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changeset 2:c1b75945752a draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit c595a7b4b556ab642ecf0396957f2959139dc4ab-dirty
author siwaa
date Mon, 09 Dec 2024 10:31:09 +0000
parents c3841488b88d
children f542f29a920c
files wine_quality.xml wine_quality.xml.VENDREDI
diffstat 2 files changed, 92 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/wine_quality.xml	Wed Dec 04 18:35:18 2024 +0000
+++ b/wine_quality.xml	Mon Dec 09 10:31:09 2024 +0000
@@ -5,23 +5,20 @@
   <requirements>
 
     <!-- singularity -->
-    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/dnn_fidlemore:6d159f79349e231deadb738f79bd293c1a8dadd3</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/dnn_fidlemore:c595a7b4b556ab642ecf0396957f2959139dc4ab</container>
 
     <!-- image locale
     <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_dnn/use/DNN/containers/fidlemore.simg</container -->
 
   </requirements>
 
-  <environment_variables>
-    <environment_variable name="FIDLE_DATASETS_DIR">/fidle-tp/datasets-fidle</environment_variable>
-  </environment_variables>
   <command detect_errors="aggressive">
     <![CDATA[
-    . /fidle-tp/fidle-env/bin/activate;
-    mkdir /fidle-tp/fidle-env/cache_dir; export TRANSFORMERS_CACHE=/fidle-tp/fidle-env/cache_dir;
-    mkdir /fidle-tp/fidle-env/mpl_dir; export MPLCONFIGDIR=/fidle-tp/fidle-env/mpl_dir;
-    /bin/bash -c "python3 $__tool_directory__/wine_quality.py -model_ckpt_filepath ${model_ckpt} -norm_config_json_filepath ${norm_config_json} -data '${datajson_text}'";
-    cp OUTPUTS/quality.txt ${quality_txt};
+    bash -e -c "source /fidle-tp/fidle-env/bin/activate &&
+    mkdir datasets-fidle &&
+    export FIDLE_DATASETS_DIR=\$(realpath -s datasets-fidle) &&
+    python3 $__tool_directory__/wine_quality.py -model_ckpt_filepath ${model_ckpt} -norm_config_json_filepath ${norm_config_json} -data '${datajson_text}' &&
+    cp OUTPUTS/quality.txt ${quality_txt}"
     ]]>
   </command>
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wine_quality.xml.VENDREDI	Mon Dec 09 10:31:09 2024 +0000
@@ -0,0 +1,86 @@
+<tool id="wine_quality" name="wine_quality" version="1.0.0">
+
+  <description>wine_quality</description>
+
+  <requirements>
+
+    <!-- singularity -->
+    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/dnn_fidlemore:6d159f79349e231deadb738f79bd293c1a8dadd3</container>
+
+    <!-- image locale
+    <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_dnn/use/DNN/containers/fidlemore.simg</container -->
+
+  </requirements>
+
+  <environment_variables>
+    <environment_variable name="FIDLE_DATASETS_DIR">/fidle-tp/datasets-fidle</environment_variable>
+  </environment_variables>
+  <command detect_errors="aggressive">
+    <![CDATA[
+    . /fidle-tp/fidle-env/bin/activate;
+    mkdir /fidle-tp/fidle-env/cache_dir; export TRANSFORMERS_CACHE=/fidle-tp/fidle-env/cache_dir;
+    mkdir /fidle-tp/fidle-env/mpl_dir; export MPLCONFIGDIR=/fidle-tp/fidle-env/mpl_dir;
+    /bin/bash -c "python3 $__tool_directory__/wine_quality.py -model_ckpt_filepath ${model_ckpt} -norm_config_json_filepath ${norm_config_json} -data '${datajson_text}'";
+    cp OUTPUTS/quality.txt ${quality_txt};
+    ]]>
+  </command>
+
+  <inputs>
+    <param name="datajson_text" optional="false" type="text" area="true"
+           label="Data of wine whose quality to be predicted (json as text)"/>
+    <param name="model_ckpt" optional="false" type="data" format="ckpt" 
+           label="model_ckpt model file (.ckpt)"/>
+    <param name="norm_config_json" optional="false" type="data" format="json" 
+           label="norm_config normalization configuration (.json)"/>
+  </inputs>
+
+  <outputs>
+    <data format="txt" name="quality_txt" label="quality (.txt)"/>
+  </outputs>
+
+  <tests>
+  </tests>
+
+  <help><![CDATA[
+
+wine_quality.xml
+
+===========================
+
+Code:
+
+----
+
+- wine_quality.py
+
+Inputs:
+
+-------
+
+- data json as text : data of wine for which quality is going to be predicted.
+
+  - example :
+
+    - {"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}
+
+- Model file (.ckpt)
+
+- Normalization configuration file (.json)
+
+Outputs:
+
+--------
+
+- Quality file (.txt)
+
+Credits:
+
+--------
+
+-  Author: Nathalie Rousse nathalie.rousse@inrae.fr
+-  Copyright: INRAE
+
+  ]]>
+  </help>
+
+</tool>