Mercurial > repos > siwaa > wine_quality_train_eval

annotate wine_quality_train_eval.xml @ 18:8916f75916b6 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 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
author siwaa
date Fri, 06 Dec 2024 19:19:52 +0000
parents e233f68fc8c6
children a9b2e3ba898b
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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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7
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8 <!-- singularity -->
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9 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/dnn_fidlemore:1906137478520a9f71a4d8996c0a8827f27aed16</container>
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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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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_variables>
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18 <command detect_errors="aggressive">
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19 <![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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20 bash -e -c "source /fidle-tp/fidle-env/bin/activate &&
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21 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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22 export FIDLE_DATASETS_DIR=\$(realpath -s datasets-fidle) &&
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23 mkdir ipython_dir &&
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24 export IPYTHONDIR=\$(realpath -s ipython_dir) &&
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dd7d99707a65 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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25 ipython profile create default &&
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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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26 mkdir cache_dir &&
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27 export TRANSFORMERS_CACHE=\$(realpath -s cache_dir) &&
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28 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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29 export MPLCONFIGDIR=\$(realpath -s mpl_dir) &&
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30 python3 $__tool_directory__/toto_wine_quality_train_eval.py -dataset_filepath ${dataset_csv} &&
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31 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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32 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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33 cp OUTPUTS/report.json ${report_json}"
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34 ]]>
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35 </command>
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37 <inputs>
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38 <param name="dataset_csv" optional="true" type="data" format="csv"
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39 label="File of dataset used to train and test the model (.csv)"/>
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40 </inputs>
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41
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42 <outputs>
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43 <data format="ckpt" name="model_ckpt"
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44 label="model_ckpt model file (.ckpt)"/>
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45 <data format="json" name="norm_config_json"
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46 label="norm_config normalization configuration (.json)"/>
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47 <data format="json" name="report_json" label="report (.json)"/>
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48 </outputs>
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50 <tests>
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51 </tests>
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53 <help><![CDATA[
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55 wine_quality_train_eval.xml
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57 ===========================
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59 Code:
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61 ----
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63 - wine_quality_train_eval.py
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65 Inputs:
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67 -------
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69 - dataset file (.csv) :
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71 File containing dataset used to train and test the model.
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73 The dataset will be splitted in 2 parts (training part, validation part).
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75 If not given, an embedded default file used.
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76
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77 Outputs:
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78
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79 --------
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80
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81 - Model file (.ckpt)
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82
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83 - Normalization configuration file (.json)
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84
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85 - Report file (.json)
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86
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87 Credits:
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88
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89 --------
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90
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91 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
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92 - Copyright: INRAE
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93
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94 ]]>
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95 </help>
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96
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97 </tool>