Mercurial > repos > goeckslab > pycaret_compare
comparison pycaret_train.xml @ 4:4aa511539199 draft default tip
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
author | goeckslab |
---|---|
date | Tue, 03 Jun 2025 19:31:16 +0000 |
parents | 009b18a75dc3 |
children |
comparison
equal
deleted
inserted
replaced
3:02f7746e7772 | 4:4aa511539199 |
---|---|
1 <tool id="pycaret_compare" name="PyCaret Model Comparison" version="@VERSION@" profile="@PROFILE@"> | 1 <tool id="pycaret_compare" name="Tabular Learner" version="@VERSION@" profile="@PROFILE@"> |
2 <description>compares different machine learning models on a dataset using PyCaret. Do feature analyses using Random Forest and LightGBM. </description> | 2 <description>applies and evaluates multiple machine learning models on a tabular dataset</description> |
3 <macros> | 3 <macros> |
4 <import>pycaret_macros.xml</import> | 4 <import>pycaret_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="python_requirements" /> | 6 <expand macro="python_requirements" /> |
7 <command> | 7 <command> |
51 #end if | 51 #end if |
52 --model_type '$model_type' | 52 --model_type '$model_type' |
53 ]]> | 53 ]]> |
54 </command> | 54 </command> |
55 <inputs> | 55 <inputs> |
56 <param name="input_file" type="data" format="csv,tabular" label="Train Dataset (CSV or TSV)" /> | 56 <param name="input_file" type="data" format="csv,tabular" label="Tabular Input Dataset" /> |
57 <param name="test_file" type="data" format="csv,tabular" optional="true" label="Test Dataset (CSV or TSV)" | 57 <param name="test_file" type="data" format="csv,tabular" optional="true" label="Tabular Test Dataset" |
58 help="If a test set is not provided, | 58 help="If a test dataset is not provided, |
59 the selected training set will be split into training, validation, and test sets. | 59 the input dataset will be split into training, validation, and test sets. |
60 If a test set is provided, the training set will only be split into training and validation sets. | 60 If a test set is provided, the input dataset will be split into training and validation sets. |
61 BTW, cross-validation is always applied by default." /> | 61 Cross-validation is applied by default during training." /> |
62 <param name="target_feature" multiple="false" type="data_column" use_header_names="true" data_ref="input_file" label="Select the target column:" /> | 62 <param name="target_feature" multiple="false" type="data_column" use_header_names="true" data_ref="input_file" label="Select the target column:" /> |
63 <conditional name="model_selection"> | 63 <conditional name="model_selection"> |
64 <param name="model_type" type="select" label="Task"> | 64 <param name="model_type" type="select" label="Task"> |
65 <option value="classification">classification</option> | 65 <option value="classification">classification</option> |
66 <option value="regression">regression</option> | 66 <option value="regression">regression</option> |
122 <param name="customize_defaults" type="select" label="Customize Default Settings?" help="Select yes if you want to customize the default settings of the experiment."> | 122 <param name="customize_defaults" type="select" label="Customize Default Settings?" help="Select yes if you want to customize the default settings of the experiment."> |
123 <option value="false" selected="true">No</option> | 123 <option value="false" selected="true">No</option> |
124 <option value="true">Yes</option> | 124 <option value="true">Yes</option> |
125 </param> | 125 </param> |
126 <when value="true"> | 126 <when value="true"> |
127 <param name="train_size" type="float" value="0.7" min="0.1" max="0.9" label="Train Size" help="Proportion of the dataset to include in the train split." /> | 127 <param name="train_size" type="float" value="0.7" min="0.1" max="0.9" label="Train Size" help="Proportion of the input dataset to include in the train split." /> |
128 <param name="normalize" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Normalize Data" help="Whether to normalize data before training." /> | 128 <param name="normalize" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Normalize Data" help="Whether to normalize data before training." /> |
129 <param name="feature_selection" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Feature Selection" help="Whether to perform feature selection." /> | 129 <param name="feature_selection" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Feature Selection" help="Whether to perform feature selection." /> |
130 <conditional name="cross_validation"> | 130 <conditional name="cross_validation"> |
131 <param name="enable_cross_validation" type="select" label="Enable Cross Validation?" help="Select whether to enable cross-validation. Default: Yes" > | 131 <param name="enable_cross_validation" type="select" label="Enable Cross Validation?" help="Select whether to enable cross-validation." > |
132 <option value="false" >No</option> | 132 <option value="false" >No</option> |
133 <option value="true" selected="true">Yes</option> | 133 <option value="true" selected="true">Yes</option> |
134 </param> | 134 </param> |
135 <when value="true"> | 135 <when value="true"> |
136 <param name="cross_validation_folds" type="integer" value="10" min="2" max="20" label="Cross Validation Folds" help="Number of folds to use for cross-validation. Default: 10" /> | 136 <param name="cross_validation_folds" type="integer" value="10" min="2" max="20" label="Cross Validation Folds" help="Number of folds to use for cross-validation." /> |
137 </when> | 137 </when> |
138 <when value="false"> | 138 <when value="false"> |
139 <!-- No additional parameters to show if the user selects 'No' --> | 139 <!-- No additional parameters to show if the user selects 'No' --> |
140 </when> | 140 </when> |
141 </conditional> | 141 </conditional> |
142 <param name="remove_outliers" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Remove Outliers" help="Whether to remove outliers from the dataset before training. Default: False" /> | 142 <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." /> |
143 <param name="remove_multicollinearity" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Remove Multicollinearity" help="Whether to remove multicollinear features before training. Default: False" /> | 143 <param name="remove_multicollinearity" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Remove Multicollinearity" help="Whether to remove multicollinear features before training." /> |
144 <param name="polynomial_features" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Polynomial Features" help="Whether to create polynomial features before training. Default: False" /> | 144 <param name="polynomial_features" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Polynomial Features" help="Whether to create polynomial features before training." /> |
145 <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 dataset. Default: False" /> | 145 <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." /> |
146 </when> | 146 </when> |
147 <when value="false"> | 147 <when value="false"> |
148 <!-- No additional parameters to show if the user selects 'No' --> | 148 <!-- No additional parameters to show if the user selects 'No' --> |
149 </when> | 149 </when> |
150 </conditional> | 150 </conditional> |
151 </inputs> | 151 </inputs> |
152 <outputs> | 152 <outputs> |
153 <data name="comparison_result" format="html" from_work_dir="comparison_result.html" label="${tool.name} analysis report on ${on_string}"/> | |
153 <data name="model" format="h5" from_work_dir="pycaret_model.h5" label="${tool.name} best model on ${on_string}" /> | 154 <data name="model" format="h5" from_work_dir="pycaret_model.h5" label="${tool.name} best model on ${on_string}" /> |
154 <data name="comparison_result" format="html" from_work_dir="comparison_result.html" label="${tool.name} Comparison result on ${on_string}"/> | 155 <data name="best_model_csv" format="csv" from_work_dir="best_model.csv" label="${tool.name} The parameters of the best model on ${on_string}" hidden="true" /> |
155 <data name="best_model_csv" format="csv" from_work_dir="best_model.csv" label="${tool.name} The prams of the best model on ${on_string}" hidden="true" /> | |
156 </outputs> | 156 </outputs> |
157 <tests> | 157 <tests> |
158 <test> | 158 <test> |
159 <param name="input_file" value="pcr.tsv"/> | 159 <param name="input_file" value="pcr.tsv"/> |
160 <param name="target_feature" value="11"/> | 160 <param name="target_feature" value="11"/> |