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comparison main_macros.xml @ 0:68aaa903052a draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
author bgruening
date Fri, 09 Aug 2019 07:09:06 -0400
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children cc49634df38f
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1 <macros>
2 <token name="@VERSION@">1.0.7.10</token>
3
4 <token name="@ENSEMBLE_VERSION@">0.2.0</token>
5
6 <xml name="python_requirements">
7 <requirements>
8 <requirement type="package" version="3.6">python</requirement>
9 <requirement type="package" version="0.7.10">Galaxy-ML</requirement>
10 <yield/>
11 </requirements>
12 </xml>
13
14 <xml name="macro_stdio">
15 <stdio>
16 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
17 </stdio>
18 </xml>
19
20
21 <!--Generic interface-->
22
23 <xml name="sl_Conditional" token_train="tabular" token_data="tabular" token_model="txt">
24 <conditional name="selected_tasks">
25 <param name="selected_task" type="select" label="Select a Classification Task">
26 <option value="train" selected="true">Train a model</option>
27 <option value="load">Load a model and predict</option>
28 </param>
29 <when value="load">
30 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
31 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
32 <param name="header" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
33 <conditional name="prediction_options">
34 <param name="prediction_option" type="select" label="Select the type of prediction">
35 <option value="predict">Predict class labels</option>
36 <option value="advanced">Include advanced options</option>
37 </param>
38 <when value="predict">
39 </when>
40 <when value="advanced">
41 </when>
42 </conditional>
43 </when>
44 <when value="train">
45 <conditional name="selected_algorithms">
46 <yield />
47 </conditional>
48 </when>
49 </conditional>
50 </xml>
51
52 <xml name="advanced_section">
53 <section name="options" title="Advanced Options" expanded="False">
54 <yield />
55 </section>
56 </xml>
57
58
59 <!--Generalized Linear Models-->
60 <xml name="loss" token_help=" " token_select="false">
61 <param argument="loss" type="select" label="Loss function" help="@HELP@">
62 <option value="squared_loss" selected="@SELECT@">squared loss</option>
63 <option value="huber">huber</option>
64 <option value="epsilon_insensitive">epsilon insensitive</option>
65 <option value="squared_epsilon_insensitive">squared epsilon insensitive</option>
66 <yield/>
67 </param>
68 </xml>
69
70 <xml name="penalty" token_help=" ">
71 <param argument="penalty" type="select" label="Penalty (regularization term)" help="@HELP@">
72 <option value="l2" selected="true">l2</option>
73 <option value="l1">l1</option>
74 <option value="elasticnet">elastic net</option>
75 <option value="none">none</option>
76 <yield/>
77 </param>
78 </xml>
79
80 <xml name="l1_ratio" token_default_value="0.15" token_help=" ">
81 <param argument="l1_ratio" type="float" value="@DEFAULT_VALUE@" label="Elastic Net mixing parameter" help="@HELP@"/>
82 </xml>
83
84 <xml name="epsilon" token_default_value="0.1" token_help="Used if loss is ‘huber’, ‘epsilon_insensitive’, or ‘squared_epsilon_insensitive’. ">
85 <param argument="epsilon" type="float" value="@DEFAULT_VALUE@" label="Epsilon (epsilon-sensitive loss functions only)" help="@HELP@"/>
86 </xml>
87
88 <xml name="learning_rate_s" token_help=" " token_selected1="false" token_selected2="false">
89 <param argument="learning_rate" type="select" optional="true" label="Learning rate schedule" help="@HELP@">
90 <option value="optimal" selected="@SELECTED1@">optimal</option>
91 <option value="constant">constant</option>
92 <option value="invscaling" selected="@SELECTED2@">inverse scaling</option>
93 <yield/>
94 </param>
95 </xml>
96
97 <xml name="eta0" token_default_value="0.0" token_help="Used with ‘constant’ or ‘invscaling’ schedules. ">
98 <param argument="eta0" type="float" value="@DEFAULT_VALUE@" label="Initial learning rate" help="@HELP@"/>
99 </xml>
100
101 <xml name="power_t" token_default_value="0.5" token_help=" ">
102 <param argument="power_t" type="float" value="@DEFAULT_VALUE@" label="Exponent for inverse scaling learning rate" help="@HELP@"/>
103 </xml>
104
105 <xml name="normalize" token_checked="false" token_help=" ">
106 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Normalize samples before training" help=" "/>
107 </xml>
108
109 <xml name="copy_X" token_checked="true" token_help=" ">
110 <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. "/>
111 </xml>
112
113 <xml name="ridge_params">
114 <expand macro="normalize"/>
115 <expand macro="alpha" default_value="1.0"/>
116 <expand macro="fit_intercept"/>
117 <expand macro="max_iter" default_value=""/>
118 <expand macro="tol" default_value="0.001" help_text="Precision of the solution. "/>
119 <!--class_weight-->
120 <expand macro="copy_X"/>
121 <param argument="solver" type="select" value="" label="Solver to use in the computational routines" help=" ">
122 <option value="auto" selected="true">auto</option>
123 <option value="svd">svd</option>
124 <option value="cholesky">cholesky</option>
125 <option value="lsqr">lsqr</option>
126 <option value="sparse_cg">sparse_cg</option>
127 <option value="sag">sag</option>
128 </param>
129 <expand macro="random_state"/>
130 </xml>
131
132 <!--Ensemble methods-->
133 <xml name="n_estimators" token_default_value="10" token_help=" ">
134 <param argument="n_estimators" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of trees in the forest" help="@HELP@"/>
135 </xml>
136
137 <xml name="max_depth" token_default_value="" token_help=" ">
138 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/>
139 </xml>
140
141 <xml name="min_samples_split" token_type="integer" token_default_value="2" token_help=" ">
142 <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@"/>
143 </xml>
144
145 <xml name="min_samples_leaf" token_type="integer" token_default_value="1" token_label="Minimum number of samples in newly created leaves" token_help=" ">
146 <param argument="min_samples_leaf" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP@"/>
147 </xml>
148
149 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" ">
150 <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@"/>
151 </xml>
152
153 <xml name="max_leaf_nodes" token_default_value="" token_help=" ">
154 <param argument="max_leaf_nodes" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum number of leaf nodes in best-first method" help="@HELP@"/>
155 </xml>
156
157 <xml name="min_impurity_decrease" token_default_value="0" token_help=" ">
158 <param argument="min_impurity_decrease" type="float" value="@DEFAULT_VALUE@" optional="true" label="The threshold value of impurity for stopping node splitting" help="@HELP@"/>
159 </xml>
160
161 <xml name="bootstrap" token_checked="true" token_help=" ">
162 <param argument="bootstrap" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Use bootstrap samples for building trees." help="@HELP@"/>
163 </xml>
164
165 <xml name="criterion" token_help=" ">
166 <param argument="criterion" type="select" label="Function to measure the quality of a split" help=" ">
167 <option value="gini" selected="true">Gini impurity</option>
168 <option value="entropy">Information gain</option>
169 <yield/>
170 </param>
171 </xml>
172
173 <xml name="criterion2" token_help="">
174 <param argument="criterion" type="select" label="Function to measure the quality of a split" >
175 <option value="mse">mse - mean squared error</option>
176 <option value="mae">mae - mean absolute error</option>
177 <yield/>
178 </param>
179 </xml>
180
181 <xml name="oob_score" token_checked="false" token_help=" ">
182 <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@"/>
183 </xml>
184
185 <xml name="max_features">
186 <conditional name="select_max_features">
187 <param argument="max_features" type="select" label="max_features">
188 <option value="auto" selected="true">auto - max_features=n_features</option>
189 <option value="sqrt">sqrt - max_features=sqrt(n_features)</option>
190 <option value="log2">log2 - max_features=log2(n_features)</option>
191 <option value="number_input">I want to type the number in or input None type</option>
192 </param>
193 <when value="auto">
194 </when>
195 <when value="sqrt">
196 </when>
197 <when value="log2">
198 </when>
199 <when value="number_input">
200 <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."/>
201 </when>
202 </conditional>
203 </xml>
204
205 <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.">
206 <param argument="verbose" type="integer" value="@DEFAULT_VALUE@" optional="true" label="Enable verbose output" help="@HELP@"/>
207 </xml>
208
209 <xml name="learning_rate" token_default_value="1.0" token_help=" ">
210 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/>
211 </xml>
212
213 <xml name="subsample" token_help=" ">
214 <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@"/>
215 </xml>
216
217 <xml name="presort">
218 <param argument="presort" type="select" label="Whether to presort the data to speed up the finding of best splits in fitting" >
219 <option value="auto" selected="true">auto</option>
220 <option value="true">true</option>
221 <option value="false">false</option>
222 </param>
223 </xml>
224
225 <!--Parameters-->
226 <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.">
227 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/>
228 </xml>
229
230 <xml name="n_clusters" token_default_value="8">
231 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/>
232 </xml>
233
234 <xml name="fit_intercept" token_checked="true">
235 <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."/>
236 </xml>
237
238 <xml name="n_iter" token_default_value="5" token_help_text="The number of passes over the training data (aka epochs). ">
239 <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
240 </xml>
241
242 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration">
243 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/>
244 </xml>
245
246 <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.">
247 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/>
248 </xml>
249
250 <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.">
251 <param argument="warm_start" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Perform warm start" help="@HELP_TEXT@"/>
252 </xml>
253
254 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term.">
255 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
256 </xml>
257
258 <!--xml name="class_weight" token_default_value="" token_help_text="">
259 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/>
260 </xml-->
261
262 <xml name="alpha" token_default_value="0.0001" token_help_text="Constant that multiplies the regularization term if regularization is used. ">
263 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/>
264 </xml>
265
266 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters.">
267 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/>
268 </xml>
269
270 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample.">
271 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/>
272 </xml>
273
274 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. ">
275 <param argument="noise" type="float" optional="true" value="@DEFAULT_VALUE@" label="Standard deviation of the Gaussian noise added to the data" help="@HELP_TEXT@"/>
276 </xml>
277
278 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. ">
279 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
280 </xml>
281
282 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" ">
283 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
284 </xml>
285
286 <xml name="n_init" token_default_value="10" >
287 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/>
288 </xml>
289
290 <xml name="init">
291 <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.">
292 <option value="k-means++">k-means++</option>
