Mercurial > repos > siwaa > gama_legacy_gen

annotate gama_legacy_gen.xml @ 3:4f6c9c14b8e4 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_gen commit f3324742c1aa0050df56ad3f868018360a10a6ab-dirty
author siwaa
date Mon, 09 Dec 2024 17:00:18 +0000
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children ad48b8d5acd4
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1 <tool id="gama_legacy_gen" name="gama_legacy_gen" version="1.0.0">
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3 <description>tool generating XML file from GAML file</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:f3324742c1aa0050df56ad3f868018360a10a6ab</container>
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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 inputs; mkdir -p outputs;
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17 cp $__tool_directory__/src/cmd_gama_headless_legacy_gen.sh .;
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18 cp ${model_gaml} inputs/model.gaml;
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19 /bin/bash cmd_gama_headless_legacy_gen.sh ${experiment_name} > outputs/GEN.txt;
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20 xmlstarlet edit --inplace --update "//Simulation/@sourcePath" --value "model.gaml" outputs/file.xml;
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21 cp outputs/file.xml ${file_xml};
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22 ]]>
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23 </command>
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25 <inputs>
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27 <param name="experiment_name" optional="false" type="text"
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28 value="prey_predator"
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29 label="experiment_name"
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30 help="name of an experiment that must exist into gaml file as 'experiment' of type': 'gui'" />
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32 <param name="model_gaml" optional="false" type="data" format="txt"
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33 label="GAML model (.gaml format)"/>
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35 </inputs>
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37 <outputs>
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38 <data format="xml" name="file_xml" label="XML file of experiment plan"/>
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39 </outputs>
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41 <tests>
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42 </tests>
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44 <help><![CDATA[
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46 Desc:
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48 -----
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50 gama_legacy_gen.xml tool, running a GAMA Headless in 'Legacy' mode, generates
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51 the XML file 'file_xml' corresponding with the experiment 'experiment_name'
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52 (of 'type': 'gui') contained into the GAML file 'model_gaml'.
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54 Inputs:
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56 - experiment_name
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57 - model_gaml
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59 Outputs:
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61 - file_xml
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63 Credits:
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64
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65 --------
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67 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
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68 - Copyright: INRAE
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70 ]]>
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71 </help>
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73 </tool>
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74