Mercurial > repos > siwaa > redelac_stics_g

annotate redelacSticsInputGenerator.xml @ 4:af7d9ca55205 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit eee8ee9f1f9a49a332d24981c79fa4f0a45e65bd"
author siwaa
date Thu, 29 Jun 2023 11:03:20 +0000
parents e344100f3354
children 4f8d87b9c246
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1 <tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.1">
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2 <description>to run generate Stics Inputs for REDELAC</description>
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3 <requirements>
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4 <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics_test:10.0.0</container>
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5 </requirements>
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6 <command detect_errors="aggressive">
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7 <![CDATA[
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8 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/JavaSTICS-1.5.1-STICS-10.0.0 . &&
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9 rm -rf JavaSTICS-1.5.1-STICS-10.0.0/config &&
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10 cp -r $__tool_directory__/config JavaSTICS-1.5.1-STICS-10.0.0 &&
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11 unzip ${Workspace} -d TMP &&
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12 export WSname=\$(ls TMP) &&
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13 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
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14 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_gen.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
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15 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_newform.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
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16 unzip ${Climat} -d TMPbis &&
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17 mv TMPbis/*/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
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18 cp ${USMs} JavaSTICS-1.5.1-STICS-10.0.0/WS/USMs.csv &&
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19 cp ${Tec} JavaSTICS-1.5.1-STICS-10.0.0/WS/Tec.csv &&
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20 cp ${Ini} JavaSTICS-1.5.1-STICS-10.0.0/WS/Ini.csv &&
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21 cp ${Station} JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
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22 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
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23 Rscript --verbose $__tool_directory__/redelacSticsInputGenerator.R &&
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24 rm WS/1* &&
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25 mv WS \$WSname &&
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26 zip -r \$WSname \$WSname &&
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27 cp \$WSname.zip ${GeneratedWorkspace}
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28 ]]>
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29 </command>
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30 <inputs>
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31 <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/>
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32 <param name="Climat" type="data" format="zip" label="Select a climat scenario (zip file)"/>
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33 <param name="USMs" type="data" format="csv" label="Select the USMs sheet (csv)"/>
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34 <param name="Tec" type="data" format="csv" label="Select the Tec sheet (csv)"/>
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35 <param name="Ini" type="data" format="csv" label="Select the Ini sheet (csv)"/>
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36 <param name="Station" type="data" format="csv" label="Select the Station sheet (csv)"/>
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37 <param name="Tag" type="text" value="" label="Outputs tag"/>
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38 </inputs>
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39 <outputs>
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40 <data format="zip" name="GeneratedWorkspace"
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41 label="GeneratedWorkspace${Tag}">
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42 </data>
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43 </outputs>
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44 <tests>
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45 </tests>
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46 <help>
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47 *The usage of this tool is restricted to the user of the stics_authorized group.*
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48
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49 *To be granted, apply to the Project Stics Team and then request to SIWAA*
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50
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51 Documentation
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52 -------------
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53 A tool to generate Stics Inputs according to a plan for REDELAC
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54
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55 Credits
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56 -------
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57 - Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team
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58 - Stics Site: https://www6.paca.inra.fr/stics_eng
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59 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
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60 - Copyright: INRAE
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61 </help>
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62 </tool>