descriptor.json

{
    "name": "SpotDetection3D-Icy",
    "container-image": {
        "image": "neubiaswg5/w_spotdetection3d-icy",
        "type": "singularity"
    },
    "schema-version": "cytomine-0.1",
    "description": "Neubias-WG5 workflow for 3D SpotDetection using Icy",
    "command-line": "python wrapper.py CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE ICY_SCALE ICY_SENSITIVITY",
    "inputs": [
        {
            "id": "cytomine_host",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Cytomine host",
            "description": "Cytomine server hostname",
            "type": "String",
            "optional": false,
            "set-by-server": true
        },
        {
            "id": "cytomine_public_key",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Cytomine public key",
            "description": "Cytomine public key",
            "type": "String",
            "optional": false,
            "set-by-server": true
        },
        {
            "id": "cytomine_private_key",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Cytomine private key",
            "description": "Cytomine private key",
            "type": "String",
            "optional": false,
            "set-by-server": true
        },
        {
            "id": "cytomine_id_project",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Cytomine project id",
            "description": "Cytomine project id",
            "type": "String",
            "optional": false,
            "set-by-server": true
        },
        {
            "id": "cytomine_id_software",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Cytomine software id",
            "description": "Cytomine software id",
            "type": "String",
            "optional": false,
            "set-by-server": true
        },
        {
            "id": "icy_scale",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Scale",
            "description": "The scale depends in a none obvious way on the size of the spots",
            "type": "Number",
            "default-value": 2,
            "optional": true,
	    "set-by-server": false
        },
        {
            "id": "icy_sensitivity",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Sensitivity",
            "description": "The lower, the more stringent",
            "type": "Number",
            "default-value": 70,
            "optional": true,
	    "set-by-server": false
        }
    ]
}