descriptor.json

{
  "name": "Create_Annotations",
  "container-image": {
    "image": "cytomineuliege/s_create_annotations",
    "type": "singularity"
  },
  "description": "Create annotations from a given threshold on a heatmap.",
  "schema-version": "cytomine-0.1",
  "command-line": "python run.py CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE CYTOMINE_TERM_IDS IMAGE_ID HEATMAP_ID THRESHOLD MIN_AREA",
  "inputs": [
    {
      "id": "cytomine_host",
      "name": "Cytomine host",
      "set-by-server": true,
      "optional": false,
      "type": "String",
      "value-key": "@ID",
      "command-line-flag": "--@id"
    },
    {
      "id": "cytomine_public_key",
      "name": "Cytomine public key",
      "set-by-server": true,
      "optional": false,
      "type": "String",
      "value-key": "@ID",
      "command-line-flag": "--@id"
    },
    {
      "id": "cytomine_private_key",
      "name": "Cytomine private key",
      "set-by-server": true,
      "optional": false,
      "type": "String",
      "value-key": "@ID",
      "command-line-flag": "--@id"
    },
    {
      "id": "cytomine_id_project",
      "name": "Cytomine project ID",
      "set-by-server": true,
      "optional": false,
      "type": "Number",
      "value-key": "@ID",
      "command-line-flag": "--@id"
    },
    {
      "id": "cytomine_id_software",
      "name": "Cytomine software ID",
      "set-by-server": true,
      "optional": false,
      "type": "Number",
      "value-key": "@ID",
      "command-line-flag": "--@id"
    },
    {
      "id": "cytomine_term_ids",
      "name": "Cytomine terms that will be associated to the annotations",
      "optional": false,
      "type": "ListDomain",
      "uri": "/api/ontology/$currentOntology$/term.json",
      "uri-print-attribute": "name",
      "uri-sort-attribute": "name",
      "value-key": "@ID",
      "command-line-flag": "--@id"
    },
    {
      "id": "image_id",
      "name": "The Cytomine image ID",
      "optional": false,
      "type": "Domain",
      "uri": "/api/project/$currentProject$/imageinstance.json",
      "uri-print-attribute": "instanceFilename",
      "uri-sort-attribute": "instanceFilename",
      "value-key": "@ID",
      "command-line-flag": "--@id"
    },
    {
      "id": "heatmap_id",
      "name": "The heatmap associated to this image",
      "optional": false,
      "type": "Domain",
      "uri": "/api/project/$currentProject$/imageinstance.json",
      "uri-print-attribute": "instanceFilename",
      "uri-sort-attribute": "instanceFilename",
      "value-key": "@ID",
      "command-line-flag": "--@id"
    },
    {
      "id": "threshold",
      "name": "Threshold",
      "optional": false,
      "type": "Number",
      "value-key": "@ID",
      "command-line-flag": "--@id"
    },
    {
      "id": "min_area",
      "name": "Minimum valid area",
      "optional": true,
      "default-value": 1000,
      "type": "Number",
      "value-key": "@ID",
      "command-line-flag": "--@id"
    }
  ]
}