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annotate gama_tool.xml @ 0:f895e266b37a draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
author siwaa
date Tue, 04 Jun 2024 15:18:01 +0000
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f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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1 <tool id="gama_tool" name="gama" version="1.0.0">
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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3 <description>tool for GAMA Platform</description>
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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5 <requirements>
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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7 <!-- singularity -->
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8 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/gama:d01c3645810b3e5bf1b21170fd24d21fe1f831ec</container>
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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10 <!-- image locale
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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11 <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_gama/use/GAMA/containers/gama.simg</container -->
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12 </requirements>
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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14 <command detect_errors="aggressive">
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15 <![CDATA[
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16 cp -fr /opt/gama-platform .;
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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17 cp $__tool_directory__/src/MY_predatorPrey.gaml gama-platform/headless/samples/predatorPrey/.;
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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18 cp $__tool_directory__/src/MY_gama-headless.sh gama-platform/headless/.;
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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19 cp $__tool_directory__/src/MY_sequential_example.py .;
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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20 cp $__tool_directory__/src/cmd_gama_headless.sh .;
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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21 cp $__tool_directory__/src/cmd_python_client.sh .;
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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22 /bin/bash cmd_gama_headless.sh > run_server.txt & sleep 20 && /bin/bash cmd_python_client.sh $nb_preys_init $nb_predators_init $nb_more_steps > run_client.txt;
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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23 cp run_server.txt ${run_server_txt};
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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24 cp run_client.txt ${run_client_txt};
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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25 cp gama-platform/headless/samples/predatorPrey/results.txt ${results_txt};
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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26 ]]>
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27 </command>
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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29 <inputs>
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31 <param name="nb_preys_init" optional="true" type="integer"
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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32 value="200" min="0" max="1000"
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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33 label="nb_preys_init" help="[0, 1000]" />
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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34
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35 <param name="nb_predators_init" optional="true" type="integer"
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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36 value="20" min="0" max="200"
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37 label="nb_predators_init" help="[0, 200]" />
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38
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39 <param name="nb_more_steps" optional="true" type="integer"
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40 value="10" min="4" max="100"
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41 label="nb_more_steps" help="[4,100]" />
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42
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43 </inputs>
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44
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45 <outputs>
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46 <data format="txt" name="run_server_txt" label="run_server_txt"/>
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47 <data format="txt" name="run_client_txt" label="run_client_txt"/>
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48 <data format="txt" name="results_txt" label="results_txt"/>
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49 </outputs>
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50
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51 <tests>
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52 </tests>
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54 <help><![CDATA[
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55
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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56 Desc:
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57
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58 -----
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59
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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60 gama_tool.xml tool running a GAMA Python client interacting with gama-server
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61 (Headless server) concerning a "Predator Prey" agent-based simulator.
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62
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63 Code: MY_sequential_example.py
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64
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65 Inputs:
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66
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67 - nb_preys_init
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68 - nb_predators_init
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69 - nb_more_steps
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70
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71 Outputs:
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72
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73 - results_txt file (.txt) : produced while running the simulator
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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74 (cf 'reflex save_result' into MY_predatorPrey.gaml).
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75 - run_server_txt file (.txt) : gama-server screen display capture
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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76 - run_client_txt file (.txt) : gama-client screen display capture
f895e266b37a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef
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77
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78 Credits:
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80 --------
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82 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
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83 - Copyright: INRAE
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85 ]]>
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86 </help>
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87
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88 </tool>