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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_train_eval commit 47b8c32e8c595ed11e4c6fe404bb75162d8cc7a4-dirty
author siwaa
date Mon, 09 Dec 2024 11:17:12 +0000
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202391eebeb6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_train_eval commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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1 <tool id="wine_quality_train_eval" name="wine_quality_train_eval"
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2 version="1.0.0">
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4 <description>wine_quality_train_eval</description>
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6 <requirements>
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8 <!-- singularity -->
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9 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/dnn_fidlemore:c595a7b4b556ab642ecf0396957f2959139dc4ab</container>
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11 <!-- image locale
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12 <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_dnn/use/DNN/containers/fidlemore.simg</container -->
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14 </requirements>
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16 <command detect_errors="aggressive">
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17 <![CDATA[
6
51f36952ccaa planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_train_eval commit e7c4e447552083db7eaecbdf139a7c359fe9becc-dirty
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18 bash -e -c "source /fidle-tp/fidle-env/bin/activate &&
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19 mkdir datasets-fidle &&
e233f68fc8c6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_train_eval commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
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20 export FIDLE_DATASETS_DIR=\$(realpath -s datasets-fidle) &&
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21 mkdir datasets-fidle/WineQuality &&
a9b2e3ba898b planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_train_eval commit c595a7b4b556ab642ecf0396957f2959139dc4ab-dirty
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22 mkdir datasets-fidle/WineQuality/origine &&
a9b2e3ba898b planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_train_eval commit c595a7b4b556ab642ecf0396957f2959139dc4ab-dirty
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23 cp /fidle-tp/datasets-fidle/WineQuality/origine/winequality-red.csv datasets-fidle/WineQuality/origine/. &&
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24 mkdir cache_dir &&
083671dfbef9 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_train_eval commit 47b8c32e8c595ed11e4c6fe404bb75162d8cc7a4-dirty
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25 export TRANSFORMERS_CACHE=\$(realpath -s cache_dir) &&
083671dfbef9 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_train_eval commit 47b8c32e8c595ed11e4c6fe404bb75162d8cc7a4-dirty
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26 mkdir mpl_dir &&
083671dfbef9 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_train_eval commit 47b8c32e8c595ed11e4c6fe404bb75162d8cc7a4-dirty
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27 export MPLCONFIGDIR=\$(realpath -s mpl_dir) &&
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28 python3 /fidlemore/model_wine_lightning/wine_quality_train_eval.py -dataset_filepath ${dataset_csv} &&
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29 cp OUTPUTS/model.ckpt ${model_ckpt} &&
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30 cp OUTPUTS/norm_config.json ${norm_config_json} &&
ce2d614cac69 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_train_eval commit e7c4e447552083db7eaecbdf139a7c359fe9becc-dirty
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31 cp OUTPUTS/report.json ${report_json}"
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32 ]]>
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33 </command>
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35 <inputs>
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36 <param name="dataset_csv" optional="true" type="data" format="csv"
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37 label="File of dataset used to train and test the model (.csv)"/>
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38 </inputs>
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39
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40 <outputs>
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41 <data format="ckpt" name="model_ckpt"
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42 label="model_ckpt model file (.ckpt)"/>
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43 <data format="json" name="norm_config_json"
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44 label="norm_config normalization configuration (.json)"/>
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45 <data format="json" name="report_json" label="report (.json)"/>
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46 </outputs>
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48 <tests>
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49 </tests>
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51 <help><![CDATA[
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53 wine_quality_train_eval.xml
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55 ===========================
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57 Code:
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59 ----
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61 - wine_quality_train_eval.py
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63 Inputs:
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65 -------
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67 - dataset file (.csv) :
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69 File containing dataset used to train and test the model.
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71 The dataset will be splitted in 2 parts (training part, validation part).
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73 If not given, an embedded default file used.
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74
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75 Outputs:
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77 --------
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202391eebeb6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_train_eval commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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79 - Model file (.ckpt)
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81 - Normalization configuration file (.json)
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83 - Report file (.json)
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85 Credits:
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87 --------
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89 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
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90 - Copyright: INRAE
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92 ]]>
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93 </help>
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95 </tool>