3, n_neighbors_ver3=3."/> | |
| 1795 </when> | |
| 1796 <when value="under_sampling.NeighbourhoodCleaningRule"> | |
| 1797 <expand macro="estimator_params_text" | |
| 1798 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, kind_sel='all', threshold_cleaning=0.5."/> | |
| 1799 </when> | |
| 1800 <when value="under_sampling.OneSidedSelection"> | |
| 1801 <expand macro="estimator_params_text" | |
| 1802 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=None, n_seeds_S=1."/> | |
| 1803 </when> | |
| 1804 <when value="under_sampling.RandomUnderSampler"> | |
| 1805 <expand macro="estimator_params_text" | |
| 1806 help="Default(=blank): sampling_strategy='auto', random_state=None, replacement=False."/> | |
| 1807 </when> | |
| 1808 <when value="under_sampling.TomekLinks"> | |
| 1809 <expand macro="estimator_params_text" | |
| 1810 help="Default(=blank): sampling_strategy='auto', random_state=None."/> | |
| 1811 </when> | |
| 1812 <when value="over_sampling.ADASYN"> | |
| 1813 <expand macro="estimator_params_text" | |
| 1814 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=5."/> | |
| 1815 </when> | |
| 1816 <when value="over_sampling.RandomOverSampler"> | |
| 1817 <expand macro="estimator_params_text" | |
| 1818 help="Default(=blank): sampling_strategy='auto', random_state=None."/> | |
| 1819 </when> | |
| 1820 <when value="over_sampling.SMOTE"> | |
| 1821 <expand macro="estimator_params_text" | |
| 1822 help="Default(=blank): sampling_strategy='auto', random_state=None, k_neighbors=5."/> | |
| 1823 </when> | |
| 1824 <when value="over_sampling.SVMSMOTE"> | |
| 1825 <expand macro="estimator_params_text" | |
| 1826 help="Default(=blank): sampling_strategy='auto', k_neighbors=5, m_neighbors=10, out_step=0.5, random_state=None, svm_estimator=None."/> | |
| 1827 </when> | |
| 1828 <when value="over_sampling.BorderlineSMOTE"> | |
| 1829 <expand macro="estimator_params_text" | |
| 1830 help="Default(=blank): sampling_strategy='auto', k_neighbors=5, kind='borderline-1', m_neighbors=10, random_state=None."/> | |
| 1831 </when> | |
| 1832 <when value="over_sampling.SMOTENC"> | |
| 1833 <expand macro="estimator_params_text" | |
| 1834 help="Default: categorical_features=[], sampling_strategy='auto', random_state=None, k_neighbors=5."/> | |
| 1835 </when> | |
| 1836 <when value="combine.SMOTEENN"> | |
| 1837 <expand macro="estimator_params_text" | |
| 1838 help="Default(=blank): sampling_strategy='auto', random_state=None, smote=None, enn=None."/> | |
| 1839 </when> | |
| 1840 <when value="combine.SMOTETomek"> | |
| 1841 <expand macro="estimator_params_text" | |
| 1842 help="Default(=blank): sampling_strategy='auto', random_state=None, smote=None, tomek=None."/> | |
| 1843 </when> | |
| 1844 <when value="Z_RandomOverSampler"> | |
| 1845 <expand macro="estimator_params_text" | |
| 1846 help="Default(=blank): sampling_strategy='auto', random_state=None, negative_thres=0, positive_thres=-1."/> | |
| 1847 </when> | |
| 1848 </conditional> | |
| 1849 </xml> | |
| 1850 | |
| 1851 <xml name="stacking_ensemble_inputs"> | |
| 1852 <section name="options" title="Advanced Options" expanded="false"> | |
| 1853 <yield/> | |
| 1854 <param argument="use_features_in_secondary" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false"/> | |
| 1855 <param argument="store_train_meta_features" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false"/> | |
| 1856 </section> | |
| 1857 </xml> | |
| 1858 | |
| 1859 <xml name="stacking_base_estimator"> | |
| 1860 <conditional name="estimator_selector"> | |
| 1861 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" > | |
| 1862 <expand macro="estimator_module_options"> | |
| 1863 <option value="custom_estimator">Load a custom estimator</option> | |
| 1864 </expand> | |
| 1865 </param> | |
| 1866 <expand macro="estimator_suboptions"> | |
| 1867 <when value="custom_estimator"> | |
| 1868 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline"/> | |
| 1869 </when> | |
| 1870 </expand> | |
| 1871 </conditional> | |
| 1872 </xml> | |
| 1873 | |
| 1874 <xml name="stacking_voting_weights"> | |
| 1875 <section name="options" title="Advanced Options" expanded="false"> | |
| 1876 <param argument="weights" type="text" value="[]" optional="true" help="Sequence of weights (float or int). Uses uniform weights if None (`[]`)."> | |
| 1877 <sanitizer> | |
| 1878 <valid initial="default"> | |
| 1879 <add value="["/> | |
| 1880 <add value="]"/> | |
| 1881 </valid> | |
| 1882 </sanitizer> | |
| 1883 </param> | |
| 1884 <yield/> | |
| 1885 </section> | |
| 1886 </xml> | |
| 1887 | |
| 1888 <xml name="preprocessors_sequence_encoders"> | |
| 1889 <conditional name="encoder_selection"> | |
| 1890 <param name="encoder_type" type="select" label="Choose the sequence encoder class"> | |
| 1891 <option value="GenomeOneHotEncoder">GenomeOneHotEncoder</option> | |
| 1892 <option value="ProteinOneHotEncoder">ProteinOneHotEncoder</option> | |
| 1893 </param> | |
| 1894 <when value="GenomeOneHotEncoder"> | |
| 1895 <expand macro="preprocessors_sequence_encoder_arguments"/> | |
| 1896 </when> | |
| 1897 <when value="ProteinOneHotEncoder"> | |
| 1898 <expand macro="preprocessors_sequence_encoder_arguments"/> | |
| 1899 </when> | |
| 1900 </conditional> | |
| 1901 </xml> | |
| 1902 | |
| 1903 <xml name="preprocessors_sequence_encoder_arguments"> | |
| 1904 <param argument="seq_length" type="integer" value="" min="0" optional="true" help="Integer. Sequence length"/> | |
| 1905 <param argument="padding" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" help="Whether to pad or truncate sequence to meet the sequence length."/> | |
| 1906 </xml> | |
| 1907 | |
| 1908 <!-- Outputs --> | |
| 1909 | |
| 1910 <xml name="output"> | |
| 1911 <outputs> | |
| 1912 <data format="tabular" name="outfile_predict"> | |
| 1913 <filter>selected_tasks['selected_task'] == 'load'</filter> | |
| 1914 </data> | |
| 1915 <data format="zip" name="outfile_fit" label="${tool.name}.${selected_tasks.selected_algorithms.selected_algorithm}"> | |
| 1916 <filter>selected_tasks['selected_task'] == 'train'</filter> | |
| 1917 </data> | |
| 1918 </outputs> | |
| 1919 </xml> | |
| 1920 | |
| 1921 <!--Citations--> | |
| 1922 <xml name="eden_citation"> | |
| 1923 <citations> | |
| 1924 <citation type="doi">10.5281/zenodo.15094</citation> | |
| 1925 </citations> | |
| 1926 </xml> | |
| 1927 | |
| 1928 <xml name="sklearn_citation"> | |
| 1929 <citations> | |
| 1930 <citation type="bibtex"> | |
| 1931 @article{scikit-learn, | |
| 1932 title={Scikit-learn: Machine Learning in {P}ython}, | |
| 1933 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V. | |
| 1934 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P. | |
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