Mercurial > repos > siwaa > redelac_stics_s

annotate redelacSticsSimulator.xml @ 2:ea8e91473dc8 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
author siwaa
date Fri, 23 Jun 2023 10:17:27 +0000
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children fa8e742b197b
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ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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1 <tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.1">
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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2 <description>to run sequences paralelly [Stics-10.0.0]</description>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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3 <requirements>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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4 <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics:10.0.0</container>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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5 </requirements>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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6 <command detect_errors="aggressive">
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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7 <![CDATA[
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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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 . &&
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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9 rm JavaSTICS-1.5.1-STICS-10.0.0/bin/stics_modulo &&
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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10 cp $__tool_directory__/stics_modulo JavaSTICS-1.5.1-STICS-10.0.0/bin &&
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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11 unzip -qq ${WorkSpace} -d TMP &&
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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12 export WSname=\$(ls TMP) &&
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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13 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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14 cp ${SuccessionPlan} JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv &&
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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15 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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16 Rscript --verbose $__tool_directory__/redelacSticsSimulator.R \${GALAXY_SLOTS:-2} &&
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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17 mv WS \$WSname &&
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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18 zip -qq -r \$WSname \$WSname &&
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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19 cp \$WSname.zip ${SimulatedWorkspace} &&
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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20 cp results.RData ${SimulationResults}
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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21 ]]>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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22 </command>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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23 <inputs>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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24 <param name="WorkSpace" type="data" format="zip" label="Select a stics Workspace(zip file)"/>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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25 <param name="SuccessionPlan" type="data" format="csv" label="Select a plan of succession (csv)"/>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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26 <param name="Tag" type="text" value="" label="Outputs tag"/>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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27 </inputs>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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28 <outputs>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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29 <data format="zip" name="SimulatedWorkspace"
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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30 label="SticsSimulatedWorkspace${Tag}">
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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31 </data>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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32 <data format="rdata" name="SimulationResults"
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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33 label="SticsOnResults${Tag}">
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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34 </data>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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35 </outputs>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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36 <tests>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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37 </tests>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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38 <help>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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39 *The usage of this tool is restricted to the user of the stics_authorized group.*
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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40
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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41 *To be granted, apply to the Project Stics Team and then request to SIWAA*
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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42
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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43 Documentation
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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44 -------------
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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45 A tool to simulate stics rotation paralelly
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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46
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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47 Credits
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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48 -------
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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49 - Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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50 - Stics Site: https://www6.paca.inra.fr/stics_eng
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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51 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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52 - Copyright: INRAE
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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53 </help>
ea8e91473dc8 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
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54 </tool>