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changeset 1:97f5c404a9d6 draft

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"planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 8269762f9e0aad13dad21b646add6fed821ed613"
author siwaa
date Wed, 17 Nov 2021 14:00:22 +0000
parents 7a2bd77a30bf
children e6bbaf03133e
files tool_AZODYN.xml tool_AZODYN.xml.bak
diffstat 2 files changed, 2 insertions(+), 60 deletions(-) [+]
line wrap: on
line diff
--- a/tool_AZODYN.xml	Tue Oct 26 09:07:12 2021 +0000
+++ b/tool_AZODYN.xml	Wed Nov 17 14:00:22 2021 +0000
@@ -1,11 +1,11 @@
 <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:358a6e682f76859d7b54f359b1ab701b79e3791e</container>
+    <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 ${crop_type} AZODYN ${file_input} ${file_outputs} 5";
+    /bin/bash -c "Rscript --verbose /data/RECORD/misc/docker/rAzodynSunflo.R ${crop_type} AZODYN ${file_input} ${file_outputs} \${GALAXY_SLOTS:-2}";
     zip temp_results.zip  simresults_*.txt;
     cp temp_results.zip ${simresults};
   </command>
--- a/tool_AZODYN.xml.bak	Tue Oct 26 09:07:12 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +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:latest</container>
-  </requirements>
-  <command detect_errors="aggressive">
-    unzip ${input_meteo}; 
-    /bin/bash -c "Rscript --verbose /data/RECORD/misc/docker/rAzodynSunflo.R ${crop_type} AZODYN ${file_input} ${file_outputs} 5";
-    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>
-