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annotate tool_AZODYN.xml @ 3:d1070fee9dc4 draft

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"planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 4861ee70e49274ed88d2b7ca37f02178ed6da471"
author siwaa
date Wed, 27 Apr 2022 09:59:49 +0000
parents e6bbaf03133e
children 5deede146fb6
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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:ub2004_vle21</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
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11 /bin/bash -c "Rscript --verbose /data/rAzodynSunflo.R ${crop_type} AZODYN internal_inputAZODYN.csv internal_outputAZODYN.csv \${GALAXY_SLOTS:-2}";
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12 zip temp_results.zip simresults_*.txt;
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13 cp temp_results.zip ${simresults};
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14 </command>
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15 <inputs>
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16 <param name="crop_type" type="select" label="Select crop to simulate">
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17 <option value="AzodynPea.vpz">Pea</option>
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18 <option value="AzodynWheat.vpz">Wheat</option>
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19 <option value="AzodynBarley.vpz">Barley</option>
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20 </param>
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21 <param name="input_meteo" type="data" format="zip" label="Wheater serie input files (zip file)"/>
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22 <param name="file_input" type="data" format="csv" label="Crop model input values"/>
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23 <param name="file_outputs" type="data" format="csv" label="Outputs to simulate"/>
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24 </inputs>
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25 <outputs>
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26 <data format="zip" name="simresults" />
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27 </outputs>
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28 <help><![CDATA[
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29 AZODYN crop models simulations
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30 ==============================
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32 Inputs:
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33 -------
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35 - Zip file of wheather series
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36 - Input values of the crop model (1 simulation per row)
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37 - Identification of the crop model output to simulate.
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39 Outputs:
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40 --------
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42 - Zip file of the crop model simulation values (1 file per output)
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44 Example:
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45 --------
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47 - Select 'Pea' as the crop model to use
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48 - Copy to your history files 'AzodynPea_meteo.zip', 'AzodynPea_input.csv' and 'AzodynPea_output.csv' from the AZODYN shared dataset.
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49 - Fill file names and choose the adequate number of cores.
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50 - And then execute
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51
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52 Credits:
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53 --------
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54
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55 - Author: Ronan Trépos ronan.trepos@inrae.fr
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56 - Wrapper Maintainer: Ronan Trépos ronan.trepos@inrae.fr
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57 - Tool Maintainer: Ronan Trépos ronan.trepos@inrae.fr
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58 - Copyright: INRAE]]>
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59 </help>
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60 </tool>
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61