293 <option value="random">random</option>
294 </param>
295 </xml>
296
297 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" ">
298 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
299 </xml>
300
301 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" ">
302 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
303 </xml>
304
305 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" ">
306 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
307 </xml>
308
309 <xml name="pos_label" token_default_value="">
310 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/>
311 </xml>
312
313 <xml name="average">
314 <param argument="average" type="select" optional="true" label="Averaging type" help=" ">
315 <option value="micro">Calculate metrics globally by counting the total true positives, false negatives and false positives. (micro)</option>
316 <option value="samples">Calculate metrics for each instance, and find their average. Only meaningful for multilabel. (samples)</option>
317 <option value="macro">Calculate metrics for each label, and find their unweighted mean. This does not take label imbalance into account. (macro)</option>
318 <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>
319 <option value="None">None</option>
320 <yield/>
321 </param>
322 </xml>
323
324 <xml name="beta">
325 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/>
326 </xml>
327
328
329 <!--Data interface-->
330
331 <xml name="samples_tabular" token_multiple1="false" token_multiple2="false">
332 <param name="infile1" type="data" format="tabular" label="Training samples dataset:"/>
333 <param name="header1" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
334 <conditional name="column_selector_options_1">
335 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/>
336 </conditional>
337 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels or target values:"/>
338 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
339 <conditional name="column_selector_options_2">
340 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE2@" infile="infile2"/>
341 </conditional>
342 <yield/>
343 </xml>
344
345 <xml name="samples_column_selector_options" token_column_option="selected_column_selector_option" token_col_name="col1" token_multiple="False" token_infile="infile1">
346 <param name="@COLUMN_OPTION@" type="select" label="Choose how to select data by column:">
347 <option value="by_index_number" selected="true">Select columns by column index number(s)</option>
348 <option value="all_but_by_index_number">All columns EXCLUDING some by column index number(s)</option>
349 <option value="by_header_name">Select columns by column header name(s)</option>
350 <option value="all_but_by_header_name">All columns EXCLUDING some by column header name(s)</option>
351 <option value="all_columns">All columns</option>
352 </param>
353 <when value="by_index_number">
354 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" use_header_names="true" data_ref="@INFILE@" label="Select target column(s):"/>
355 </when>
356 <when value="all_but_by_index_number">
357 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" use_header_names="true" data_ref="@INFILE@" label="Select target column(s):"/>
358 </when>
359 <when value="by_header_name">
360 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2"/>
361 </when>
362 <when value="all_but_by_header_name">
363 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2"/>
364 </when>
365 <when value="all_columns">
366 </when>
367 </xml>
368
369 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False">
370 <conditional name="true_columns">
371 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:">
372 <option value="tabular" selected="true">Tabular</option>
373 <option value="sparse">Sparse</option>
374 </param>
375 <when value="tabular">
376 <param name="infile1" type="data" label="@LABEL1@"/>
377 <param name="col1" type="data_column" data_ref="infile1" label="Select the target column:"/>
378 </when>
379 <when value="sparse">
380 <param name="infile1" type="data" format="txt" label="@LABEL1@"/>
381 </when>
382 </conditional>
383 <conditional name="predicted_columns">
384 <param name="selected_input2" type="select" label="Select the input type of predicted labels dataset:">
385 <option value="tabular" selected="true">Tabular</option>
386 <option value="sparse">Sparse</option>
387 </param>
388 <when value="tabular">
389 <param name="infile2" type="data" label="@LABEL2@"/>
390 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
391 </when>
392 <when value="sparse">
393 <param name="infile2" type="data" format="txt" label="@LABEL1@"/>
394 </when>
395 </conditional>
396 </xml>
397
398 <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False">
399 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/>
400 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
401 <conditional name="column_selector_options_1">
402 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/>
403 </conditional>
404 <param name="infile2" type="data" format="tabular" label="@LABEL2@"/>
405 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
406 <conditional name="column_selector_options_2">
407 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE@" infile="infile2"/>
408 </conditional>
409 </xml>
410
411 <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.">
412 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
413 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>
414 </repeat>
415 </xml>
416
417 <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="">
418 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
419 <expand macro="input_tabular_target"/>
420 </xml>
421
422 <xml name="sl_mixed_input">
423 <conditional name="input_options">
424 <param name="selected_input" type="select" label="Select input type:">
425 <option value="tabular" selected="true">tabular data</option>
426 <option value="sparse">sparse matrix</option>
427 <option value="seq_fasta">sequnences in a fasta file</option>
428 <option value="refseq_and_interval">reference genome and intervals</option>
429 </param>
430 <when value="tabular">
431 <expand macro="samples_tabular" multiple1="true" multiple2="false"/>
432 </when>
433 <when value="sparse">
434 <expand macro="sparse_target"/>
435 </when>
436 <when value="seq_fasta">
437 <expand macro="inputs_seq_fasta"/>
438 </when>
439 <when value="refseq_and_interval">
440 <expand macro="inputs_refseq_and_interval"/>
441 </when>
442 </conditional>
443 </xml>
444
445 <xml name="input_tabular_target">
446 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels or target values:"/>
447 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" />
448 <conditional name="column_selector_options_2">
449 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="false" infile="infile2"/>
450 </conditional>
451 </xml>
452
453 <xml name="inputs_seq_fasta">
454 <param name="fasta_path" type="data" format="fasta" label="Dataset containing fasta genomic/protein sequences" help="Sequences will be one-hot encoded to arrays."/>
455 <expand macro="input_tabular_target"/>
456 </xml>
457
458 <xml name="inputs_refseq_and_interval">
459 <param name="ref_genome_file" type="data" format="fasta" label="Dataset containing reference genomic sequence"/>
460 <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."/>
461 <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`."/>
462 <param name="infile2" type="data" format="tabular" label="Dataset containing the feature list for prediction"/>
463 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" />
464 <conditional name="column_selector_options_2">
465 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="true" infile="infile2"/>
466 </conditional>
467 </xml>
468
469 <!--Advanced options-->
470 <xml name="nn_advanced_options">
471 <section name="options" title="Advanced Options" expanded="False">
472 <yield/>
473 <param argument="weights" type="select" label="Weight function" help="Used in prediction.">
474 <option value="uniform" selected="true">Uniform weights. All points in each neighborhood are weighted equally. (Uniform)</option>
475 <option value="distance">Weight points by the inverse of their distance. (Distance)</option>
476 </param>
477 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" ">
478 <option value="auto" selected="true">Auto</option>
479 <option value="ball_tree">BallTree</option>
480 <option value="kd_tree">KDTree</option>
481 <option value="brute">Brute-force</option>
482 </param>
483 <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."/>
484 <!--param name="metric"-->
485 <!--param name="p"-->
486 <!--param name="metric_params"-->
487 </section>
488 </xml>
489
490 <xml name="svc_advanced_options">
491 <section name="options" title="Advanced Options" expanded="False">
492 <yield/>
493 <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.">
494 <option value="rbf" selected="true">rbf</option>
495 <option value="linear">linear</option>
496 <option value="poly">poly</option>
497 <option value="sigmoid">sigmoid</option>
498 <option value="precomputed">precomputed</option>
499 </param>
500 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
501 <!--TODO: param argument="gamma" float, optional (default=’auto’) -->
502 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)"
503 help="Independent term in kernel function. dafault: 0.0 "/>
504 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
505 label="Use the shrinking heuristic" help=" "/>
506 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
507 label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/>
508 <!-- param argument="cache_size"-->
509 <!--expand macro="class_weight"/-->
510 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/>
511 <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."/>
512 <!--param argument="decision_function_shape"-->
513 <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."/>
514 </section>
515 </xml>
516
517 <xml name="spectral_clustering_advanced_options">
518 <section name="options" title="Advanced Options" expanded="False">
519 <expand macro="n_clusters"/>
520 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use.">
521 <option value="arpack" selected="true">arpack</option>
522 <option value="lobpcg">lobpcg</option>
523 <option value="amg">amg</option>
524 <!--None-->
525 </param>
526 <expand macro="random_state"/>
527 <expand macro="n_init"/>
528 <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''."/>
529 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. ">
530 <option value="rbf" selected="true">RBF</option>
531 <option value="precomputed">precomputed</option>
532 <option value="nearest_neighbors">Nearset neighbors</option>
533 </param>
534 <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''"/>
535 <!--param argument="eigen_tol"-->
536 <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space.">
537 <option value="kmeans" selected="true">kmeans</option>
538 <option value="discretize">discretize</option>
539 </param>
540 <param argument="degree" type="integer" optional="true" value="3"
541 label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
542 <param argument="coef0" type="integer" optional="true" value="1"
543 label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/>
544 <!--param argument="kernel_params"-->
545 </section>
546 </xml>
547
548 <xml name="minibatch_kmeans_advanced_options">
549 <section name="options" title="Advanced Options" expanded="False">
550 <expand macro="n_clusters"/>
551 <expand macro="init"/>
552 <expand macro="n_init" default_value="3"/>
553 <expand macro="max_iter" default_value="100"/>
554 <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ."/>
555 <expand macro="random_state"/>
556 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/>
557 <!--param argument="compute_labels"-->
558 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help="
559 Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia).
