Mercurial > repos > goeckslab > ludwig_experiment

comparison ludwig_experiment.xml @ 3:116e0e254dab draft

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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 0bcd53b5df7cbdb4b6fb69b4a25f53abc2dfd2aa
author goeckslab
date Tue, 18 Mar 2025 20:51:27 +0000
parents e1c7d044b759
children 5a39f429fad1
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2:e1c7d044b759 3:116e0e254dab
90 </command> 90 </command>
91 <configfiles> 91 <configfiles>
92 <inputs name="inputs" /> 92 <inputs name="inputs" />
93 </configfiles> 93 </configfiles>
94 <inputs> 94 <inputs>
95 <param argument="config" type="data" format="yaml" label="Select the dataset containing model configuration" /> 95 <param argument="config" type="data" format="yaml" label="Experiment configuration" />
96 <param argument="model_load_path" type="data" format="ludwig_model" optional="true" label="Load a pretrained model as initialization" help="Optional." /> 96 <param argument="model_load_path" type="data" format="ludwig_model" optional="true" label="Pretrained model for initialization" help="Optional." />
97 <param argument="model_resume_path" type="data" format="ludwig_model" optional="true" label="Load a pretained model to resume training" help="Optional." /> 97 <param argument="model_resume_path" type="data" format="ludwig_model" optional="true" label="Pretained model resuming training" help="Optional." />
98 <param argument="dataset" type="data" format="tabular,csv,h5,json,txt" optional="true" label="Input dataset" /> 98 <param argument="dataset" type="data" format="tabular,csv,h5,json,txt" optional="true" label="Experiment dataset" />
99 <param argument="training_set" type="data" format="tabular,csv,h5,json" optional="true" label="Input traning dataset" /> 99 <param argument="training_set" type="data" format="tabular,csv,h5,json" optional="true" label="Experiment training dataset" />
100 <param argument="validation_set" type="data" format="tabular,csv,h5,json" optional="true" label="Input validation dataset" /> 100 <param argument="validation_set" type="data" format="tabular,csv,h5,json" optional="true" label="Experiment validation dataset" />
101 <param argument="test_set" type="data" format="tabular,csv,h5,json" optional="true" label="Input test dataset" /> 101 <param argument="test_set" type="data" format="tabular,csv,h5,json" optional="true" label="Experiment test dataset" />
102 <param argument="training_set_metadata" type="data" format="json" optional="true" label="Training set metadata" /> 102 <param argument="training_set_metadata" type="data" format="json" optional="true" label="Metadata for training dataset" />
103 <param argument="data_format" type="select" label="Data format"> 103 <param argument="data_format" type="select" label="Data format">
104 <option value="auto" selected="true">auto</option> 104 <option value="auto" selected="true">auto</option>
105 <option value="tsv">tsv</option> 105 <option value="tsv">tsv</option>
106 <option value="csv">csv</option> 106 <option value="csv">csv</option>
107 <option value="h5">h5</option> 107 <option value="h5">h5</option>
108 <option value="json">json</option> 108 <option value="json">json</option>
109 </param> 109 </param>
110 <param argument="eval_split" type="select" label="Select the split portion for evaluation"> 110 <param argument="eval_split" type="select" label="Dataset split to use for evaluation">
111 <option value="training">training</option> 111 <option value="training">training</option>
112 <option value="validation">validation</option> 112 <option value="validation">validation</option>
113 <option value="test" selected="true">test</option> 113 <option value="test" selected="true">test</option>
114 <option value="full">full</option> 114 <option value="full">full</option>
115 </param> 115 </param>
116 <param argument="k_fold" type="integer" value="" optional="true" label="number of folds for a k-fold cross validation run" min="2" max="10"/> 116 <param argument="k_fold" type="integer" value="" optional="true" label="Number of folds for a k-fold cross validation run" min="2" max="10"/>
117 <param argument="random_seed" type="integer" value="42" label="Randomness seed" min="0" max="999999"/> 117 <param argument="random_seed" type="integer" value="42" label="Random seed (set for reproducibility)" min="0" max="999999"/>
118 <param argument="disable_parallel_threads" type="boolean" checked="false" label="Whether to disable parallel threads for reproducibility?" /> 118 <param argument="disable_parallel_threads" type="boolean" checked="false" label="Disable parallel threads for reproducibility?" />
119 <!-- <param argument="skip_save_predictions" type="boolean" checked="false" label="Whether to skip saving predictions?" /> --> 119 <!-- <param argument="skip_save_predictions" type="boolean" checked="false" label="Whether to skip saving predictions?" /> -->
120 <param name="raw_data" type="data" format="zip" optional="true" label="Raw data" help="Optional. Needed for images."/> 120 <param name="raw_data" type="data" format="zip" optional="true" label="Raw data" help="Needed when using unstructured data (e.g., images) not included in experiment dataset file."/>
121 </inputs> 121 </inputs>
122 <outputs> 122 <outputs>
123 <data format="ludwig_model" name="output_model" label="${tool.name} trained model on ${on_string}" /> 123 <data format="ludwig_model" name="output_model" label="${tool.name} trained model on ${on_string}" />
124 <data format="html" name="output_report" from_work_dir="ludwig_experiment_report.html" label="${tool.name} report on ${on_string}" /> 124 <data format="html" name="output_report" from_work_dir="ludwig_experiment_report.html" label="${tool.name} report on ${on_string}" />
125 <collection type="list" name="output_pred_csv" label="${tool.name} predictions CSVs/experiment stats on ${on_string}" > 125 <collection type="list" name="output_pred_csv" label="${tool.name} predictions CSVs/experiment stats on ${on_string}" >