Mercurial > repos > siwaa > wine_quality_predict

changeset 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
files wine_quality_predict.xml wine_quality_predict.xml.original
diffstat 2 files changed, 96 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/wine_quality_predict.xml	Wed Dec 04 18:35:11 2024 +0000
+++ b/wine_quality_predict.xml	Fri Dec 06 19:17:19 2024 +0000
@@ -17,11 +17,19 @@
   </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 /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}";
-    cp OUTPUTS/report.json ${report_json};
+
+    bash -e -c "source /fidle-tp/fidle-env/bin/activate &&
+    mkdir datasets-fidle &&
+    export FIDLE_DATASETS_DIR=\$(realpath -s datasets-fidle) &&
+    mkdir ipython_dir &&
+    export IPYTHONDIR=\$(realpath -s ipython_dir) &&
+    ipython profile create default &&
+    mkdir cache_dir &&
+    export TRANSFORMERS_CACHE=\$(realpath -s cache_dir) &&
+    mkdir mpl_dir &&
+    export MPLCONFIGDIR=\$(realpath -s mpl_dir) &&
+    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} &&
+    cp OUTPUTS/report.json ${report_json}"
     ]]>
   </command>
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wine_quality_predict.xml.original	Fri Dec 06 19:17:19 2024 +0000
@@ -0,0 +1,83 @@
+<tool id="wine_quality_predict" name="wine_quality_predict" version="1.0.0">
+
+  <description>wine_quality_predict</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 /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}";
+    cp OUTPUTS/report.json ${report_json};
+    ]]>
+  </command>
+
+  <inputs>
+    <param name="data_json" optional="false" type="data" format="json"
+           label="File of data of wine whose quality to be predicted (.json)"/>
+    <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="json" name="report_json" label="report (.json)"/>
+  </outputs>
+
+  <tests>
+  </tests>
+
+  <help><![CDATA[
+
+wine_quality_predict.xml
+
+===========================
+
+Code:
+
+----
+
+- wine_quality_predict.py
+
+Inputs:
+
+-------
+
+- data file (.json) :
+  File containing data of wine for which quality is going to be predicted.
+
+- Model file (.ckpt)
+
+- Normalization configuration file (.json)
+
+Outputs:
+
+--------
+
+- Report file (.json)
+
+Credits:
+
+--------
+
+-  Author: Nathalie Rousse nathalie.rousse@inrae.fr
+-  Copyright: INRAE
+
+  ]]>
+  </help>
+
+</tool>