560 To disable, set max_no_improvement to None. "/>
561 <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 )"/>
562 <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."/>
563 </section>
564 </xml>
565
566 <xml name="kmeans_advanced_options">
567 <section name="options" title="Advanced Options" expanded="False">
568 <expand macro="n_clusters"/>
569 <expand macro="init"/>
570 <expand macro="n_init"/>
571 <expand macro="max_iter"/>
572 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence."/>
573 <!--param argument="precompute_distances"/-->
574 <expand macro="random_state"/>
575 <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."/>
576 <expand macro="kmeans_algorithm"/>
577 </section>
578 </xml>
579
580 <xml name="kmeans_algorithm">
581 <param argument="algorithm" type="select" label="K-means algorithm to use:">
582 <option value="auto" selected="true">auto</option>
583 <option value="full">full</option>
584 <option value="elkan">elkan</option>
585 </param>
586 </xml>
587
588 <xml name="birch_advanced_options">
589 <section name="options" title="Advanced Options" expanded="False">
590 <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."/>
591 <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."/>
592 <expand macro="n_clusters" default_value="3"/>
593 <!--param argument="compute_labels"/-->
594 </section>
595 </xml>
596
597 <xml name="dbscan_advanced_options">
598 <section name="options" title="Advanced Options" expanded="False">
599 <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."/>
600 <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."/>
601 <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."/>
602 <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.">
603 <option value="auto" selected="true">auto</option>
604 <option value="ball_tree">ball_tree</option>
605 <option value="kd_tree">kd_tree</option>
606 <option value="brute">brute</option>
607 </param>
608 <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."/>
609 </section>
610 </xml>
611
612 <xml name="clustering_algorithms_options">
613 <conditional name="algorithm_options">
614 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
615 <option value="KMeans" selected="true">KMeans</option>
616 <option value="SpectralClustering">Spectral Clustering</option>
617 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
618 <option value="DBSCAN">DBSCAN</option>
619 <option value="Birch">Birch</option>
620 </param>
621 <when value="KMeans">
622 <expand macro="kmeans_advanced_options"/>
623 </when>
624 <when value="DBSCAN">
625 <expand macro="dbscan_advanced_options"/>
626 </when>
627 <when value="Birch">
628 <expand macro="birch_advanced_options"/>
629 </when>
630 <when value="SpectralClustering">
631 <expand macro="spectral_clustering_advanced_options"/>
632 </when>
633 <when value="MiniBatchKMeans">
634 <expand macro="minibatch_kmeans_advanced_options"/>
635 </when>
636 </conditional>
637 </xml>
638
639 <xml name="distance_metrics">
640 <param argument="metric" type="select" label="Distance metric" help=" ">
641 <option value="euclidean" selected="true">euclidean</option>
642 <option value="cityblock">cityblock</option>
643 <option value="cosine">cosine</option>
644 <option value="l1">l1</option>
645 <option value="l2">l2</option>
646 <option value="manhattan">manhattan</option>
647 <yield/>
648 </param>
649 </xml>
650
651 <xml name="distance_nonsparse_metrics">
652 <option value="braycurtis">braycurtis</option>
653 <option value="canberra">canberra</option>
654 <option value="chebyshev">chebyshev</option>
655 <option value="correlation">correlation</option>
656 <option value="dice">dice</option>
657 <option value="hamming">hamming</option>
658 <option value="jaccard">jaccard</option>
659 <option value="kulsinski">kulsinski</option>
660 <option value="mahalanobis">mahalanobis</option>
661 <option value="matching">matching</option>
662 <option value="minkowski">minkowski</option>
663 <option value="rogerstanimoto">rogerstanimoto</option>
664 <option value="russellrao">russellrao</option>
665 <option value="seuclidean">seuclidean</option>
666 <option value="sokalmichener">sokalmichener</option>
667 <option value="sokalsneath">sokalsneath</option>
668 <option value="sqeuclidean">sqeuclidean</option>
669 <option value="yule">yule</option>
670 </xml>
671
672 <xml name="pairwise_kernel_metrics">
673 <param argument="metric" type="select" label="Pirwise Kernel metric" help=" ">
674 <option value="rbf" selected="true">rbf</option>
675 <option value="sigmoid">sigmoid</option>
676 <option value="polynomial">polynomial</option>
677 <option value="linear" selected="true">linear</option>
678 <option value="chi2">chi2</option>
679 <option value="additive_chi2">additive_chi2</option>
680 </param>
681 </xml>
682
683 <xml name="sparse_pairwise_metric_functions">
684 <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:">
685 <option value="euclidean_distances" selected="true">Euclidean distance matrix</option>
686 <option value="pairwise_distances">Distance matrix</option>
687 <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option>
688 <yield/>
689 </param>
690 </xml>
691
692 <xml name="pairwise_metric_functions">
693 <option value="additive_chi2_kernel" >Additive chi-squared kernel</option>
694 <option value="chi2_kernel">Exponential chi-squared kernel</option>
695 <option value="linear_kernel">Linear kernel</option>
696 <option value="manhattan_distances">L1 distances</option>
697 <option value="pairwise_kernels">Kernel</option>
698 <option value="polynomial_kernel">Polynomial kernel</option>
699 <option value="rbf_kernel">Gaussian (rbf) kernel</option>
700 <option value="laplacian_kernel">Laplacian kernel</option>
701 </xml>
702
703 <xml name="sparse_pairwise_condition">
704 <when value="pairwise_distances">
705 <section name="options" title="Advanced Options" expanded="False">
706 <expand macro="distance_metrics">
707 <yield/>
708 </expand>
709 </section>
710 </when>
711 <when value="euclidean_distances">
712 <section name="options" title="Advanced Options" expanded="False">
713 <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
714 label="Return squared Euclidean distances" help=" "/>
715 </section>
716 </when>
717 </xml>
718
719 <xml name="argmin_distance_condition">
720 <when value="pairwise_distances_argmin">
721 <section name="options" title="Advanced Options" expanded="False">
722 <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed."/>
723 <expand macro="distance_metrics">
724 <yield/>
725 </expand>
726 <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run."/>
727 </section>
728 </when>
729 </xml>
730
731 <xml name="sparse_preprocessors">
732 <param name="selected_pre_processor" type="select" label="Select a preprocessor:">
733 <option value="StandardScaler" selected="true">Standard Scaler (Standardizes features by removing the mean and scaling to unit variance)</option>
734 <option value="Binarizer">Binarizer (Binarizes data)</option>
735 <option value="MaxAbsScaler">Max Abs Scaler (Scales features by their maximum absolute value)</option>
736 <option value="Normalizer">Normalizer (Normalizes samples individually to unit norm)</option>
737 <yield/>
738 </param>
739 </xml>
740
741 <xml name="sparse_preprocessors_ext">
742 <expand macro="sparse_preprocessors">
743 <option value="KernelCenterer">Kernel Centerer (Centers a kernel matrix)</option>
744 <option value="MinMaxScaler">Minmax Scaler (Scales features to a range)</option>
745 <option value="PolynomialFeatures">Polynomial Features (Generates polynomial and interaction features)</option>
746 <option value="RobustScaler">Robust Scaler (Scales features using outlier-invariance statistics)</option>
747 </expand>
748 </xml>
749
750 <xml name="sparse_preprocessor_options">
751 <when value="Binarizer">
752 <section name="options" title="Advanced Options" expanded="False">
753 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
754 label="Use a copy of data for precomputing binarization" help=" "/>
755 <param argument="threshold" type="float" optional="true" value="0.0"
756 label="Threshold"
757 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. "/>
758 </section>
759 </when>
760 <when value="StandardScaler">
761 <section name="options" title="Advanced Options" expanded="False">
762 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
763 label="Use a copy of data for performing inplace scaling" help=" "/>
764 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
765 label="Center the data before scaling" help=" "/>
766 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
767 label="Scale the data to unit variance (or unit standard deviation)" help=" "/>
768 </section>
769 </when>
770 <when value="MaxAbsScaler">
771 <section name="options" title="Advanced Options" expanded="False">
772 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
773 label="Use a copy of data for precomputing scaling" help=" "/>
774 </section>
775 </when>
776 <when value="Normalizer">
777 <section name="options" title="Advanced Options" expanded="False">
778 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" ">
779 <option value="l1" selected="true">l1</option>
780 <option value="l2">l2</option>
781 <option value="max">max</option>
782 </param>
783 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
784 label="Use a copy of data for precomputing row normalization" help=" "/>
785 </section>
786 </when>
787 <yield/>
788 </xml>
789
790 <xml name="sparse_preprocessor_options_ext">
791 <expand macro="sparse_preprocessor_options">
792 <when value="KernelCenterer">
793 <section name="options" title="Advanced Options" expanded="False">
794 </section>
795 </when>
796 <when value="MinMaxScaler">
797 <section name="options" title="Advanced Options" expanded="False">
798 <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)"/>
799 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
800 label="Use a copy of data for precomputing normalization" help=" "/>
801 </section>
802 </when>
803 <when value="PolynomialFeatures">
804 <section name="options" title="Advanced Options" expanded="False">
805 <param argument="degree" type="integer" optional="true" value="2" label="The degree of the polynomial features " help=""/>
806 <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) "/>
807 <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 "/>
808 </section>
809 </when>
810 <when value="RobustScaler">
811 <section name="options" title="Advanced Options" expanded="False">
812 <!--=True, =True, copy=True-->
813 <param argument="with_centering" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
814 label="Center the data before scaling" help=" "/>
815 <param argument="with_scaling" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
816 label="Scale the data to interquartile range" help=" "/>
817 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
