cwlVersion: v1.2

$namespaces:
  s: https://schema.org/
  cwltool: http://commonwl.org/cwltool#

$graph:
- class: CommandLineTool

  id: get_dir_pyopia_pipeline

  baseCommand: python
  arguments:
  - /opt/get-dir.py
  - --dir_name
  - valueFrom: $( inputs.dir_name )
  - valueFrom: |
      ${ return inputs.directory ? ["--directory", inputs.directory] : [] }
  - valueFrom: |
      ${ return inputs.s3_endpoint ? ["--s3_endpoint", inputs.s3_endpoint] : [] }
  - valueFrom: |
      ${ return inputs.s3_region ? ["--s3_region", inputs.s3_region] : [] }
  - valueFrom: |
      ${ return inputs.s3_access_key ? ["--s3_access_key", inputs.s3_access_key] : [] }
  - valueFrom: |
      ${ return inputs.s3_secret_key ? ["--s3_secret_key", inputs.s3_secret_key] : [] }
  - valueFrom: |
      ${ return inputs.s3_session_token ? ["--s3_session_token", inputs.s3_session_token] : [] }
  - valueFrom: |
      ${ return inputs.s3_bucket_name ? ["--s3_bucket", inputs.s3_bucket_name] : [] }
  - valueFrom: |
      ${ return inputs.s3_path ? ["--s3_path", inputs.s3_path] : [] }

  inputs:
    dir_name:
      type: string?
      doc: Name of the output directory
      default: pyopia_inputs
    directory:
      type:
        - string?
        - Directory?
      doc: URL to download the directory or local path
    s3_endpoint:
      type: string?
      doc: S3 storage endpoint
    s3_region:
      type: string?
      doc: S3 storage region
    s3_access_key:
      type: string?
      doc: S3 storage access_key
    s3_secret_key:
      type: string?
      doc: S3 storage secret_key
    s3_session_token:
      type: string?
      doc: S3 storage region
    s3_bucket_name:
      type: string?
      doc: S3 storage bucket
    s3_path:
      type: string?
      doc: S3 path to the directory

  outputs:
    images:
      type: Directory
      doc: Input image directory
      outputBinding:
        glob: "$(inputs.dir_name)/images"
    auxiliary_data:
      type: File
      doc: Auxiliary data file
      outputBinding:
        glob: "$(inputs.dir_name)/auxillarydata/auxillary_data.csv"
    config:
      type: File
      doc: Configuration file
      outputBinding:
        glob: "$(inputs.dir_name)/config.toml"
    metadata:
      type: File
      doc: Metadata file
      outputBinding:
        glob: "$(inputs.dir_name)/metadata.json"
    model_classifier:
      type: File?
      doc: Model classifier file
      outputBinding:
        glob: "$(inputs.dir_name)/*.keras"

  requirements:
    NetworkAccess:
      networkAccess: true
    ResourceRequirement: {}
    InlineJavascriptRequirement: {}
    DockerRequirement:
      dockerPull: iliad-repository.inesctec.pt/get-dir:0.1.0


  s:name: get_dir_pyopia_pipeline
  s:description: Tool to download images from a URL or S3 storage
  s:keywords:
    - s3
    - storage
  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:author:
    - class: s:Person
      s:name: Miguel Correia
      s:email: miguel.r.correia@inesctec.pt
  s:dateCreated: "2025-11-13T17:16:45Z"