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author | goeckslab |
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date | Tue, 07 Jan 2025 22:46:16 +0000 |
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<tool id="ludwig_evaluate" name="Ludwig Evaluate" version="@VERSION@" profile="@PROFILE@"> <description>loads a pretrained model and evaluates its performance by comparing its predictions with ground truth</description> <macros> <import>ludwig_macros.xml</import> </macros> <expand macro="python_requirements_gpu" /> <expand macro="macro_stdio" /> <version_command>echo "@VERSION@"</version_command> <command> <![CDATA[ #import re mkdir -p outputs && #if $dataset #set $sanitized_dataset = re.sub('[^\w\-_\.]', '_', $dataset.element_identifier.strip()) ln -sf '$dataset' "./${sanitized_dataset}"; #end if #if $raw_data unzip -o -q '$raw_data' -d ./; #end if python '$__tool_directory__/ludwig_evaluate.py' #if $model_path --model_path '$model_path.extra_files_path' #end if #if $dataset --dataset "./${sanitized_dataset}" #end if #if $disable_parallel_threads --disable_parallel_threads #end if --output_directory "./outputs" --data_format '$data_format' --split '$split' --backend local --skip_save_unprocessed_output && mkdir -p '$output_report.extra_files_path' && cp outputs/*.json outputs/*.parquet '$output_report.extra_files_path' && echo "Evaluation is Done!" ]]> </command> <configfiles> <inputs name="inputs" /> </configfiles> <inputs> <param name="model_path" type="data" format="ludwig_model" label="Load the pretrained model" /> <param name="dataset" type="data" format="tabular,csv,h5,json,txt" label="Input dataset" /> <param name="data_format" type="select" label="Data format"> <option value="auto" selected="true">auto</option> <option value="tsv">tsv</option> <option value="csv">csv</option> <option value="h5">h5</option> <option value="json">json</option> </param> <param name="split" type="select" label="Select the split portion to test the model on"> <option value="training">training</option> <option value="validation">validation</option> <option value="test">test</option> <option value="full" selected="true">full</option> </param> <param name="batch_size" type="integer" value="128" optional="true" label="Batch size" min="1" max="4096"/> <param name="disable_parallel_threads" type="boolean" checked="false" label="Whether to disable parallel threads for reproducibility?" /> <param name="raw_data" type="data" format="zip" optional="true" label="Raw data" help="Optional. Needed for images."/> </inputs> <outputs> <collection type="list" name="output_pred_csv" label="${tool.name} predictions CSV/json on ${on_string}" > <discover_datasets pattern="(?P<designation>predictions_parquet\.csv)" format="csv" directory="outputs" /> <discover_datasets pattern="(?P<designation>.+)\.json" format="json" directory="outputs" /> <discover_datasets pattern="(?P<designation>.+)\.png" format="png" directory="outputs" /> </collection> <data format="html" name="output_report" from_work_dir="outputs/ludwig_evaluate_report.html" label="${tool.name} report on ${on_string}" /> </outputs> <tests> <test expect_num_outputs="2"> <param name="model_path" value="" ftype="ludwig_model"> <composite_data value="temp_model01/model_hyperparameters.json" /> <composite_data value="temp_model01/model_weights" /> <composite_data value="temp_model01/training_set_metadata.json" /> <composite_data value="temp_model01/training_progress.json" /> </param> <param name="dataset" value="temperature_la.csv" ftype="csv" /> <param name="split" value="test" /> <output name="output_report" ftype="html"> <assert_contents> <has_text text="Evaluate" /> </assert_contents> </output> <output_collection name="output_pred_csv"> <element name="predictions_parquet.csv"> <assert_contents> <has_n_columns n="1" /> </assert_contents> </element> </output_collection> </test> </tests> <help> <![CDATA[ **What it does** This tool conducts `ludwig evaluate`. **Input** - a trained ludwig model. - dataset to be evaluate. **Output** - report in html. - a collection of prediction results. ]]> </help> <expand macro="macro_citations" /> </tool>