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changeset 1:935e06766216 draft

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"planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/3a14800d8c700f5acdf49d564adc9fe820aa1c25 commit 3a14800d8c700f5acdf49d564adc9fe820aa1c25-dirty"
author siwaa
date Thu, 25 Aug 2022 10:49:25 +0000
parents 53d753cb6b81
children a08cdfcedd4c
files test-data/inputs/sunflo_input.csv test-data/inputs/sunflo_meteo.zip test-data/inputs/sunflo_output.csv tool_SUNFLO.xml tool_SUNFLO.xml.bak tool_defaults_SUNFLO.xml
diffstat 6 files changed, 71 insertions(+), 54 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputs/sunflo_input.csv	Thu Aug 25 10:49:25 2022 +0000
@@ -0,0 +1,5 @@
+sunflo_climat.meteo_file;itk.densite
+exmeteo_1.txt;7
+exmeteo_1.txt;5
+exmeteo_2.txt;7
+exmeteo_2.txt;5
Binary file test-data/inputs/sunflo_meteo.zip has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputs/sunflo_output.csv	Thu Aug 25 10:49:25 2022 +0000
@@ -0,0 +1,3 @@
+id;path;integration
+RDT;viewStatic/sunflo,sunflo_bio,performances:elaboration_rendement.photo_RDT_aFinMATURATION;last
+LAI;viewDbg/sunflo,sunflo_bio:croissance_plante.LAI;all
--- a/tool_SUNFLO.xml	Wed Dec 15 13:10:41 2021 +0000
+++ b/tool_SUNFLO.xml	Thu Aug 25 10:49:25 2022 +0000
@@ -1,11 +1,11 @@
 <tool id="SUNFLO" name="SUNFLO crop model simulations" version="1.0.0">
   <description></description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/record/record/azodyn_sunflo:187cf18876225903f7ab06915374a0277ad83130</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/record/record/azodyn_sunflo:ub2004_vle21</container>
   </requirements>
   <command detect_errors="aggressive">
     unzip ${input_meteo}; 
-    /bin/bash -c "Rscript --verbose /data/RECORD/misc/docker/rAzodynSunflo.R sunflo_web.vpz sunflo ${file_input} ${file_outputs} \${GALAXY_SLOTS:-2}";
+    /bin/bash -c "Rscript --verbose /data/rAzodynSunflo.R sunflo_web.vpz sunflo ${file_input} ${file_outputs} \${GALAXY_SLOTS:-2}";
     zip temp_results.zip  simresults_*.txt;
     cp temp_results.zip ${simresults};
   </command>
@@ -17,6 +17,26 @@
   <outputs>
     <data format="zip" name="simresults" />
   </outputs>
+  <tests>
+    <test>
+    <param name="input_meteo" value="inputs/sunflo_meteo.zip" ftype="zip" />
+    <param name="file_input" value="inputs/sunflo_input.csv" ftype="csv" />
+    <param name="file_outputs" value="inputs/sunflo_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="0.007252155941" />
+      </has_archive_member>
+      <has_archive_member path="simresults_RDT.txt">
+	<has_text text="29.639416530" />
+	<has_text text="29.411414411" />
+      </has_archive_member>
+    </assert_contents>
+    </output>
+  </test>
+</tests>
+
   <help><![CDATA[
 SUNFLO crop model simulations
 =============================
--- a/tool_SUNFLO.xml.bak	Wed Dec 15 13:10:41 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-<tool id="SUNFLO" name="SUNFLO crop model simulations" version="1.0.0">
-  <description></description>
-  <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/record/record/azodyn_sunflo:latest</container>
-  </requirements>
-  <command detect_errors="aggressive">
-    unzip ${input_meteo}; 
-    /bin/bash -c "Rscript --verbose /data/RECORD/misc/docker/rAzodynSunflo.R sunflo_web.vpz sunflo ${file_input} ${file_outputs} \${GALAXY_SLOTS:-2}";
-    zip temp_results.zip  simresults_*.txt;
-    cp temp_results.zip ${simresults};
-  </command>
-  <inputs>
-    <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[
-SUNFLO crop model 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:
---------
-
-- Copy to your history files 'sunflo_meteo.zip', 'sunflo_input.csv' and 'sunflo_output.csv' from the SUNFLO 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>
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_defaults_SUNFLO.xml	Thu Aug 25 10:49:25 2022 +0000
@@ -0,0 +1,41 @@
+<tool id="SUNFLOdefaults" name="SUNFLO crop model 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 sunflo_web.vpz sunflo";
+    cp file_default_input.csv ${inputs};
+    cp file_default_output.csv ${outputs};
+  </command>
+  <inputs>
+  </inputs>
+  <outputs>
+    <data format="csv" name="inputs" label="Sunflo default inputs"/>
+    <data format="csv" name="outputs" label="Sunflo default outputs"/>
+  </outputs>
+    <tests>
+    <test>
+      <output name="inputs">
+	<assert_contents>
+	  <has_text text="simulation_engine.duration;simulation_engine.begin" />
+	  <has_text text="AUZ_2006.txt;Jour;sunflo" />
+	</assert_contents>
+      </output>
+      <output name="outputs">
+	<assert_contents>
+	  <has_text text="id;path;integration" />
+	  <has_text text="INN;viewDbg/sunflo,sunflo_bio,contraintes:contrainte_azote.INN;all" />
+	</assert_contents>
+      </output>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+Sunflo crop model default inputs and outputs provider
+
+Full documentation is available here : https://siwaa.toulouse.inrae.fr/ in section "Tool Tuto > Sunflo tool"
+]]>
+  </help>
+</tool>
+