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annotate REDELACparallelSticsRsequence-10.0.xml @ 1:50dd120308af draft default tip

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"planemo upload for repository https://forgemia.inra.fr/redelac"
author siwaa
date Mon, 12 Jun 2023 16:06:00 +0000
parents 21e91d3b7068
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21e91d3b7068 "planemo upload for repository https://forgemia.inra.fr/redelac"
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1 <tool id="REDELACparallelSticsRsequence-10.0.0" name="redelacparallelsticsrsequence-10.0.0" version="1.0.0">
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2 <description>to run sequences paralelly 4 REDELAC[Stics-10.0.0]</description>
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3 <requirements>
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4 <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics_redelac: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 unzip ${WorkSpace} -d TMP &&
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10 export WSname=\$(ls TMP) &&
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11 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
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12 cp ${SuccessionPlan} JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv &&
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13 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
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14 Rscript --verbose $__tool_directory__/REDELACparallelSticsRsequence.R &&
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15 mv WS \$WSname &&
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16 zip -r \$WSname \$WSname &&
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17 cp \$WSname.zip ${SimulatedWorkspace} &&
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18 cp results.RData ${SimulationResults}
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="WorkSpace" type="data" format="zip" label="Select a stics Workspace(zip file)"/>
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23 <param name="SuccessionPlan" type="data" format="csv" label="Select a plan (xlsx)"/>
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24 </inputs>
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25 <outputs>
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26 <data format="zip" name="SimulatedWorkspace"
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27 label="Stics simulated Workspace">
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28 </data>
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29 <data format="rdata" name="SimulationResults"
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30 label="Stics simulations results">
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31 </data>
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32 </outputs>
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33 <tests>
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34 </tests>
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35 <help>
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36 *The usage of this tool is restricted to the user of the stics_authorized group.*
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37
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38 *To be granted, apply to the Project Stics Team and then request to SIWAA*
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39
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40 Documentation
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41 -------------
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42 A tool to simulate stics rotation paralelly
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43
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44 Credits
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45 -------
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46 - Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team
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47 - Stics Site: https://www6.paca.inra.fr/stics_eng
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48 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
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49 - Copyright: INRAE
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50 </help>
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51 </tool>