818 label="Use a copy of data for inplace scaling" help=" "/>
819 </section>
820 </when>
821 </expand>
822 </xml>
823
824 <xml name="cv_splitter">
825 <option value="default" selected="true">default splitter</option>
826 <option value="KFold">KFold</option>
827 <option value="StratifiedKFold">StratifiedKFold</option>
828 <option value="LeaveOneOut">LeaveOneOut</option>
829 <option value="LeavePOut">LeavePOut</option>
830 <option value="RepeatedKFold">RepeatedKFold</option>
831 <option value="RepeatedStratifiedKFold">RepeatedStratifiedKFold</option>
832 <option value="ShuffleSplit">ShuffleSplit</option>
833 <option value="StratifiedShuffleSplit">StratifiedShuffleSplit</option>
834 <option value="TimeSeriesSplit">TimeSeriesSplit</option>
835 <option value="PredefinedSplit">PredefinedSplit</option>
836 <option value="OrderedKFold">OrderedKFold</option>
837 <option value="RepeatedOrderedKFold">RepeatedOrderedKFold</option>
838 <yield/>
839 </xml>
840
841 <xml name="cv_splitter_options">
842 <when value="default">
843 <expand macro="cv_n_splits"/>
844 </when>
845 <when value="KFold">
846 <expand macro="cv_n_splits"/>
847 <expand macro="cv_shuffle"/>
848 <expand macro="random_state"/>
849 </when>
850 <when value="StratifiedKFold">
851 <expand macro="cv_n_splits"/>
852 <expand macro="cv_shuffle"/>
853 <expand macro="random_state"/>
854 </when>
855 <when value="LeaveOneOut">
856 </when>
857 <when value="LeavePOut">
858 <param argument="p" type="integer" value="" label="p" help="Integer. Size of the test sets."/>
859 </when>
860 <when value="RepeatedKFold">
861 <expand macro="cv_n_splits" value="5"/>
862 <param argument="n_repeats" type="integer" value="10" label="n_repeats" help="Number of times cross-validator needs to be repeated." />
863 <expand macro="random_state" />
864 </when>
865 <when value="RepeatedStratifiedKFold">
866 <expand macro="cv_n_splits" value="5"/>
867 <param argument="n_repeats" type="integer" value="10" label="n_repeats" help="Number of times cross-validator needs to be repeated." />
868 <expand macro="random_state" />
869 </when>
870 <when value="ShuffleSplit">
871 <expand macro="cv_n_splits" value="10" help="Number of re-shuffling and splitting iterations."/>
872 <expand macro="cv_test_size" value="0.1" />
873 <expand macro="random_state"/>
874 </when>
875 <when value="StratifiedShuffleSplit">
876 <expand macro="cv_n_splits" value="10" help="Number of re-shuffling and splitting iterations."/>
877 <expand macro="cv_test_size" value="0.1" />
878 <expand macro="random_state"/>
879 </when>
880 <when value="TimeSeriesSplit">
881 <expand macro="cv_n_splits"/>
882 <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." />
883 </when>
884 <when value="PredefinedSplit">
885 <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'."/>
886 </when>
887 <when value="OrderedKFold">
888 <expand macro="cv_n_splits"/>
889 <expand macro="cv_shuffle"/>
890 <expand macro="random_state"/>
891 </when>
892 <when value="RepeatedOrderedKFold">
893 <expand macro="cv_n_splits"/>
894 <param argument="n_repeats" type="integer" value="5"/>
895 <expand macro="random_state"/>
896 </when>
897 <yield/>
898 </xml>
899
900 <xml name="cv">
901 <conditional name="cv_selector">
902 <param name="selected_cv" type="select" label="Select the cv splitter:">
903 <expand macro="cv_splitter">
904 <option value="GroupKFold">GroupKFold</option>
905 <option value="GroupShuffleSplit">GroupShuffleSplit</option>
906 <option value="LeaveOneGroupOut">LeaveOneGroupOut</option>
907 <option value="LeavePGroupsOut">LeavePGroupsOut</option>
908 </expand>
909 </param>
910 <expand macro="cv_splitter_options">
911 <when value="GroupKFold">
912 <expand macro="cv_n_splits"/>
913 <expand macro="cv_groups" />
914 </when>
915 <when value="GroupShuffleSplit">
916 <expand macro="cv_n_splits" value="5"/>
917 <expand macro="cv_test_size"/>
918 <expand macro="random_state"/>
919 <expand macro="cv_groups"/>
920 </when>
921 <when value="LeaveOneGroupOut">
922 <expand macro="cv_groups"/>
923 </when>
924 <when value="LeavePGroupsOut">
925 <param argument="n_groups" type="integer" value="" label="n_groups" help="Number of groups (p) to leave out in the test split." />
926 <expand macro="cv_groups"/>
927 </when>
928 </expand>
929 </conditional>
930 </xml>
931
932 <xml name="cv_reduced" token_label="Select the cv splitter">
933 <conditional name="cv_selector">
934 <param name="selected_cv" type="select" label="@LABEL@">
935 <expand macro="cv_splitter"/>
936 </param>
937 <expand macro="cv_splitter_options"/>
938 </conditional>
939 </xml>
940
941 <xml name="cv_n_splits" token_value="3" token_help="Number of folds. Must be at least 2.">
942 <param argument="n_splits" type="integer" value="@VALUE@" min="1" label="n_splits" help="@HELP@"/>
943 </xml>
944
945 <xml name="cv_shuffle">
946 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to shuffle data before splitting" />
947 </xml>
948
949 <xml name="cv_test_size" token_value="0.2">
950 <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 "/>
951 </xml>
952
953 <xml name="cv_groups" >
954 <section name="groups_selector" title="Groups column selector" expanded="true">
955 <param name="infile_g" type="data" format="tabular" label="Choose dataset containing groups info:"/>
956 <param name="header_g" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
957 <conditional name="column_selector_options_g">
958 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option_g" col_name="col_g" multiple="False" infile="infile_g"/>
959 </conditional>
960 </section>
961 </xml>
962
963 <xml name="train_test_split_params">
964 <conditional name="split_algos">
965 <param name="shuffle" type="select" label="Select the splitting method">
966 <option value="None">No shuffle</option>
967 <option value="simple" selected="true">ShuffleSplit</option>
968 <option value="stratified">StratifiedShuffleSplit -- target values serve as class labels</option>
969 <option value="group">GroupShuffleSplit or split by group names</option>
970 </param>
971 <when value="None">
972 <expand macro="train_test_split_test_size"/>
973 </when>
974 <when value="simple">
975 <expand macro="train_test_split_test_size"/>
976 <expand macro="random_state"/>
977 </when>
978 <when value="stratified">
979 <expand macro="train_test_split_test_size"/>
980 <expand macro="random_state"/>
981 </when>
982 <when value="group">
983 <expand macro="train_test_split_test_size" optional="true"/>
984 <expand macro="random_state"/>
985 <param argument="group_names" type="text" value="" optional="true" label="Type in group names instead"
986 help="For example: chr6, chr7. This parameter is optional. If used, it will override the holdout size and random seed."/>
987 <yield/>
988 </when>
989 </conditional>
990 <!--param argument="train_size" type="float" optional="True" value="" label="Train size:"/>-->
991 </xml>
992
993 <xml name="train_test_split_test_size" token_optional="false">
994 <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."/>
995 </xml>
996
997 <xml name="feature_selection_algorithms">
998 <option value="SelectKBest" selected="true">SelectKBest - Select features according to the k highest scores</option>
999 <option value="GenericUnivariateSelect">GenericUnivariateSelect - Univariate feature selector with configurable strategy</option>
1000 <option value="SelectPercentile">SelectPercentile - Select features according to a percentile of the highest scores</option>
1001 <option value="SelectFpr">SelectFpr - Filter: Select the p-values below alpha based on a FPR test</option>
1002 <option value="SelectFdr">SelectFdr - Filter: Select the p-values for an estimated false discovery rate</option>
1003 <option value="SelectFwe">SelectFwe - Filter: Select the p-values corresponding to Family-wise error rate</option>
1004 <option value="VarianceThreshold">VarianceThreshold - Feature selector that removes all low-variance features</option>
1005 <option value="SelectFromModel">SelectFromModel - Meta-transformer for selecting features based on importance weights</option>
1006 <option value="RFE">RFE - Feature ranking with recursive feature elimination</option>
1007 <option value="RFECV">RFECV - Feature ranking with recursive feature elimination and cross-validated selection of the best number of features</option>
1008 <yield/>
1009 </xml>
1010
1011 <xml name="feature_selection_algorithm_details">
1012 <when value="GenericUnivariateSelect">
1013 <expand macro="feature_selection_score_function" />
1014 <section name="options" title="Advanced Options" expanded="False">
1015 <param argument="mode" type="select" label="Feature selection mode">
1016 <option value="percentile">percentile</option>
1017 <option value="k_best">k_best</option>
1018 <option value="fpr">fpr</option>
1019 <option value="fdr">fdr</option>
1020 <option value="fwe">fwe</option>
1021 </param>
1022 <param argument="param" type="float" value="" optional="true" label="Parameter of the corresponding mode" help="float or int depending on the feature selection mode" />
1023 </section>
1024 </when>
1025 <when value="SelectPercentile">
1026 <expand macro="feature_selection_score_function" />
1027 <section name="options" title="Advanced Options" expanded="False">
1028 <param argument="percentile" type="integer" value="10" optional="True" label="Percent of features to keep" />
1029 </section>
1030 </when>
1031 <when value="SelectKBest">
1032 <expand macro="feature_selection_score_function" />
1033 <section name="options" title="Advanced Options" expanded="False">
1034 <param argument="k" type="integer" value="10" optional="True" label="Number of top features to select" help="No 'all' option is supported." />
1035 </section>
1036 </when>
1037 <when value="SelectFpr">
1038 <expand macro="feature_selection_score_function" />
1039 <section name="options" title="Advanced Options" expanded="False">
1040 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest p-value for features to be kept."/>
1041 </section>
1042 </when>
1043 <when value="SelectFdr">
1044 <expand macro="feature_selection_score_function" />
1045 <section name="options" title="Advanced Options" expanded="False">
1046 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/>
1047 </section>
1048 </when>
1049 <when value="SelectFwe">
1050 <expand macro="feature_selection_score_function" />
1051 <section name="options" title="Advanced Options" expanded="False">
1052 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/>
1053 </section>
1054 </when>
1055 <when value="VarianceThreshold">
1056 <section name="options" title="Options" expanded="False">
1057 <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."/>
1058 </section>
1059 </when>
1060 </xml>
1061
1062 <xml name="feature_selection_SelectFromModel">
1063 <when value="SelectFromModel">
1064 <conditional name="model_inputter">
