# HG changeset patch
# User siwaa
# Date 1661424477 0
# Node ID 49c988e63e6bcd80fe66b1e28e2167b13c65eab6
# Parent  5deede146fb6143990e2d020a320747907e5e67d
"planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/3a14800d8c700f5acdf49d564adc9fe820aa1c25 commit 3a14800d8c700f5acdf49d564adc9fe820aa1c25-dirty"

diff -r 5deede146fb6 -r 49c988e63e6b test-data/inputs/AzodynPea_input.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputs/AzodynPea_input.csv	Thu Aug 25 10:47:57 2022 +0000
@@ -0,0 +1,5 @@
+cPlant.coef_tot_a;condClimate.meteo_file
+1.25;meteo1.csv
+1.5;meteo1.csv
+1.0;meteo2.csv
+1.25;meteo2.csv
diff -r 5deede146fb6 -r 49c988e63e6b test-data/inputs/AzodynPea_meteo.zip
Binary file test-data/inputs/AzodynPea_meteo.zip has changed
diff -r 5deede146fb6 -r 49c988e63e6b test-data/inputs/AzodynPea_output.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputs/AzodynPea_output.csv	Thu Aug 25 10:47:57 2022 +0000
@@ -0,0 +1,3 @@
+id;path;integration
+LAI;view/AzodynPea:PlantGrowthPea.LAI;all
+MS;view/AzodynPea:PlantGrowthPea.MS;all
diff -r 5deede146fb6 -r 49c988e63e6b tool_AZODYN.xml
--- a/tool_AZODYN.xml	Tue May 03 10:17:50 2022 +0000
+++ b/tool_AZODYN.xml	Thu Aug 25 10:47:57 2022 +0000
@@ -24,6 +24,26 @@
   <outputs>
     <data format="zip" name="simresults" />
   </outputs>
+  <tests>
+  <test>
+    <param name="crop_type" value="AzodynPea.vpz" />
+    <param name="input_meteo" value="inputs/AzodynPea_meteo.zip" ftype="zip" />
+    <param name="file_input" value="inputs/AzodynPea_input.csv" ftype="csv" />
+    <param name="file_outputs" value="inputs/AzodynPea_output.csv" ftype="csv" />
+    <output name="simresults">
+    <assert_contents>
+      <has_archive_member path="simresults_LAI.txt">
+	<has_text text="0;0;0;0" />
+	<has_text text="0.02230323" />
+      </has_archive_member>
+      <has_archive_member path="simresults_MS.txt">
+	<has_text text="0;0;0;0" />
+	<has_text text="1.568" />
+      </has_archive_member>
+    </assert_contents>
+    </output>
+  </test>
+</tests>
   <help><![CDATA[
 AZODYN crop models simulations
 ==============================
diff -r 5deede146fb6 -r 49c988e63e6b tool_AZODYN.xml.bak
--- a/tool_AZODYN.xml.bak	Tue May 03 10:17:50 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
-<tool id="AZODYN" name="AZODYN crop models simulations" version="1.0.0">
-  <description></description>
-  <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/record/record/azodyn_sunflo:ub2004_vle21</container>
-  </requirements>
-  <command detect_errors="aggressive">
-    unzip ${input_meteo}; 
-    dos2unix -n ${file_input} internal_inputAZODYN.csv;
-    dos2unix -n ${file_outputs} internal_outputAZODYN.csv; 
-    /bin/bash -c "Rscript --verbose /data/rAzodynSunflo.R ${crop_type} AZODYN internal_inputAZODYN.csv internal_outputAZODYN.csv \${GALAXY_SLOTS:-2}";
-    zip temp_results.zip  simresults_*.txt;
-    cp temp_results.zip ${simresults};
-  </command>
-  <inputs>
-    <param name="crop_type" type="select"  label="Select crop to simulate">
-      <option value="AzodynPea.vpz">Pea</option>
-      <option value="AzodynWheat.vpz">Wheat</option>
-      <option value="AzodynBarley.vpz">Barley</option>
-    </param>
-    <param name="input_meteo" type="data" format="zip" label="Wheater serie input files (zip file)"/>
-    <param name="file_input" type="data" format="csv" label="Crop model input values"/>
-    <param name="file_outputs" type="data" format="csv" label="Outputs to simulate"/>
-  </inputs>
-  <outputs>
-    <data format="zip" name="simresults" />
-  </outputs>
-  <help><![CDATA[
-AZODYN crop models simulations
-==============================
-
-Inputs:
--------
-
-- Zip file of wheather series
-- Input values of the crop model (1 simulation per row)
-- Identification of the crop model output to simulate.
-
-Outputs:
---------
-
-- Zip file of the crop model simulation values (1 file per output)
-
-Example:
---------
-
-- Select 'Pea' as the crop model to use
-- Copy to your history files 'AzodynPea_meteo.zip', 'AzodynPea_input.csv' and 'AzodynPea_output.csv' from the AZODYN shared dataset.
-- Fill file names and choose the adequate number of cores.
-- And then execute 
-
-Credits:
---------
-
--  Author: Ronan Trépos ronan.trepos@inrae.fr
--  Wrapper Maintainer: Ronan Trépos ronan.trepos@inrae.fr
--  Tool Maintainer: Ronan Trépos ronan.trepos@inrae.fr
--  Copyright: INRAE]]>
-  </help>
-</tool>
-
diff -r 5deede146fb6 -r 49c988e63e6b tool_defaults_AZODYN.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_defaults_AZODYN.xml	Thu Aug 25 10:47:57 2022 +0000
@@ -0,0 +1,46 @@
+<tool id="AZODYNdefaults" name="AZODYN crop models default inputs and outputs" version="1.0.0">
+  <description></description>
+  <requirements>
+    <container type="singularity">docker://registry.forgemia.inra.fr/record/record/azodyn_sunflo:ub2004_vle21</container>
+  </requirements>
+  <command detect_errors="aggressive">
+    /bin/bash -c "Rscript --verbose /data/rDefaultAzodynSunflo.R ${crop_type} AZODYN";
+    cp file_default_input.csv ${inputs};
+    cp file_default_output.csv ${outputs};
+  </command>
+  <inputs>
+    <param name="crop_type" type="select"  label="Select crop">
+      <option value="AzodynPea.vpz">Pea</option>
+      <option value="AzodynWheat.vpz">Wheat</option>
+      <option value="AzodynBarley.vpz">Barley</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="csv" name="inputs" label="Azodyn default inputs"/>
+    <data format="csv" name="outputs" label="Azodyn default outputs"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="crop_type" value="AzodynPea.vpz" />
+      <output name="inputs">
+	<assert_contents>
+	  <has_text text="simulation_engine.duration;simulation_engine.begin" />
+	  <has_text text="Breteniere_1991_2018.csv;AZODYN" />
+	</assert_contents>
+      </output>
+      <output name="outputs">
+	<assert_contents>
+	  <has_text text="id;path;integration" />
+	  <has_text text="Des_cumul;view/AzodynPea:Frost.Des_cumul;all" />
+	</assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[
+Azodyn crop models default inputs and outputs provider
+
+Full documentation is available here : https://siwaa.toulouse.inrae.fr/ in section "Tool Tuto > Azodyn tool"
+]]>
+  </help>
+</tool>
+