Mercurial > repos > siwaa > azodyn

annotate tool_AZODYN.xml @ 8:b72b6d36bf94 draft

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"planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/6309b0ebe4ac2f7b979d28fb46f90c7719beb87b commit 6309b0ebe4ac2f7b979d28fb46f90c7719beb87b-dirty"
author siwaa
date Tue, 17 Jan 2023 09:28:15 +0000
parents 420fa749a5f9
children ead8d0406cdb
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8
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1 <tool id="AZODYN" name="AZODYN crop models simulations" version="1.3.0">
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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:image-azodynsunflo-1.3</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 dos2unix -n ${file_input} internal_inputAZODYN.csv;
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9 dos2unix -n ${file_outputs} internal_outputAZODYN.csv;
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10 /bin/bash -c "Rscript --verbose /data/rAzodynSunflo.R ${crop_type} AZODYN internal_inputAZODYN.csv internal_outputAZODYN.csv \${GALAXY_SLOTS:-2}";
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11 zip temp_results.zip simresults_*.txt;
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12 cp temp_results.zip ${simresults};
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13 </command>
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14 <inputs>
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15 <param name="crop_type" type="select" label="Select crop to simulate">
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16 <option value="AzodynPea.vpz">Pea</option>
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17 <option value="AzodynWheat.vpz">Wheat</option>
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18 <option value="AzodynBarley.vpz">Barley</option>
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19 </param>
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20 <param name="input_meteo" type="data" format="zip" label="Wheater serie input files (zip file)"/>
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21 <param name="file_input" type="data" format="csv" label="Crop model input values"/>
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22 <param name="file_outputs" type="data" format="csv" label="Outputs to simulate"/>
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23 </inputs>
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24 <outputs>
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25 <data format="zip" name="simresults" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="crop_type" value="AzodynPea.vpz" />
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30 <param name="input_meteo" value="inputs/AzodynPea_meteo.zip" ftype="zip" />
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31 <param name="file_input" value="inputs/AzodynPea_input.csv" ftype="csv" />
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32 <param name="file_outputs" value="inputs/AzodynPea_output.csv" ftype="csv" />
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33 <output name="simresults">
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34 <assert_contents>
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35 <has_archive_member path="simresults_LAI.txt">
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36 <has_text text="0;0;0;0" />
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37 <has_text text="0.02230323" />
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38 </has_archive_member>
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39 <has_archive_member path="simresults_MS.txt">
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40 <has_text text="0;0;0;0" />
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41 <has_text text="1.568" />
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42 </has_archive_member>
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43 </assert_contents>
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44 </output>
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45 </test>
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46 </tests>
0
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47 <help><![CDATA[
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48 AZODYN crop models simulations
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49 ==============================
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50
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51 Inputs:
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52 -------
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53
7a2bd77a30bf "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 358a6e682f76859d7b54f359b1ab701b79e3791e-dirty"
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54 - Zip file of wheather series
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55 - Input values of the crop model (1 simulation per row)
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56 - Identification of the crop model output to simulate.
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57
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58 Outputs:
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59 --------
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60
7a2bd77a30bf "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 358a6e682f76859d7b54f359b1ab701b79e3791e-dirty"
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61 - Zip file of the crop model simulation values (1 file per output)
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62
7a2bd77a30bf "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 358a6e682f76859d7b54f359b1ab701b79e3791e-dirty"
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63 Example:
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64 --------
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65
7a2bd77a30bf "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 358a6e682f76859d7b54f359b1ab701b79e3791e-dirty"
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66 - Select 'Pea' as the crop model to use
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67 - Copy to your history files 'AzodynPea_meteo.zip', 'AzodynPea_input.csv' and 'AzodynPea_output.csv' from the AZODYN shared dataset.
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68 - Fill file names and choose the adequate number of cores.
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69 - And then execute
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70
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71 Credits:
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72 --------
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73
7a2bd77a30bf "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 358a6e682f76859d7b54f359b1ab701b79e3791e-dirty"
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74 - Author: Ronan Trépos ronan.trepos@inrae.fr
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75 - Wrapper Maintainer: Ronan Trépos ronan.trepos@inrae.fr
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76 - Tool Maintainer: Ronan Trépos ronan.trepos@inrae.fr
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77 - Copyright: INRAE]]>
7a2bd77a30bf "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 358a6e682f76859d7b54f359b1ab701b79e3791e-dirty"
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78 </help>
7a2bd77a30bf "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 358a6e682f76859d7b54f359b1ab701b79e3791e-dirty"
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79 </tool>
7a2bd77a30bf "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 358a6e682f76859d7b54f359b1ab701b79e3791e-dirty"
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80