1065 <param name="input_mode" type="select" label="Construct a new estimator from a selection list?" >
1066 <option value="new" selected="true">Yes</option>
1067 <option value="prefitted">No. Load a prefitted estimator</option>
1068 </param>
1069 <when value="new">
1070 <expand macro="estimator_selector_fs"/>
1071 </when>
1072 <when value="prefitted">
1073 <param name="fitted_estimator" type="data" format='zip' label="Load a prefitted estimator" />
1074 </when>
1075 </conditional>
1076 <expand macro="feature_selection_SelectFromModel_options"/>
1077 </when>
1078 </xml>
1079
1080 <xml name="feature_selection_SelectFromModel_no_prefitted">
1081 <when value="SelectFromModel">
1082 <conditional name="model_inputter">
1083 <param name="input_mode" type="select" label="Construct a new estimator from a selection list?" >
1084 <option value="new" selected="true">Yes</option>
1085 </param>
1086 <when value="new">
1087 <expand macro="estimator_selector_all"/>
1088 </when>
1089 </conditional>
1090 <expand macro="feature_selection_SelectFromModel_options"/>
1091 </when>
1092 </xml>
1093
1094 <xml name="feature_selection_SelectFromModel_options">
1095 <section name="options" title="Advanced Options" expanded="False">
1096 <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'." />
1097 <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. " />
1098 <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."/>
1099 </section>
1100 </xml>
1101
1102 <xml name="feature_selection_RFE">
1103 <when value="RFE">
1104 <yield/>
1105 <section name="options" title="Advanced Options" expanded="False">
1106 <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." />
1107 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
1108 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
1109 </section>
1110 </when>
1111 </xml>
1112
1113 <xml name="feature_selection_RFECV_fs">
1114 <when value="RFECV">
1115 <yield/>
1116 <section name="options" title="Advanced Options" expanded="False">
1117 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
1118 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/>
1119 <expand macro="cv"/>
1120 <expand macro="scoring_selection"/>
1121 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
1122 </section>
1123 </when>
1124 </xml>
1125
1126 <xml name="feature_selection_RFECV_pipeline">
1127 <when value="RFECV">
1128 <yield/>
1129 <section name="options" title="Advanced Options" expanded="False">
1130 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
1131 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/>
1132 <expand macro="cv_reduced"/>
1133 <!-- TODO: group splitter support-->
1134 <expand macro="scoring_selection"/>
1135 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
1136 </section>
1137 </when>
1138 </xml>
1139
1140 <xml name="feature_selection_DyRFECV_fs">
1141 <when value="DyRFECV">
1142 <yield/>
1143 <section name="options" title="Advanced Options" expanded="False">
1144 <param argument="step" type="text" size="30" value="1" label="step" optional="true" help="Default = 1. Support float, int and list." >
1145 <sanitizer>
1146 <valid initial="default">
1147 <add value="["/>
1148 <add value="]"/>
1149 </valid>
1150 </sanitizer>
1151 </param>
1152 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/>
1153 <expand macro="cv"/>
1154 <expand macro="scoring_selection"/>
1155 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
1156 </section>
1157 </when>
1158 </xml>
1159
1160 <xml name="feature_selection_pipeline">
1161 <!--compare to `feature_selection_fs`, no fitted estimator for SelectFromModel and no custom estimator for RFE and RFECV-->
1162 <conditional name="fs_algorithm_selector">
1163 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm">
1164 <expand macro="feature_selection_algorithms"/>
1165 </param>
1166 <expand macro="feature_selection_algorithm_details"/>
1167 <expand macro="feature_selection_SelectFromModel_no_prefitted"/>
1168 <expand macro="feature_selection_RFE">
1169 <expand macro="estimator_selector_all"/>
1170 </expand>
1171 <expand macro="feature_selection_RFECV_pipeline">
1172 <expand macro="estimator_selector_all"/>
1173 </expand>
1174 <!-- TODO: add DyRFECV to pipeline-->
1175 </conditional>
1176 </xml>
1177
1178 <xml name="feature_selection_fs">
1179 <conditional name="fs_algorithm_selector">
1180 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm">
1181 <expand macro="feature_selection_algorithms">
1182 <option value="DyRFECV">DyRFECV - Extended RFECV with changeable steps</option>
1183 </expand>
1184 </param>
1185 <expand macro="feature_selection_algorithm_details"/>
1186 <expand macro="feature_selection_SelectFromModel"/>
1187 <expand macro="feature_selection_RFE">
1188 <expand macro="estimator_selector_fs"/>
1189 </expand>
1190 <expand macro="feature_selection_RFECV_fs">
1191 <expand macro="estimator_selector_fs"/>
1192 </expand>
1193 <expand macro="feature_selection_DyRFECV_fs">
1194 <expand macro="estimator_selector_fs"/>
1195 </expand>
1196 </conditional>
1197 </xml>
1198
1199 <xml name="feature_selection_score_function">
1200 <param argument="score_func" type="select" label="Select a score function">
1201 <option value="chi2">chi2 - Compute chi-squared stats between each non-negative feature and class</option>
1202 <option value="f_classif">f_classif - Compute the ANOVA F-value for the provided sample</option>
1203 <option value="f_regression">f_regression - Univariate linear regression tests</option>
1204 <option value="mutual_info_classif">mutual_info_classif - Estimate mutual information for a discrete target variable</option>
1205 <option value="mutual_info_regression">mutual_info_regression - Estimate mutual information for a continuous target variable</option>
1206 </param>
1207 </xml>
1208
1209 <xml name="model_validation_common_options">
1210 <expand macro="cv"/>
1211 <expand macro="verbose"/>
1212 <yield/>
1213 </xml>
1214
1215 <xml name="scoring_selection">
1216 <conditional name="scoring">
1217 <param name="primary_scoring" type="select" multiple="false" label="Select the primary metric (scoring):" help="Metric to refit the best estimator.">
1218 <option value="default" selected="true">default with estimator</option>
1219 <option value="accuracy">Classification -- 'accuracy'</option>
1220 <option value="balanced_accuracy">Classification -- 'balanced_accuracy'</option>
1221 <option value="average_precision">Classification -- 'average_precision'</option>
1222 <option value="f1">Classification -- 'f1'</option>
1223 <option value="f1_micro">Classification -- 'f1_micro'</option>
1224 <option value="f1_macro">Classification -- 'f1_macro'</option>
1225 <option value="f1_weighted">Classification -- 'f1_weighted'</option>
1226 <option value="f1_samples">Classification -- 'f1_samples'</option>
1227 <option value="neg_log_loss">Classification -- 'neg_log_loss'</option>
1228 <option value="precision">Classification -- 'precision'</option>
1229 <option value="precision_micro">Classification -- 'precision_micro'</option>
1230 <option value="precision_macro">Classification -- 'precision_macro'</option>
1231 <option value="precision_wighted">Classification -- 'precision_wighted'</option>
1232 <option value="precision_samples">Classification -- 'precision_samples'</option>
1233 <option value="recall">Classification -- 'recall'</option>
1234 <option value="recall_micro">Classification -- 'recall_micro'</option>
1235 <option value="recall_macro">Classification -- 'recall_macro'</option>
1236 <option value="recall_wighted">Classification -- 'recall_wighted'</option>
1237 <option value="recall_samples">Classification -- 'recall_samples'</option>
1238 <option value="roc_auc">Classification -- 'roc_auc'</option>
1239 <option value="explained_variance">Regression -- 'explained_variance'</option>
1240 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option>
1241 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option>
1242 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option>
1243 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option>
1244 <option value="r2">Regression -- 'r2'</option>
1245 <option value="binarize_auc_scorer">anomaly detection -- binarize_auc_scorer</option>
1246 <option value="binarize_average_precision_scorer">anomaly detection -- binarize_average_precision_scorer</option>
1247 </param>
1248 <when value="default"/>
1249 <when value="accuracy"><expand macro="secondary_scoring_selection_classification"/></when>
1250 <when value="balanced_accuracy"><expand macro="secondary_scoring_selection_classification"/></when>
1251 <when value="average_precision"><expand macro="secondary_scoring_selection_classification"/></when>
1252 <when value="f1"><expand macro="secondary_scoring_selection_classification"/></when>
1253 <when value="f1_micro"><expand macro="secondary_scoring_selection_classification"/></when>
1254 <when value="f1_macro"><expand macro="secondary_scoring_selection_classification"/></when>
1255 <when value="f1_weighted"><expand macro="secondary_scoring_selection_classification"/></when>
1256 <when value="f1_samples"><expand macro="secondary_scoring_selection_classification"/></when>
1257 <when value="neg_log_loss"><expand macro="secondary_scoring_selection_classification"/></when>
1258 <when value="precision"><expand macro="secondary_scoring_selection_classification"/></when>
1259 <when value="precision_micro"><expand macro="secondary_scoring_selection_classification"/></when>
1260 <when value="precision_macro"><expand macro="secondary_scoring_selection_classification"/></when>
1261 <when value="precision_wighted"><expand macro="secondary_scoring_selection_classification"/></when>
1262 <when value="precision_samples"><expand macro="secondary_scoring_selection_classification"/></when>
1263 <when value="recall"><expand macro="secondary_scoring_selection_classification"/></when>
1264 <when value="recall_micro"><expand macro="secondary_scoring_selection_classification"/></when>
1265 <when value="recall_macro"><expand macro="secondary_scoring_selection_classification"/></when>
1266 <when value="recall_wighted"><expand macro="secondary_scoring_selection_classification"/></when>
1267 <when value="recall_samples"><expand macro="secondary_scoring_selection_classification"/></when>
1268 <when value="roc_auc"><expand macro="secondary_scoring_selection_classification"/></when>
1269 <when value="explained_variance"><expand macro="secondary_scoring_selection_regression"/></when>
1270 <when value="neg_mean_absolute_error"><expand macro="secondary_scoring_selection_regression"/></when>
1271 <when value="neg_mean_squared_error"><expand macro="secondary_scoring_selection_regression"/></when>
1272 <when value="neg_mean_squared_log_error"><expand macro="secondary_scoring_selection_regression"/></when>
1273 <when value="neg_median_absolute_error"><expand macro="secondary_scoring_selection_regression"/></when>
