cwlVersion: v1.2

$namespaces:
  s: https://schema.org/
  edam: http://edamontology.org/

$graph:

- class: CommandLineTool

  id: aquaculture_norway

  baseCommand: python
  arguments:
  - /aquaculturedemo/runnorkystforecast.py
  - --aqua_site_file
  - valueFrom: $( inputs.aqua_site_file )
  - --aqua_site_distances_files
  - valueFrom: $( inputs.aqua_site_distances_files )
  - --aqua_opendrift_particles_per_site
  - valueFrom: $( inputs.aqua_opendrift_particles_per_site )
  - --aqua_opendrift_simulation_duration_hours
  - valueFrom: $( inputs.aqua_opendrift_simulation_duration_hours )
  # - --aqua_opendrift_output_file
  # - valueFrom: $( inputs.aqua_opendrift_output_file )
  - --aqua_connectivity_number_of_neighbours
  - valueFrom: $( inputs.aqua_connectivity_number_of_neighbours )
  - --aqua_connectivity_radius
  - valueFrom: $( inputs.aqua_connectivity_radius )
  # - --aqua_connectivity_output_file
  # - valueFrom: $( inputs.aqua_connectivity_output_file )
  # - --aqua_connectivity_output_file_with_locality_id
  # - valueFrom: $( inputs.aqua_connectivity_output_file_with_locality_id )
  - valueFrom: $(
        function () {
          if (inputs.starttime) {
            return ["--starttime", inputs.starttime];
          } else {
            return [];
          }
        }())
  inputs:
    aqua_site_file:
      type: string
      doc: aqua_site_file
    aqua_site_distances_files:
      type: string
      doc: aqua_site_distances_files
    aqua_opendrift_particles_per_site:
      type: int
      doc: aqua_opendrift_particles_per_site
    aqua_opendrift_simulation_duration_hours:
      type: int
      doc: aqua_opendrift_simulation_duration_hours
    # aqua_opendrift_output_file:
    #   type: string
    #   doc: aqua_opendrift_output_file
    aqua_connectivity_number_of_neighbours:
      type: int
      doc: aqua_connectivity_number_of_neighbours
    aqua_connectivity_radius:
      type: int
      doc: aqua_connectivity_radius
    # aqua_connectivity_output_file:
    #   type: string
    #   doc: aqua_connectivity_output_file
    # aqua_connectivity_output_file_with_locality_id:
    #   type: string
    #   doc: aqua_connectivity_output_file_with_locality_id
    starttime:
      type: string?
      doc: The start time of the simulation

  outputs:
    simulation:
      format: edam:format_3650 # NetCDF
      type: File
      outputBinding:
        glob: "modeloutput/salmon_midnor.nc"
    connectivity:
      format: edam:format_3620 # xlsx
      type: File
      outputBinding:
        glob: "modeloutput/salmon_midnor_connectivity.xlsx"
    connectivity_with_locality_id:
      format: edam:format_3620 # xlsx
      type: File
      outputBinding:
        glob: "modeloutput/salmon_midnor_connectivity_withLocalityId.xlsx"

  requirements:
    NetworkAccess:
      networkAccess: true
    EnvVarRequirement:
      envDef:
        PATH: /opt/miniconda3/envs/opendrift/bin:/opt/conda/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
    ResourceRequirement: {}
    InlineJavascriptRequirement: {}
    DockerRequirement:
      dockerPull: iliad-repository.inesctec.pt/aquaculture-norway:0.0.1

  s:name: aquaculture_norway
  s:description:
  s:keywords:
    - opendrift
  s:programmingLanguage: python
  s:softwareVersion: 0.1.0
  s:producer:
    class: s:Organization
    s:name: INESCTEC
    s:url: https://inesctec.pt
    s:address:
        class: s:PostalAddress
        s:addressCountry: PT
  s:sourceOrganization:
    - class: s:Organization
      s:name: INESCTEC
      s:url: https://inesctec.pt
      s:address:
          class: s:PostalAddress
          s:addressCountry: PT
  s:contributor:
    - class: s:Person
      s:name: Miguel Correia
      s:email: miguel.r.correia@inesctec.pt
  s:codeRepository: https://pipe-drive.inesctec.pt/application-packages/tools/openoil-simulation-duth/aquaculture_norway_duth_0_1_0.cwl
  s:dateCreated: "2025-05-12T12:31:30Z"