Mercurial > repos > goeckslab > tabular_learner

comparison tabular_learner.xml @ 5:3d42f82b3c7f draft

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planemo upload for repository https://github.com/goeckslab/gleam commit 4a11e8a4c4e9daa884bddedfa47090476c517667
author goeckslab
date Thu, 31 Jul 2025 15:41:07 +0000
parents 11fdac5affb3
children ba45bc057d70
comparison
equal deleted inserted replaced
4:11fdac5affb3 5:3d42f82b3c7f
20 #if $tune_model 20 #if $tune_model
21 --tune_model 21 --tune_model
22 #end if 22 #end if
23 #if $customize_defaults == "true" 23 #if $customize_defaults == "true"
24 #if $train_size 24 #if $train_size
25 --train_size '$train_size' 25 --train_size '$train_size'
26 #end if 26 #end if
27 #if $normalize 27 #if $normalize
28 --normalize 28 --normalize
29 #end if 29 #end if
30 #if $feature_selection 30 #if $feature_selection
31 --feature_selection 31 --feature_selection
32 #end if 32 #end if
33 #if $enable_cross_validation == "true" 33 #if $enable_cross_validation == "true"
34 --cross_validation 34 --cross_validation
35 #if $cross_validation_folds 35 #if $cross_validation_folds
36 --cross_validation_folds '$cross_validation_folds' 36 --cross_validation_folds '$cross_validation_folds'
37 #end if 37 #end if
38 #end if 38 #end if
39 #if $enable_cross_validation == "false" 39 #if $enable_cross_validation == "false"
40 --no_cross_validation 40 --no_cross_validation
41 #end if 41 #end if
42 #if $remove_outliers 42 #if $remove_outliers
43 --remove_outliers 43 --remove_outliers
44 #end if 44 #end if
45 #if $remove_multicollinearity 45 #if $remove_multicollinearity
46 --remove_multicollinearity 46 --remove_multicollinearity
47 #end if 47 #end if
48 #if $polynomial_features 48 #if $polynomial_features
49 --polynomial_features 49 --polynomial_features
50 #end if 50 #end if
51 #if $fix_imbalance 51 #if $fix_imbalance
52 --fix_imbalance 52 --fix_imbalance
53 #end if
54 #if $probability_threshold
55 --probability_threshold '$probability_threshold'
53 #end if 56 #end if
54 #end if 57 #end if
55 #if $test_file 58 #if $test_file
56 --test_file '$test_file' 59 --test_file '$test_file'
57 #end if 60 #end if
58 --model_type '$model_type' 61 --model_type '$model_type'
59 ]]> 62 ]]>
60 </command> 63 </command>
61 <inputs> 64 <inputs>
62 <param name="input_file" type="data" format="csv,tabular" label="Tabular Input Dataset" /> 65 <param name="input_file" type="data" format="csv,tabular" label="Tabular Input Dataset" />
148 </conditional> 151 </conditional>
149 <param name="remove_outliers" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Remove Outliers" help="Whether to remove outliers from the input dataset before training." /> 152 <param name="remove_outliers" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Remove Outliers" help="Whether to remove outliers from the input dataset before training." />
150 <param name="remove_multicollinearity" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Remove Multicollinearity" help="Whether to remove multicollinear features before training." /> 153 <param name="remove_multicollinearity" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Remove Multicollinearity" help="Whether to remove multicollinear features before training." />
151 <param name="polynomial_features" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Polynomial Features" help="Whether to create polynomial features before training." /> 154 <param name="polynomial_features" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Polynomial Features" help="Whether to create polynomial features before training." />
152 <param name="fix_imbalance" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Fix Imbalance" help="ONLY for classfication! Whether to use SMOTE or similar methods to fix imbalance in the input dataset." /> 155 <param name="fix_imbalance" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Fix Imbalance" help="ONLY for classfication! Whether to use SMOTE or similar methods to fix imbalance in the input dataset." />
156 <param name="probability_threshold" type="float" min="0.0" max="1.0" value="0.5" label="Classification Probability Threshold" help="Only applies to classification. Probability above which a prediction is considered positive. Default is 0.5." />
153 </when> 157 </when>
154 <when value="false"> 158 <when value="false">
155 <!-- No additional parameters to show if the user selects 'No' --> 159 <!-- No additional parameters to show if the user selects 'No' -->
156 </when> 160 </when>
157 </conditional> 161 </conditional>
173 <param name="feature_selection" value="true"/> 177 <param name="feature_selection" value="true"/>
174 <param name="enable_cross_validation" value="true"/> 178 <param name="enable_cross_validation" value="true"/>
175 <param name="cross_validation_folds" value="5"/> 179 <param name="cross_validation_folds" value="5"/>
176 <param name="remove_outliers" value="true"/> 180 <param name="remove_outliers" value="true"/>
177 <param name="remove_multicollinearity" value="true"/> 181 <param name="remove_multicollinearity" value="true"/>
182 <param name="probability_threshold" value="0.4" />
178 <output name="model" file="expected_model_classification_customized.h5" compare="sim_size"/> 183 <output name="model" file="expected_model_classification_customized.h5" compare="sim_size"/>
179 <output name="comparison_result"> 184 <output name="comparison_result">
180 <assert_contents> 185 <assert_contents>
181 <has_text text="Validation Summary" /> 186 <has_text text="Validation Summary" />
182 <has_text text="Test Summary" /> 187 <has_text text="Test Summary" />
195 <param name="normalize" value="true"/> 200 <param name="normalize" value="true"/>
196 <param name="feature_selection" value="true"/> 201 <param name="feature_selection" value="true"/>
197 <param name="enable_cross_validation" value="false"/> 202 <param name="enable_cross_validation" value="false"/>
198 <param name="remove_outliers" value="true"/> 203 <param name="remove_outliers" value="true"/>
199 <param name="remove_multicollinearity" value="true"/> 204 <param name="remove_multicollinearity" value="true"/>
205 <param name="probability_threshold" value="0.6" />
200 <output name="model" file="expected_model_classification_customized_cross_off.h5" compare="sim_size"/> 206 <output name="model" file="expected_model_classification_customized_cross_off.h5" compare="sim_size"/>
201 <output name="comparison_result"> 207 <output name="comparison_result">
202 <assert_contents> 208 <assert_contents>
203 <has_text text="Validation Summary" /> 209 <has_text text="Validation Summary" />
204 <has_text text="Test Summary" /> 210 <has_text text="Test Summary" />