1274 <when value="r2"><expand macro="secondary_scoring_selection_regression"/></when>
1275 <when value="binarize_auc_scorer"><expand macro="secondary_scoring_selection_anormaly"/></when>
1276 <when value="binarize_average_precision_scorer"><expand macro="secondary_scoring_selection_anormaly"/></when>
1277 </conditional>
1278 </xml>
1279
1280 <xml name="secondary_scoring_selection_classification">
1281 <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.">
1282 <option value="accuracy">Classification -- 'accuracy'</option>
1283 <option value="balanced_accuracy">Classification -- 'balanced_accuracy'</option>
1284 <option value="average_precision">Classification -- 'average_precision'</option>
1285 <option value="f1">Classification -- 'f1'</option>
1286 <option value="f1_micro">Classification -- 'f1_micro'</option>
1287 <option value="f1_macro">Classification -- 'f1_macro'</option>
1288 <option value="f1_weighted">Classification -- 'f1_weighted'</option>
1289 <option value="f1_samples">Classification -- 'f1_samples'</option>
1290 <option value="neg_log_loss">Classification -- 'neg_log_loss'</option>
1291 <option value="precision">Classification -- 'precision'</option>
1292 <option value="precision_micro">Classification -- 'precision_micro'</option>
1293 <option value="precision_macro">Classification -- 'precision_macro'</option>
1294 <option value="precision_wighted">Classification -- 'precision_wighted'</option>
1295 <option value="precision_samples">Classification -- 'precision_samples'</option>
1296 <option value="recall">Classification -- 'recall'</option>
1297 <option value="recall_micro">Classification -- 'recall_micro'</option>
1298 <option value="recall_macro">Classification -- 'recall_macro'</option>
1299 <option value="recall_wighted">Classification -- 'recall_wighted'</option>
1300 <option value="recall_samples">Classification -- 'recall_samples'</option>
1301 <option value="roc_auc">Classification -- 'roc_auc'</option>
1302 </param>
1303 </xml>
1304
1305 <xml name="secondary_scoring_selection_regression">
1306 <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.">
1307 <option value="explained_variance">Regression -- 'explained_variance'</option>
1308 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option>
1309 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option>
1310 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option>
1311 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option>
1312 <option value="r2">Regression -- 'r2'</option>
1313 </param>
1314 </xml>
1315
1316 <xml name="secondary_scoring_selection_anormaly">
1317 <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.">
1318 <option value="binarize_auc_scorer">anomaly detection -- binarize_auc_scorer</option>
1319 <option value="binarize_average_precision_scorer">anomaly detection -- binarize_average_precision_scorer</option>
1320 </param>
1321 </xml>
1322
1323 <xml name="pre_dispatch" token_type="hidden" token_default_value="all" token_help="Number of predispatched jobs for parallel execution">
1324 <param argument="pre_dispatch" type="@TYPE@" value="@DEFAULT_VALUE@" optional="true" label="pre_dispatch" help="@HELP@"/>
1325 </xml>
1326
1327 <xml name="search_cv_estimator">
1328 <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing pipeline/estimator object"/>
1329 <section name="search_params_builder" title="Search parameters Builder" expanded="true">
1330 <param name="infile_params" type="data" format="tabular" optional="true" label="Choose the dataset containing parameter names" help="This dataset could be the output of `get_params` in the `Estimator Attributes` tool."/>
1331 <repeat name="param_set" min="1" max="30" title="Parameter settings for search:">
1332 <param name="sp_name" type="select" optional="true" label="Choose a parameter name (with current value)">
1333 <options from_dataset="infile_params" startswith="@">
1334 <column name="name" index="2"/>
1335 <column name="value" index="1"/>
1336 <filter type="unique_value" name="unique_param" column="1"/>
1337 </options>
1338 </param>
1339 <param name="sp_list" type="text" value="" optional="true" label="Search list" help="list or array-like, for example: [1, 10, 100, 1000], [True, False] and ['auto', 'sqrt', None]. See `help` section for more examples">
1340 <sanitizer>
1341 <valid initial="default">
1342 <add value="&apos;"/>
1343 <add value="&quot;"/>
1344 <add value="["/>
1345 <add value="]"/>
1346 </valid>
1347 </sanitizer>
1348 </param>
1349 </repeat>
1350 </section>
1351 </xml>
1352
1353 <xml name="estimator_and_hyperparameter">
1354 <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing pipeline/estimator object"/>
1355 <section name="hyperparams_swapping" title="Hyperparameter Swapping" expanded="false">
1356 <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."/>
1357 <repeat name="param_set" min="1" max="30" title="New hyperparameter setting">
1358 <param name="sp_name" type="select" optional="true" label="Choose a parameter name (with current value)">
1359 <options from_dataset="infile_params" startswith="@">
1360 <column name="name" index="2"/>
1361 <column name="value" index="1"/>
1362 <filter type="unique_value" name="unique_param" column="1"/>
1363 </options>
1364 </param>
1365 <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.">
1366 <sanitizer>
1367 <valid initial="default">
1368 <add value="&apos;"/>
1369 <add value="&quot;"/>
1370 </valid>
1371 </sanitizer>
1372 </param>
1373 </repeat>
1374 </section>
1375 </xml>
1376
1377 <xml name="search_cv_options">
1378 <expand macro="scoring_selection"/>
1379 <expand macro="model_validation_common_options"/>
1380 <!--expand macro="pre_dispatch" default_value="2*n_jobs" help="Controls the number of jobs that get dispatched during parallel execution"/-->
1381 <param argument="iid" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="iid" help="If True, data is identically distributed across the folds"/>
1382 <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."/>
1383 <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."/>
1384 <param argument="return_train_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="return_train_score" help=""/>
1385 </xml>
1386
1387 <xml name="estimator_module_options">
1388 <option value="svm" selected="true">sklearn.svm</option>
1389 <option value="linear_model">sklearn.linear_model</option>
1390 <option value="ensemble">sklearn.ensemble</option>
1391 <option value="naive_bayes">sklearn.naive_bayes</option>
1392 <option value="tree">sklearn.tree</option>
1393 <option value="neighbors">sklearn.neighbors</option>
1394 <option value="xgboost">xgboost</option>
1395 <yield/>
1396 </xml>
1397
1398 <xml name="estimator_suboptions">
1399 <when value="svm">
1400 <param name="selected_estimator" type="select" label="Choose estimator class:">
1401 <option value="LinearSVC" selected="true">LinearSVC</option>
1402 <option value="LinearSVR">LinearSVR</option>
1403 <option value="NuSVC">NuSVC</option>
1404 <option value="NuSVR">NuSVR</option>
1405 <option value="OneClassSVM">OneClassSVM</option>
1406 <option value="SVC">SVC</option>
1407 <option value="SVR">SVR</option>
1408 </param>
1409 <expand macro="estimator_params_text"/>
1410 </when>
1411 <when value="linear_model">
1412 <param name="selected_estimator" type="select" label="Choose estimator class:">
1413 <option value="ARDRegression" selected="true">ARDRegression</option>
1414 <option value="BayesianRidge">BayesianRidge</option>
1415 <option value="ElasticNet">ElasticNet</option>
1416 <option value="ElasticNetCV">ElasticNetCV</option>
1417 <option value="HuberRegressor">HuberRegressor</option>
1418 <option value="Lars">Lars</option>
1419 <option value="LarsCV">LarsCV</option>
1420 <option value="Lasso">Lasso</option>
1421 <option value="LassoCV">LassoCV</option>
1422 <option value="LassoLars">LassoLars</option>
1423 <option value="LassoLarsCV">LassoLarsCV</option>
1424 <option value="LassoLarsIC">LassoLarsIC</option>
1425 <option value="LinearRegression">LinearRegression</option>
1426 <option value="LogisticRegression">LogisticRegression</option>
1427 <option value="LogisticRegressionCV">LogisticRegressionCV</option>
1428 <option value="MultiTaskLasso">MultiTaskLasso</option>
1429 <option value="MultiTaskElasticNet">MultiTaskElasticNet</option>
1430 <option value="MultiTaskLassoCV">MultiTaskLassoCV</option>
1431 <option value="MultiTaskElasticNetCV">MultiTaskElasticNetCV</option>
1432 <option value="OrthogonalMatchingPursuit">OrthogonalMatchingPursuit</option>
1433 <option value="OrthogonalMatchingPursuitCV">OrthogonalMatchingPursuitCV</option>
1434 <option value="PassiveAggressiveClassifier">PassiveAggressiveClassifier</option>
1435 <option value="PassiveAggressiveRegressor">PassiveAggressiveRegressor</option>
1436 <option value="Perceptron">Perceptron</option>
1437 <option value="RANSACRegressor">RANSACRegressor</option>
1438 <option value="Ridge">Ridge</option>
1439 <option value="RidgeClassifier">RidgeClassifier</option>
1440 <option value="RidgeClassifierCV">RidgeClassifierCV</option>
1441 <option value="RidgeCV">RidgeCV</option>
1442 <option value="SGDClassifier">SGDClassifier</option>
1443 <option value="SGDRegressor">SGDRegressor</option>
1444 <option value="TheilSenRegressor">TheilSenRegressor</option>
1445 </param>
1446 <expand macro="estimator_params_text"/>
1447 </when>
1448 <when value="ensemble">
1449 <param name="selected_estimator" type="select" label="Choose estimator class:">
1450 <option value="AdaBoostClassifier" selected="true">AdaBoostClassifier</option>
1451 <option value="AdaBoostRegressor">AdaBoostRegressor</option>
1452 <option value="BaggingClassifier">BaggingClassifier</option>
1453 <option value="BaggingRegressor">BaggingRegressor</option>
1454 <option value="ExtraTreesClassifier">ExtraTreesClassifier</option>
1455 <option value="ExtraTreesRegressor">ExtraTreesRegressor</option>
1456 <option value="GradientBoostingClassifier">GradientBoostingClassifier</option>
1457 <option value="GradientBoostingRegressor">GradientBoostingRegressor</option>
1458 <option value="IsolationForest">IsolationForest</option>
1459 <option value="RandomForestClassifier">RandomForestClassifier</option>
1460 <option value="RandomForestRegressor">RandomForestRegressor</option>
1461 <option value="RandomTreesEmbedding">RandomTreesEmbedding</option>
1462 <!--option value="VotingClassifier">VotingClassifier</option-->
1463 </param>
1464 <expand macro="estimator_params_text"/>
1465 </when>
1466 <when value="naive_bayes">
1467 <param name="selected_estimator" type="select" label="Choose estimator class:">
1468 <option value="BernoulliNB" selected="true">BernoulliNB</option>
1469 <option value="GaussianNB">GaussianNB</option>
1470 <option value="MultinomialNB">MultinomialNB</option>
1471 </param>
1472 <expand macro="estimator_params_text"/>
1473 </when>
1474 <when value="tree">
