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changeset 0:7a2bd77a30bf draft

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"planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 358a6e682f76859d7b54f359b1ab701b79e3791e-dirty"
author siwaa
date Tue, 26 Oct 2021 09:07:12 +0000
parents
children 97f5c404a9d6
files tool_AZODYN.xml tool_AZODYN.xml.bak
diffstat 2 files changed, 116 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_AZODYN.xml	Tue Oct 26 09:07:12 2021 +0000
@@ -0,0 +1,58 @@
+<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>
+  </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>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_AZODYN.xml.bak	Tue Oct 26 09:07:12 2021 +0000
@@ -0,0 +1,58 @@
+<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>
+