Mercurial > repos > siwaa > wine_quality_predict

annotate wine_quality_predict.xml @ 2:4d31508e95c6 draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
author siwaa
date Fri, 06 Dec 2024 19:17:19 +0000
parents f9637dc4e18a
children 01bf4f689614
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605f9329d94e planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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1 <tool id="wine_quality_predict" name="wine_quality_predict" version="1.0.0">
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3 <description>wine_quality_predict</description>
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5 <requirements>
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7 <!-- singularity -->
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8 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/dnn_fidlemore:6d159f79349e231deadb738f79bd293c1a8dadd3</container>
605f9329d94e planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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10 <!-- image locale
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11 <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_dnn/use/DNN/containers/fidlemore.simg</container -->
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13 </requirements>
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15 <environment_variables>
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16 <environment_variable name="FIDLE_DATASETS_DIR">/fidle-tp/datasets-fidle</environment_variable>
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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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21 bash -e -c "source /fidle-tp/fidle-env/bin/activate &&
4d31508e95c6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
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22 mkdir datasets-fidle &&
4d31508e95c6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
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23 export FIDLE_DATASETS_DIR=\$(realpath -s datasets-fidle) &&
4d31508e95c6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
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24 mkdir ipython_dir &&
4d31508e95c6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
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25 export IPYTHONDIR=\$(realpath -s ipython_dir) &&
4d31508e95c6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
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26 ipython profile create default &&
4d31508e95c6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
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27 mkdir cache_dir &&
4d31508e95c6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
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28 export TRANSFORMERS_CACHE=\$(realpath -s cache_dir) &&
4d31508e95c6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
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29 mkdir mpl_dir &&
4d31508e95c6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
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30 export MPLCONFIGDIR=\$(realpath -s mpl_dir) &&
4d31508e95c6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
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31 python3 /fidlemore/model_wine_lightning/wine_quality_predict.py -model_ckpt_filepath ${model_ckpt} -norm_config_json_filepath ${norm_config_json} -data_json_filepath ${data_json} &&
4d31508e95c6 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
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32 cp OUTPUTS/report.json ${report_json}"
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33 ]]>
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34 </command>
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36 <inputs>
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37 <param name="data_json" optional="false" type="data" format="json"
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38 label="File of data of wine whose quality to be predicted (.json)"/>
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39 <param name="model_ckpt" optional="false" type="data" format="ckpt"
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40 label="model_ckpt model file (.ckpt)"/>
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41 <param name="norm_config_json" optional="false" type="data" format="json"
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42 label="norm_config normalization configuration (.json)"/>
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43 </inputs>
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44
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45 <outputs>
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46 <data format="json" name="report_json" label="report (.json)"/>
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47 </outputs>
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49 <tests>
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50 </tests>
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52 <help><![CDATA[
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54 wine_quality_predict.xml
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56 ===========================
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58 Code:
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60 ----
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62 - wine_quality_predict.py
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64 Inputs:
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66 -------
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68 - data file (.json) :
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69 File containing data of wine for which quality is going to be predicted.
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71 - Model file (.ckpt)
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73 - Normalization configuration file (.json)
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75 Outputs:
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79 - Report file (.json)
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81 Credits:
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85 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
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86 - Copyright: INRAE
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88 ]]>
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89 </help>
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91 </tool>