1475 <param name="selected_estimator" type="select" label="Choose estimator class:">
1476 <option value="DecisionTreeClassifier" selected="true">DecisionTreeClassifier</option>
1477 <option value="DecisionTreeRegressor">DecisionTreeRegressor</option>
1478 <option value="ExtraTreeClassifier">ExtraTreeClassifier</option>
1479 <option value="ExtraTreeRegressor">ExtraTreeRegressor</option>
1480 </param>
1481 <expand macro="estimator_params_text"/>
1482 </when>
1483 <when value="neighbors">
1484 <param name="selected_estimator" type="select" label="Choose estimator class:">
1485 <option value="KNeighborsClassifier" selected="true">KNeighborsClassifier</option>
1486 <option value="KNeighborsRegressor">KNeighborsRegressor</option>
1487 <!--option value="BallTree">BallTree</option-->
1488 <!--option value="KDTree">KDTree</option-->
1489 <option value="KernelDensity">KernelDensity</option>
1490 <option value="LocalOutlierFactor">LocalOutlierFactor</option>
1491 <option value="RadiusNeighborsClassifier">RadiusNeighborsClassifier</option>
1492 <option value="RadiusNeighborsRegressor">RadiusNeighborsRegressor</option>
1493 <option value="NearestCentroid">NearestCentroid</option>
1494 <option value="NearestNeighbors">NearestNeighbors</option>
1495 </param>
1496 <expand macro="estimator_params_text"/>
1497 </when>
1498 <when value="xgboost">
1499 <param name="selected_estimator" type="select" label="Choose estimator class:">
1500 <option value="XGBRegressor" selected="true">XGBRegressor</option>
1501 <option value="XGBClassifier">XGBClassifier</option>
1502 </param>
1503 <expand macro="estimator_params_text"/>
1504 </when>
1505 <yield/>
1506 </xml>
1507
1508 <xml name="estimator_selector_all">
1509 <conditional name="estimator_selector">
1510 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" >
1511 <expand macro="estimator_module_options"/>
1512 </param>
1513 <expand macro="estimator_suboptions"/>
1514 </conditional>
1515 </xml>
1516
1517 <xml name="estimator_selector_fs">
1518 <conditional name="estimator_selector">
1519 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" >
1520 <expand macro="estimator_module_options">
1521 <option value="custom_estimator">Load a custom estimator</option>
1522 </expand>
1523 </param>
1524 <expand macro="estimator_suboptions">
1525 <when value="custom_estimator">
1526 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline:"/>
1527 </when>
1528 </expand>
1529 </conditional>
1530 </xml>
1531
1532 <xml name="estimator_params_text" token_label="Type in parameter settings if different from default:" token_default_value=''
1533 token_help="Dictionary-capable, e.g., C=1, kernel='linear'. No double quotes. Leave this box blank for default estimator.">
1534 <param name="text_params" type="text" value="@DEFAULT_VALUE@" optional="true" label="@LABEL@" help="@HELP@">
1535 <sanitizer>
1536 <valid initial="default">
1537 <add value="&apos;"/>
1538 </valid>
1539 </sanitizer>
1540 </param>
1541 </xml>
1542
1543 <xml name="kernel_approximation_all">
1544 <conditional name="kernel_approximation_selector">
1545 <param name="select_algorithm" type="select" label="Choose a kernel approximation algorithm:">
1546 <option value="Nystroem" selected="true">Nystroem</option>
1547 <option value="RBFSampler">RBFSampler</option>
1548 <option value="AdditiveChi2Sampler">AdditiveChi2Sampler</option>
1549 <option value="SkewedChi2Sampler">SkewedChi2Sampler</option>
1550 </param>
1551 <when value="Nystroem">
1552 <expand macro="estimator_params_text"
1553 help="Default(=blank): coef0=None, degree=None, gamma=None, kernel='rbf', kernel_params=None, n_components=100, random_state=None. No double quotes"/>
1554 </when>
1555 <when value="RBFSampler">
1556 <expand macro="estimator_params_text"
1557 help="Default(=blank): gamma=1.0, n_components=100, random_state=None."/>
1558 </when>
1559 <when value="AdditiveChi2Sampler">
1560 <expand macro="estimator_params_text"
1561 help="Default(=blank): sample_interval=None, sample_steps=2."/>
1562 </when>
1563 <when value="SkewedChi2Sampler">
1564 <expand macro="estimator_params_text"
1565 help="Default(=blank): n_components=100, random_state=None, skewedness=1.0."/>
1566 </when>
1567 </conditional>
1568 </xml>
1569
1570 <xml name="matrix_decomposition_all">
1571 <conditional name="matrix_decomposition_selector">
1572 <param name="select_algorithm" type="select" label="Choose a matrix decomposition algorithm:">
1573 <option value="DictionaryLearning" selected="true">DictionaryLearning</option>
1574 <option value="FactorAnalysis">FactorAnalysis</option>
1575 <option value="FastICA">FastICA</option>
1576 <option value="IncrementalPCA">IncrementalPCA</option>
1577 <option value="KernelPCA">KernelPCA</option>
1578 <option value="LatentDirichletAllocation">LatentDirichletAllocation</option>
1579 <option value="MiniBatchDictionaryLearning">MiniBatchDictionaryLearning</option>
1580 <option value="MiniBatchSparsePCA">MiniBatchSparsePCA</option>
1581 <option value="NMF">NMF</option>
1582 <option value="PCA">PCA</option>
1583 <option value="SparsePCA">SparsePCA</option>
1584 <!--option value="SparseCoder">SparseCoder</option-->
1585 <option value="TruncatedSVD">TruncatedSVD</option>
1586 </param>
1587 <when value="DictionaryLearning">
1588 <expand macro="estimator_params_text"
1589 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."/>
1590 </when>
1591 <when value="FactorAnalysis">
1592 <expand macro="estimator_params_text"
1593 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."/>
1594 </when>
1595 <when value="FastICA">
1596 <expand macro="estimator_params_text"
1597 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."/>
1598 </when>
1599 <when value="IncrementalPCA">
1600 <expand macro="estimator_params_text"
1601 help="Default(=blank): batch_size=None, copy=True, n_components=None, whiten=False."/>
1602 </when>
1603 <when value="KernelPCA">
1604 <expand macro="estimator_params_text"
1605 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."/>
1606 </when>
1607 <when value="LatentDirichletAllocation">
1608 <expand macro="estimator_params_text"
1609 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."/>
1610 </when>
1611 <when value="MiniBatchDictionaryLearning">
1612 <expand macro="estimator_params_text"
1613 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."/>
1614 </when>
1615 <when value="MiniBatchSparsePCA">
1616 <expand macro="estimator_params_text"
1617 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."/>
1618 </when>
1619 <when value="NMF">
1620 <expand macro="estimator_params_text"
1621 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."/>
1622 </when>
1623 <when value="PCA">
1624 <expand macro="estimator_params_text"
1625 help="Default(=blank): copy=True, iterated_power='auto', n_components=None, random_state=None, svd_solver='auto', tol=0.0, whiten=False."/>
1626 </when>
1627 <when value="SparsePCA">
1628 <expand macro="estimator_params_text"
1629 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."/>
1630 </when>
1631 <when value="TruncatedSVD">
1632 <expand macro="estimator_params_text"
1633 help="Default(=blank): algorithm='randomized', n_components=2, n_iter=5, random_state=None, tol=0.0."/>
1634 </when>
1635 </conditional>
1636 </xml>
1637
1638 <xml name="FeatureAgglomeration">
1639 <conditional name="FeatureAgglomeration_selector">
1640 <param name="select_algorithm" type="select" label="Choose the algorithm:">
1641 <option value="FeatureAgglomeration" selected="true">FeatureAgglomeration</option>
1642 </param>
1643 <when value="FeatureAgglomeration">
1644 <expand macro="estimator_params_text"
1645 help="Default(=blank): affinity='euclidean', compute_full_tree='auto', connectivity=None, linkage='ward', memory=None, n_clusters=2, pooling_func=np.mean."/>
1646 </when>
1647 </conditional>
1648 </xml>
1649
1650 <xml name="skrebate">
1651 <conditional name="skrebate_selector">
1652 <param name="select_algorithm" type="select" label="Choose the algorithm:">
1653 <option value="ReliefF">ReliefF</option>
1654 <option value="SURF">SURF</option>
1655 <option value="SURFstar">SURFstar</option>
1656 <option value="MultiSURF">MultiSURF</option>
1657 <option value="MultiSURFstar">MultiSURFstar</option>
1658 <!--option value="TuRF">TuRF</option> -->
1659 </param>
1660 <when value="ReliefF">
1661 <expand macro="estimator_params_text"
1662 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, n_neighbors=100, verbose=False."/>
1663 </when>
1664 <when value="SURF">
1665 <expand macro="estimator_params_text"
1666 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False."/>
1667 </when>
1668 <when value="SURFstar">
1669 <expand macro="estimator_params_text"
1670 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False."/>
1671 </when>
1672 <when value="MultiSURF">
1673 <expand macro="estimator_params_text"
1674 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False."/>
1675 </when>
1676 <when value="MultiSURFstar">
1677 <expand macro="estimator_params_text"
1678 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False."/>
1679 </when>
1680 <!--when value="TuRF">
1681 <expand macro="estimator_params_text"
1682 help="Default(=blank): core_algorithm='ReliefF', discrete_threshold=10, n_features_to_select=10, n_neighbors=100, pct=0.5, verbose=False."/>
1683 </when> -->
1684 </conditional>
1685 </xml>
1686
1687 <xml name="imbalanced_learn_sampling">
1688 <conditional name="imblearn_selector">
1689 <param name="select_algorithm" type="select" label="Choose the algorithm:">
1690 <option value="under_sampling.ClusterCentroids" selected="true">under_sampling.ClusterCentroids</option>
1691 <option value="under_sampling.CondensedNearestNeighbour">under_sampling.CondensedNearestNeighbour</option>
1692 <option value="under_sampling.EditedNearestNeighbours">under_sampling.EditedNearestNeighbours</option>
1693 <option value="under_sampling.RepeatedEditedNearestNeighbours">under_sampling.RepeatedEditedNearestNeighbours</option>
1694 <option value="under_sampling.AllKNN">under_sampling.AllKNN</option>
1695 <option value="under_sampling.InstanceHardnessThreshold">under_sampling.InstanceHardnessThreshold</option>
1696 <option value="under_sampling.NearMiss">under_sampling.NearMiss</option>
1697 <option value="under_sampling.NeighbourhoodCleaningRule">under_sampling.NeighbourhoodCleaningRule</option>
1698 <option value="under_sampling.OneSidedSelection">under_sampling.OneSidedSelection</option>
1699 <option value="under_sampling.RandomUnderSampler">under_sampling.RandomUnderSampler</option>
1700 <option value="under_sampling.TomekLinks">under_sampling.TomekLinks</option>
1701 <option value="over_sampling.ADASYN">over_sampling.ADASYN</option>
1702 <option value="over_sampling.RandomOverSampler">over_sampling.RandomOverSampler</option>
1703 <option value="over_sampling.SMOTE">over_sampling.SMOTE</option>
1704 <option value="over_sampling.SVMSMOTE">over_sampling.SVMSMOTE</option>
