Mercurial > repos > siwaa > wine_quality_train_eval

annotate wine_quality_train_eval.xml @ 6:51f36952ccaa draft

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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 e7c4e447552083db7eaecbdf139a7c359fe9becc-dirty
author siwaa
date Thu, 05 Dec 2024 11:45:31 +0000
parents d30ad788a0ae
children 92c6d97ef171
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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:6d159f79349e231deadb738f79bd293c1a8dadd3</container>
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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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 <environment_variables>
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17 <environment_variable name="FIDLE_DATASETS_DIR">/fidle-tp/datasets-fidle</environment_variable>
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18 </environment_variables>
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19 <command detect_errors="aggressive">
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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20 <![CDATA[
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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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21 bash -e -c "source /fidle-tp/fidle-env/bin/activate &&
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d490c7a4c63b 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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22 mkdir cache_dir &&
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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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23 mkdir mpl_dir &&
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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24 export TRANSFORMERS_CACHE=\$(realpath -s cache_dir) &&
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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25 export MPLCONFIGDIR=\$(realpath -s mpl_dir) &&
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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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26 cp /fidlemore/model_wine_lightning/wine_quality_train_eval.py wine_quality_train_eval.py &&
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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27 python3 wine_quality_train_eval.py -dataset_filepath ${dataset_csv} &&
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28 cp OUTPUTS/model.ckpt ${model_ckpt} &&
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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29 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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30 cp OUTPUTS/report.json ${report_json}"
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31 ]]>
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32 </command>
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34 <inputs>
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35 <param name="dataset_csv" optional="true" type="data" format="csv"
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36 label="File of dataset used to train and test the model (.csv)"/>
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37 </inputs>
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38
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39 <outputs>
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40 <data format="ckpt" name="model_ckpt"
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41 label="model_ckpt model file (.ckpt)"/>
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42 <data format="json" name="norm_config_json"
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43 label="norm_config normalization configuration (.json)"/>
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44 <data format="json" name="report_json" label="report (.json)"/>
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45 </outputs>
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47 <tests>
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48 </tests>
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50 <help><![CDATA[
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52 wine_quality_train_eval.xml
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54 ===========================
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56 Code:
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58 ----
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60 - wine_quality_train_eval.py
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62 Inputs:
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64 -------
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66 - dataset file (.csv) :
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68 File containing dataset used to train and test the model.
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70 The dataset will be splitted in 2 parts (training part, validation part).
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72 If not given, an embedded default file used.
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74 Outputs:
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75
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78 - Model file (.ckpt)
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80 - Normalization configuration file (.json)
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82 - Report file (.json)
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84 Credits:
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86 --------
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88 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
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89 - Copyright: INRAE
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91 ]]>
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92 </help>
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94 </tool>