Mercurial > repos > siwaa > sunflo

annotate tool_SUNFLO.xml @ 5:b4b957727dec draft default tip

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"planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/cc4805e05de7961381e752d96eff34bf06144f48 commit cc4805e05de7961381e752d96eff34bf06144f48-dirty"
author patrick_chabrier
date Mon, 17 Jun 2024 11:04:10 +0000
parents 64b9de83b8e6
children
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5
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1 <tool id="SUNFLO" name="SUNFLO crop model simulations" version="1.3.1">
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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 --allow-chown *
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9 dos2unix -n ${file_input} internal_inputSUNFLO.csv;
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10 dos2unix -n ${file_outputs} internal_outputSUNFLO.csv;
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11 /bin/bash -c "Rscript --verbose /data/rAzodynSunflo.R sunflo_simple.vpz sunflo internal_inputSUNFLO.csv internal_outputSUNFLO.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="input_meteo" type="data" format="zip" label="Wheater serie input files (zip file)"/>
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17 <param name="file_input" type="data" format="csv" label="Crop model input values"/>
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18 <param name="file_outputs" type="data" format="csv" label="Outputs to simulate"/>
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19 </inputs>
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20 <outputs>
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21 <data format="zip" name="simresults" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input_meteo" value="inputs/sunflo_meteo.zip" ftype="zip" />
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26 <param name="file_input" value="inputs/sunflo_input.csv" ftype="csv" />
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27 <param name="file_outputs" value="inputs/sunflo_output.csv" ftype="csv" />
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28 <output name="simresults">
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29 <assert_contents>
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30 <has_archive_member path="simresults_LAI.txt">
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31 <has_text text="0;0;0;0" />
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32 <has_text text="0.007303977383" />
1
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33 </has_archive_member>
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34 <has_archive_member path="simresults_RDT.txt">
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35 <has_text text="25.004733605" />
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36 <has_text text="25.084471273" />
1
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37 </has_archive_member>
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38 </assert_contents>
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39 </output>
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40 </test>
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41 </tests>
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42
0
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43 <help><![CDATA[
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44 SUNFLO crop model simulations
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45 =============================
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46
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47 Inputs:
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48 -------
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49
53d753cb6b81 "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 67ecf5a057de84342a865b7346fe9d096e795298-dirty"
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50 - Zip file of wheather series
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51 - Input values of the crop model (1 simulation per row)
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52 - Identification of the crop model output to simulate.
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53
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54 Outputs:
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55 --------
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56
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57 - Zip file of the crop model simulation values (1 file per output)
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58
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59 Example:
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60 --------
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61
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62 - Copy to your history files 'sunflo_meteo.zip', 'sunflo_input.csv' and 'sunflo_output.csv' from the SUNFLO shared dataset.
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63 - Fill file names and choose the adequate number of cores.
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64 - And then execute
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65
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66 Credits:
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67 --------
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68
53d753cb6b81 "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 67ecf5a057de84342a865b7346fe9d096e795298-dirty"
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69 - Author: Ronan Trépos ronan.trepos@inrae.fr
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70 - Wrapper Maintainer: Ronan Trépos ronan.trepos@inrae.fr
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71 - Tool Maintainer: Ronan Trépos ronan.trepos@inrae.fr
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72 - Copyright: INRAE]]>
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73 </help>
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74 </tool>
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75