1705 <option value="over_sampling.BorderlineSMOTE">over_sampling.BorderlineSMOTE</option>
1706 <option value="over_sampling.SMOTENC">over_sampling.SMOTENC</option>
1707 <option value="combine.SMOTEENN">combine.SMOTEENN</option>
1708 <option value="combine.SMOTETomek">combine.SMOTETomek</option>
1709 <option value="Z_RandomOverSampler">Z_RandomOverSampler - for regression</option>
1710 </param>
1711 <when value="under_sampling.ClusterCentroids">
1712 <expand macro="estimator_params_text"
1713 help="Default(=blank): sampling_strategy='auto', random_state=None, estimator=None, voting='auto'."/>
1714 </when>
1715 <when value="under_sampling.CondensedNearestNeighbour">
1716 <expand macro="estimator_params_text"
1717 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=None, n_seeds_S=1."/>
1718 </when>
1719 <when value="under_sampling.EditedNearestNeighbours">
1720 <expand macro="estimator_params_text"
1721 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, max_iter=100, kind_sel='all'."/>
1722 </when>
1723 <when value="under_sampling.RepeatedEditedNearestNeighbours">
1724 <expand macro="estimator_params_text"
1725 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, max_iter=100, kind_sel='all'."/>
1726 </when>
1727 <when value="under_sampling.AllKNN">
1728 <expand macro="estimator_params_text"
1729 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, kind_sel='all', allow_minority=False."/>
1730 </when>
1731 <when value="under_sampling.InstanceHardnessThreshold">
1732 <expand macro="estimator_params_text"
1733 help="Default(=blank): estimator=None, sampling_strategy='auto', random_state=None, cv=5."/>
1734 </when>
1735 <when value="under_sampling.NearMiss">
1736 <expand macro="estimator_params_text"
1737 help="Default(=blank): sampling_strategy='auto', random_state=None, version=1, n_neighbors=3, n_neighbors_ver3=3."/>
1738 </when>
1739 <when value="under_sampling.NeighbourhoodCleaningRule">
1740 <expand macro="estimator_params_text"
1741 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, kind_sel='all', threshold_cleaning=0.5."/>
1742 </when>
1743 <when value="under_sampling.OneSidedSelection">
1744 <expand macro="estimator_params_text"
1745 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=None, n_seeds_S=1."/>
1746 </when>
1747 <when value="under_sampling.RandomUnderSampler">
1748 <expand macro="estimator_params_text"
1749 help="Default(=blank): sampling_strategy='auto', random_state=None, replacement=False."/>
1750 </when>
1751 <when value="under_sampling.TomekLinks">
1752 <expand macro="estimator_params_text"
1753 help="Default(=blank): sampling_strategy='auto', random_state=None."/>
1754 </when>
1755 <when value="over_sampling.ADASYN">
1756 <expand macro="estimator_params_text"
1757 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=5."/>
1758 </when>
1759 <when value="over_sampling.RandomOverSampler">
1760 <expand macro="estimator_params_text"
1761 help="Default(=blank): sampling_strategy='auto', random_state=None."/>
1762 </when>
1763 <when value="over_sampling.SMOTE">
1764 <expand macro="estimator_params_text"
1765 help="Default(=blank): sampling_strategy='auto', random_state=None, k_neighbors=5."/>
1766 </when>
1767 <when value="over_sampling.SVMSMOTE">
1768 <expand macro="estimator_params_text"
1769 help="Default(=blank): sampling_strategy='auto', k_neighbors=5, m_neighbors=10, out_step=0.5, random_state=None, svm_estimator=None."/>
1770 </when>
1771 <when value="over_sampling.BorderlineSMOTE">
1772 <expand macro="estimator_params_text"
1773 help="Default(=blank): sampling_strategy='auto', k_neighbors=5, kind='borderline-1', m_neighbors=10, random_state=None."/>
1774 </when>
1775 <when value="over_sampling.SMOTENC">
1776 <expand macro="estimator_params_text"
1777 help="Default: categorical_features=[], sampling_strategy='auto', random_state=None, k_neighbors=5."/>
1778 </when>
1779 <when value="combine.SMOTEENN">
1780 <expand macro="estimator_params_text"
1781 help="Default(=blank): sampling_strategy='auto', random_state=None, smote=None, enn=None."/>
1782 </when>
1783 <when value="combine.SMOTETomek">
1784 <expand macro="estimator_params_text"
1785 help="Default(=blank): sampling_strategy='auto', random_state=None, smote=None, tomek=None."/>
1786 </when>
1787 <when value="Z_RandomOverSampler">
1788 <expand macro="estimator_params_text"
1789 help="Default(=blank): sampling_strategy='auto', random_state=None, negative_thres=0, positive_thres=-1."/>
1790 </when>
1791 </conditional>
1792 </xml>
1793
1794 <xml name="stacking_ensemble_inputs">
1795 <section name="options" title="Advanced Options" expanded="false">
1796 <yield/>
1797 <param argument="use_features_in_secondary" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false"/>
1798 <param argument="store_train_meta_features" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false"/>
1799 </section>
1800 </xml>
1801
1802 <xml name="stacking_base_estimator">
1803 <conditional name="estimator_selector">
1804 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" >
1805 <expand macro="estimator_module_options">
1806 <option value="custom_estimator">Load a custom estimator</option>
1807 </expand>
1808 </param>
1809 <expand macro="estimator_suboptions">
1810 <when value="custom_estimator">
1811 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline"/>
1812 </when>
1813 </expand>
1814 </conditional>
1815 </xml>
1816
1817 <xml name="stacking_voting_weights">
1818 <section name="options" title="Advanced Options" expanded="false">
1819 <param argument="weights" type="text" value="[]" optional="true" help="Sequence of weights (float or int). Uses uniform weights if None (`[]`).">
1820 <sanitizer>
1821 <valid initial="default">
1822 <add value="["/>
1823 <add value="]"/>
1824 </valid>
1825 </sanitizer>
1826 </param>
1827 <yield/>
1828 </section>
1829 </xml>
1830
1831 <xml name="preprocessors_sequence_encoders">
1832 <conditional name="encoder_selection">
1833 <param name="encoder_type" type="select" label="Choose the sequence encoder class">
1834 <option value="GenomeOneHotEncoder">GenomeOneHotEncoder</option>
1835 <option value="ProteinOneHotEncoder">ProteinOneHotEncoder</option>
1836 </param>
1837 <when value="GenomeOneHotEncoder">
1838 <expand macro="preprocessors_sequence_encoder_arguments"/>
1839 </when>
1840 <when value="ProteinOneHotEncoder">
1841 <expand macro="preprocessors_sequence_encoder_arguments"/>
1842 </when>
1843 </conditional>
1844 </xml>
1845
1846 <xml name="preprocessors_sequence_encoder_arguments">
1847 <param argument="seq_length" type="integer" value="" min="0" optional="true" help="Integer. Sequence length"/>
1848 <param argument="padding" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" help="Whether to pad or truncate sequence to meet the sequence length."/>
1849 </xml>
1850
1851 <!-- Outputs -->
1852
1853 <xml name="output">
1854 <outputs>
1855 <data format="tabular" name="outfile_predict">
1856 <filter>selected_tasks['selected_task'] == 'load'</filter>
1857 </data>
1858 <data format="zip" name="outfile_fit" label="${tool.name}.${selected_tasks.selected_algorithms.selected_algorithm}">
1859 <filter>selected_tasks['selected_task'] == 'train'</filter>
1860 </data>
1861 </outputs>
1862 </xml>
1863
1864 <!--Citations-->
1865 <xml name="eden_citation">
1866 <citations>
1867 <citation type="doi">10.5281/zenodo.15094</citation>
1868 </citations>
1869 </xml>
1870
1871 <xml name="sklearn_citation">
1872 <citations>
1873 <citation type="bibtex">
1874 @article{scikit-learn,
1875 title={Scikit-learn: Machine Learning in {P}ython},
1876 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
1877 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
1878 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
1879 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
1880 journal={Journal of Machine Learning Research},
1881 volume={12},
1882 pages={2825--2830},
1883 year={2011}
1884 }
1885 </citation>
1886 <yield/>
1887 </citations>
1888 </xml>
1889
1890 <xml name="scipy_citation">
1891 <citations>
1892 <citation type="bibtex">
1893 @Misc{,
1894 author = {Eric Jones and Travis Oliphant and Pearu Peterson and others},
1895 title = {{SciPy}: Open source scientific tools for {Python}},
1896 year = {2001--},
1897 url = "http://www.scipy.org/",
1898 note = {[Online; accessed 2016-04-09]}
1899 }
1900 </citation>
1901 </citations>
1902 </xml>
1903
1904 <xml name="skrebate_citation">
1905 <citation type="bibtex">
1906 @article{DBLP:journals/corr/abs-1711-08477,
1907 author = {Ryan J. Urbanowicz and
1908 Randal S. Olson and
1909 Peter Schmitt and
1910 Melissa Meeker and
1911 Jason H. Moore},
1912 title = {Benchmarking Relief-Based Feature Selection Methods},
1913 journal = {CoRR},
1914 volume = {abs/1711.08477},
1915 year = {2017},
1916 url = {http://arxiv.org/abs/1711.08477},
1917 archivePrefix = {arXiv},
1918 eprint = {1711.08477},
1919 timestamp = {Mon, 13 Aug 2018 16:46:04 +0200},
1920 biburl = {https://dblp.org/rec/bib/journals/corr/abs-1711-08477},
1921 bibsource = {dblp computer science bibliography, https://dblp.org}
1922 }
1923 </citation>
1924 </xml>
1925
1926 <xml name="xgboost_citation">
1927 <citation type="bibtex">
1928 @inproceedings{Chen:2016:XST:2939672.2939785,
1929 author = {Chen, Tianqi and Guestrin, Carlos},
1930 title = {{XGBoost}: A Scalable Tree Boosting System},
1931 booktitle = {Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining},
1932 series = {KDD '16},
1933 year = {2016},
1934 isbn = {978-1-4503-4232-2},
1935 location = {San Francisco, California, USA},
1936 pages = {785--794},
1937 numpages = {10},
1938 url = {http://doi.acm.org/10.1145/2939672.2939785},
1939 doi = {10.1145/2939672.2939785},
1940 acmid = {2939785},
1941 publisher = {ACM},
1942 address = {New York, NY, USA},
1943 keywords = {large-scale machine learning},
1944 }
1945 </citation>
1946 </xml>
1947
1948 <xml name="imblearn_citation">
1949 <citation type="bibtex">
1950 @article{JMLR:v18:16-365,
1951 author = {Guillaume Lema{{\^i}}tre and Fernando Nogueira and Christos K. Aridas},
1952 title = {Imbalanced-learn: A Python Toolbox to Tackle the Curse of Imbalanced Datasets in Machine Learning},
1953 journal = {Journal of Machine Learning Research},
1954 year = {2017},
1955 volume = {18},
1956 number = {17},
1957 pages = {1-5},
1958 url = {http://jmlr.org/papers/v18/16-365.html}
1959 }
1960 </citation>
1961 </xml>
1962
1963 <xml name="selene_citation">
1964 <citation type="bibtex">
1965 @article{chen2019selene,
1966 title={Selene: a PyTorch-based deep learning library for sequence data},
1967 author={Chen, Kathleen M and Cofer, Evan M and Zhou, Jian and Troyanskaya, Olga G},
1968 journal={Nature methods},
1969 volume={16},
1970 number={4},
1971 pages={315},
1972 year={2019},
1973 publisher={Nature Publishing Group}
1974 }
1975 </citation>
1976 </xml>
1977
1978 </macros>