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"planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit 40258eb06e8909d55406fd6f6f1b71fddc3c158d"
author siwaa
date Thu, 10 Apr 2025 15:22:42 +0000
parents 50112d3941d8
children
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f2840b46b353 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit 40258eb06e8909d55406fd6f6f1b71fddc3c158d"
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1 <tool id="inSiliCow" name="inSiliCow" version="1.0.1">
0
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2 <description>to run the inSiliCow simulator</description>
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3 <requirements>
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4 <container type="singularity">docker://registry.forgemia.inra.fr/insilicow/insilicow-container:6d9cbffcf24d3af29b244ea3543c53b4298077de</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 echo "=================" &&
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9 env &&
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10 echo "=================" &&
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11 cp -r /insilicow-simulator . &&
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12 cd insilicow-simulator/scripts &&
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13 cp $__tool_directory__/inSiliCow-run.sh . &&
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14 cp $__tool_directory__/inSiliCow-post.sh . &&
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15 rm -rf examples/e* &&
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16 unzip -d tmp ${in} &&
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17 configDir=\$(ls -1 tmp) &&
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18 mv tmp/* examples &&
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19 pwd && ls && echo \$configDir &&
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20 chmod u+x ./inSiliCow-run.sh &&
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21 TERM="xterm-256color" ./inSiliCow-run.sh \$configDir &&
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22 cd out &&
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23 zip -r j* * &&
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24 mv *.zip ${out}
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25 ]]>
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26 </command>
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27 <inputs>
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28 <param name="in" type="data" format="zip" label="Select a inSiliCow config folder (zip file)"/>
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29 </inputs>
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30 <outputs>
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31 <data format="zip" name="out"
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32 label="inSiliCowOutputs">
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33 </data>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="in" value="input/example_00.zip" ftype="zip" />
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38 <output name="out" ftype="zip" >
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39 <assert_contents>
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40 <has_archive_member path=".*/out/farmer.sh">
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41 <has_size value="0" negate="true" />
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42 </has_archive_member>
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43 <has_archive_member path=".*/in/explan.txt">
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44 <has_size value="0" negate="true" />
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45 <has_text text="end_year" />
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46 <has_text text="1971" />
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47 </has_archive_member>
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48 <has_archive_member path=".*/out/sim_1/events.sqlite">
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49 <has_size value="0" negate="true" />
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50 </has_archive_member>
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51 <has_archive_member path=".*/out/sim_1/states.txt">
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52 <has_size value="0" negate="true" />
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53 <has_text text="CALF" />
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54 </has_archive_member>
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55 <has_archive_member path=".*/out/sim_1/cows/nb_cows.txt">
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56 <has_text text="126" />
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57 </has_archive_member>
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58 </assert_contents>
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59 </output>
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60 </test>
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61 </tests>
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62 <help>
1
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63 *The usage of this tool is restricted to the user of the insilicow Galaxy/SIWAA group.*
0
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64
1
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65 *To be granted, apply to the insilicow Project Team and then request to SIWAA*
0
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66
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67 Documentation
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68 -------------
1
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69 A tool to launch the inSiliCow dairy cow herd simulator
0
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70
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71 Credits
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72 -------
1
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73 - Wrappedt tool authors: Olivier Martin (MoSAR) &lt;olivier.martin-mosar@inrae.fr&gt;, Pierre Blavy &lt;pierre.blavy@inrae.fr&gt;
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74 - Insilicow project site: https://digitbio.hub.inrae.fr/rubriques-verticales2/nos-actions/projets-phares/projet-phare-insilicow-2024-2028
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75 - Insilicow repository: https://forgemia.inra.fr/insilicow
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76 - Underlying container maintainer: Eric Casellas &lt;eric.casellas@inrae.fr&gt;
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77 - Galaxy tool maintainer: Patrick Chabrier &lt;patrick.chabrier@inrae.fr&gt;
0
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78 - Copyright: INRAE
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79 </help>
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80 </tool>