Mercurial > repos > siwaa > gama_legacy_run

annotate gama_legacy_run.xml @ 0:986f43279bca draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_run commit 14769577c04bcb2781b2d240f1f57a2342169cce-dirty
author siwaa
date Fri, 02 Aug 2024 18:03:16 +0000
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986f43279bca planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_run commit 14769577c04bcb2781b2d240f1f57a2342169cce-dirty
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1 <tool id="gama_legacy_run" name="gama_legacy_run" version="1.0.0">
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2
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3 <description>tool running an experiment plan XML file associated with a GAML file (GAMA Headless Legacy mode)</description>
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5 <requirements>
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7 <!-- singularity -->
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8 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/gama_headless:e45168638437055475beeaa614611cb315a56fca</container>
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9
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10 <!-- image locale
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11 <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_gama/use/GAMA_HEADLESS_LEGACY/containers/gama_headless.simg</container -->
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12 </requirements>
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14 <command detect_errors="aggressive">
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15 <![CDATA[
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16 mkdir -p software; mkdir -p exp;
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17 cp $__tool_directory__/src/MY_gama-headless.sh .;
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18 cp $__tool_directory__/src/cmd_gama_headless_legacy_run.sh .;
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19 cp ${model_gaml} exp/model.gaml;
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20 cp ${file_xml} exp/file.xml;
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21 xmlstarlet edit --inplace --update "//Simulation/@sourcePath" --value "model.gaml" exp/file.xml;
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22 xmlstarlet edit --inplace --update "//Simulation/@finalStep" --value "${final_step}" exp/file.xml;
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23 cp -fr /opt/gama-platform software/.;
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24 cp MY_gama-headless.sh software/gama-platform/headless/. ;
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25 chmod -R 777 software;
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26 /bin/bash cmd_gama_headless_legacy_run.sh > exp/RUN.txt;
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27 rm -fr exp/outputs/.workspace*;
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28 zip -r tmp_result exp;
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29 mv tmp_result.zip ${result_zip};
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30 ]]>
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31 </command>
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32
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33 <inputs>
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34
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35 <param name="file_xml" optional="false" type="data" format="xml"
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36 label="XML file of experiment plan (.xml format)"/>
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37
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38 <param name="model_gaml" optional="false" type="data" format="txt"
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39 label="GAML model (.gaml format)"/>
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40
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41 <param name="final_step" optional="true" type="integer"
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42 value="1000" min="10" max="2000"
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43 label="final_step"
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44 help="'finalStep' attribute of 'experiment' tag [10, 2000]" />
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45
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46 </inputs>
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47
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48 <outputs>
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49 <data format="zip" name="result_zip" label=".zip file of results folder"/>
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50 </outputs>
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51
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52 <tests>
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53 </tests>
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54
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55 <help><![CDATA[
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56
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57 Desc:
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58
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59 -----
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60
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61 gama_legacy_run.xml tool, running a GAMA Headless in 'Legacy' mode, runs
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62 an experiment plan XML file 'file_xml' (such as XML file generated by
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63 gama_legacy_gen.xml tool) associated with its GAML file 'model_gaml',
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64 allowing some modifications of the plan : 'final_step' modification.
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65
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66 Inputs:
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67
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68 - file_xml
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69 - model_gaml
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70 - final_step
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71
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72 Outputs:
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73
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74 - result_zip
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75
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76 Credits:
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77
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78 --------
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79
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80 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
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81 - Copyright: INRAE
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82
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83 ]]>
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84 </help>
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85
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86 </tool>
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87