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annotate tool_AZODYN.xml @ 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
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children 97f5c404a9d6
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7a2bd77a30bf "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 358a6e682f76859d7b54f359b1ab701b79e3791e-dirty"
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1 <tool id="AZODYN" name="AZODYN crop models simulations" version="1.0.0">
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2 <description></description>
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3 <requirements>
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4 <container type="singularity">docker://registry.forgemia.inra.fr/record/record/azodyn_sunflo:358a6e682f76859d7b54f359b1ab701b79e3791e</container>
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5 </requirements>
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6 <command detect_errors="aggressive">
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7 unzip ${input_meteo};
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8 /bin/bash -c "Rscript --verbose /data/RECORD/misc/docker/rAzodynSunflo.R ${crop_type} AZODYN ${file_input} ${file_outputs} 5";
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9 zip temp_results.zip simresults_*.txt;
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10 cp temp_results.zip ${simresults};
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11 </command>
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12 <inputs>
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13 <param name="crop_type" type="select" label="Select crop to simulate">
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14 <option value="AzodynPea.vpz">Pea</option>
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15 <option value="AzodynWheat.vpz">Wheat</option>
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16 <option value="AzodynBarley.vpz">Barley</option>
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17 </param>
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18 <param name="input_meteo" type="data" format="zip" label="Wheater serie input files (zip file)"/>
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19 <param name="file_input" type="data" format="csv" label="Crop model input values"/>
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20 <param name="file_outputs" type="data" format="csv" label="Outputs to simulate"/>
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21 </inputs>
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22 <outputs>
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23 <data format="zip" name="simresults" />
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24 </outputs>
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25 <help><![CDATA[
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26 AZODYN crop models simulations
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27 ==============================
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29 Inputs:
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30 -------
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32 - Zip file of wheather series
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33 - Input values of the crop model (1 simulation per row)
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34 - Identification of the crop model output to simulate.
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36 Outputs:
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37 --------
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39 - Zip file of the crop model simulation values (1 file per output)
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7a2bd77a30bf "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 358a6e682f76859d7b54f359b1ab701b79e3791e-dirty"
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41 Example:
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42 --------
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7a2bd77a30bf "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 358a6e682f76859d7b54f359b1ab701b79e3791e-dirty"
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44 - Select 'Pea' as the crop model to use
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45 - Copy to your history files 'AzodynPea_meteo.zip', 'AzodynPea_input.csv' and 'AzodynPea_output.csv' from the AZODYN shared dataset.
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46 - Fill file names and choose the adequate number of cores.
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47 - And then execute
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48
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49 Credits:
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50 --------
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51
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52 - Author: Ronan Trépos ronan.trepos@inrae.fr
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53 - Wrapper Maintainer: Ronan Trépos ronan.trepos@inrae.fr
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54 - Tool Maintainer: Ronan Trépos ronan.trepos@inrae.fr
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55 - Copyright: INRAE]]>
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56 </help>
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57 </tool>
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58