<tool id="gama_legacy_run" name="gama_legacy_run" version="1.0.0">

  <description>tool running an experiment plan XML file associated with a GAML file</description>

  <requirements>

    <!-- singularity -->
    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/gama_headless:0356ba7eb250433405698597a802d8a6b4e04967</container>

    <!-- image locale
    <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_gama/use/GAMA_HEADLESS_LEGACY/containers/gama_headless.simg</container -->
  </requirements>

  <command detect_errors="aggressive">
    <![CDATA[
    mkdir -p software; mkdir -p exp;
    cp $__tool_directory__/src/MY_gama-headless.sh .;
    cp $__tool_directory__/src/cmd_gama_headless_legacy_run.sh .;
    cp ${model_gaml} exp/model.gaml;
    cp ${file_xml} exp/file.xml;
    xmlstarlet edit --inplace --update "//Simulation/@sourcePath" --value "model.gaml" exp/file.xml;
    xmlstarlet edit --inplace --update "//Simulation/@finalStep" --value "${final_step}" exp/file.xml;
    cp -fr /opt/gama-platform software/.;
    cp MY_gama-headless.sh software/gama-platform/headless/. ;
    chmod -R 777 software;
    /bin/bash cmd_gama_headless_legacy_run.sh > exp/RUN.txt;
    rm -fr exp/outputs/.workspace*;
    zip -r tmp_result exp;
    mv tmp_result.zip ${result_zip};
    ]]>
  </command>

  <inputs>

    <param name="file_xml" optional="false" type="data" format="xml"
           label="XML file of experiment plan (.xml format)"/>

    <param name="model_gaml" optional="false" type="data" format="txt"
           label="GAML model (.gaml format)"/>

    <param name="final_step" optional="true" type="integer"
           value="1000" min="10" max="2000"
           label="final_step"
           help="'finalStep' attribute of 'experiment' tag [10, 2000]" />

  </inputs>

  <outputs>
    <data format="zip" name="result_zip" label=".zip file of results folder"/>
  </outputs>

  <tests>
  </tests>

  <help><![CDATA[

Desc:

-----

gama_legacy_run.xml tool, running a GAMA Headless in 'Legacy' mode, runs
an experiment plan XML file 'file_xml' (such as XML file generated by
gama_legacy_gen.xml tool) associated with its GAML file 'model_gaml',
allowing some modifications of the plan : 'final_step' modification.

Inputs:

  - file_xml
  - model_gaml
  - final_step

Outputs:

  - result_zip

Credits:

--------

-  Author: Nathalie Rousse nathalie.rousse@inrae.fr
-  Copyright: INRAE

  ]]>
  </help>

</tool>