Mercurial > repos > siwaa > wine_quality

annotate wine_quality.xml @ 1:c3841488b88d draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
author siwaa
date Wed, 04 Dec 2024 18:35:18 +0000
parents 143b15001522
children c1b75945752a
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
siwaa
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1 <tool id="wine_quality" name="wine_quality" version="1.0.0">
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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3 <description>wine_quality</description>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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5 <requirements>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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7 <!-- singularity -->
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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8 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/dnn_fidlemore:6d159f79349e231deadb738f79bd293c1a8dadd3</container>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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10 <!-- image locale
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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11 <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_dnn/use/DNN/containers/fidlemore.simg</container -->
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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13 </requirements>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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15 <environment_variables>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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16 <environment_variable name="FIDLE_DATASETS_DIR">/fidle-tp/datasets-fidle</environment_variable>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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17 </environment_variables>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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18 <command detect_errors="aggressive">
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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19 <![CDATA[
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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20 . /fidle-tp/fidle-env/bin/activate;
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c3841488b88d planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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21 mkdir /fidle-tp/fidle-env/cache_dir; export TRANSFORMERS_CACHE=/fidle-tp/fidle-env/cache_dir;
c3841488b88d planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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22 mkdir /fidle-tp/fidle-env/mpl_dir; export MPLCONFIGDIR=/fidle-tp/fidle-env/mpl_dir;
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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23 /bin/bash -c "python3 $__tool_directory__/wine_quality.py -model_ckpt_filepath ${model_ckpt} -norm_config_json_filepath ${norm_config_json} -data '${datajson_text}'";
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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24 cp OUTPUTS/quality.txt ${quality_txt};
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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25 ]]>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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26 </command>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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28 <inputs>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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29 <param name="datajson_text" optional="false" type="text" area="true"
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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30 label="Data of wine whose quality to be predicted (json as text)"/>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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31 <param name="model_ckpt" optional="false" type="data" format="ckpt"
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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32 label="model_ckpt model file (.ckpt)"/>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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33 <param name="norm_config_json" optional="false" type="data" format="json"
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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34 label="norm_config normalization configuration (.json)"/>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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35 </inputs>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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37 <outputs>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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38 <data format="txt" name="quality_txt" label="quality (.txt)"/>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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39 </outputs>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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41 <tests>
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42 </tests>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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44 <help><![CDATA[
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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46 wine_quality.xml
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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48 ===========================
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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50 Code:
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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52 ----
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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54 - wine_quality.py
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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56 Inputs:
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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58 -------
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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60 - data json as text : data of wine for which quality is going to be predicted.
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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62 - example :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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64 - {"fixed acidity": 11.2, "volatile acidity": 0.28, "citric acid": 0.56, "residual sugar": 1.9, "chlorides": 0.075, "free sulfur dioxide": 17, "total sulfur dioxide": 60, "density": 0.998, "pH": 3.16, "sulphates": 0.58, "alcohol": 9.8}
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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66 - Model file (.ckpt)
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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68 - Normalization configuration file (.json)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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70 Outputs:
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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72 --------
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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74 - Quality file (.txt)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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76 Credits:
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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78 --------
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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80 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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81 - Copyright: INRAE
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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82
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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83 ]]>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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84 </help>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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85
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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86 </tool>