rule all:
    input:
        "outputs/slide_{index}.csv"

rule read_and_convert:
  input:
      "data/slide_{index}.xml"
  output:
      temp("tmp/geojson/slide_{index}.geojson")
  script:
      "scripts/convert_aperio.py"

rule create_subjects:
    input:
        image_data_set="data/slide_{index}.svs",
        spatial_objects="tmp/geojson/slide_{index}.geojson"
    output:
        temp("tmp/subjects/slide_{index}_subjects.ttl")
    script:
        "scripts/create_subjects.py"

rule calculate_image_feature:
    input:
        "tmp/subjects/slide_{index}_subjects.ttl"
    output:
        "outputs/slide_{index}.csv"
    script:
        "scripts/calculate_area.py"
