Mercurial > repos > siwaa > sunflo

annotate tool_SUNFLO.xml @ 1:935e06766216 draft

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"planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/3a14800d8c700f5acdf49d564adc9fe820aa1c25 commit 3a14800d8c700f5acdf49d564adc9fe820aa1c25-dirty"
author siwaa
date Thu, 25 Aug 2022 10:49:25 +0000
parents 53d753cb6b81
children a08cdfcedd4c
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1 <tool id="SUNFLO" name="SUNFLO crop model 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 /bin/bash -c "Rscript --verbose /data/rAzodynSunflo.R sunflo_web.vpz sunflo ${file_input} ${file_outputs} \${GALAXY_SLOTS:-2}";
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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="input_meteo" type="data" format="zip" label="Wheater serie input files (zip file)"/>
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14 <param name="file_input" type="data" format="csv" label="Crop model input values"/>
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15 <param name="file_outputs" type="data" format="csv" label="Outputs to simulate"/>
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16 </inputs>
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17 <outputs>
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18 <data format="zip" name="simresults" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input_meteo" value="inputs/sunflo_meteo.zip" ftype="zip" />
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23 <param name="file_input" value="inputs/sunflo_input.csv" ftype="csv" />
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24 <param name="file_outputs" value="inputs/sunflo_output.csv" ftype="csv" />
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25 <output name="simresults">
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26 <assert_contents>
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27 <has_archive_member path="simresults_LAI.txt">
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28 <has_text text="0;0;0;0" />
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29 <has_text text="0.007252155941" />
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30 </has_archive_member>
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31 <has_archive_member path="simresults_RDT.txt">
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32 <has_text text="29.639416530" />
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33 <has_text text="29.411414411" />
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34 </has_archive_member>
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35 </assert_contents>
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36 </output>
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37 </test>
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38 </tests>
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39
0
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40 <help><![CDATA[
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41 SUNFLO crop model simulations
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42 =============================
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43
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44 Inputs:
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45 -------
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46
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47 - Zip file of wheather series
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48 - Input values of the crop model (1 simulation per row)
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49 - Identification of the crop model output to simulate.
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50
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51 Outputs:
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52 --------
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53
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54 - Zip file of the crop model simulation values (1 file per output)
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55
53d753cb6b81 "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 67ecf5a057de84342a865b7346fe9d096e795298-dirty"
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56 Example:
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57 --------
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58
53d753cb6b81 "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 67ecf5a057de84342a865b7346fe9d096e795298-dirty"
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59 - Copy to your history files 'sunflo_meteo.zip', 'sunflo_input.csv' and 'sunflo_output.csv' from the SUNFLO shared dataset.
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60 - Fill file names and choose the adequate number of cores.
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61 - And then execute
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62
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63 Credits:
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64 --------
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65
53d753cb6b81 "planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 67ecf5a057de84342a865b7346fe9d096e795298-dirty"
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66 - Author: Ronan Trépos ronan.trepos@inrae.fr
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67 - Wrapper Maintainer: Ronan Trépos ronan.trepos@inrae.fr
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68 - Tool Maintainer: Ronan Trépos ronan.trepos@inrae.fr
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69 - Copyright: INRAE]]>
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70 </help>
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71 </tool>
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72