Mercurial > repos > goeckslab > tabular_learner
comparison tabular_learner.xml @ 5:3d42f82b3c7f draft
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 |
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| 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" /> |