{
    "params": {
        "pdb": {
            "type": "file",
            "description": "Path pattern to PDB files for pKa prediction",
            "default": "/mnt/OmicNAS/private/old/olamide/propka/input/1HPX.pdb",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.pdb",
            "examples": [
                "/mnt/OmicNAS/private/old/olamide/propka/input/protein.pdb",
                "/mnt/OmicNAS/private/old/olamide/propka/input/*.pdb"
            ],
            "pattern": ".*\\.pdb$",
            "enum": [],
            "validation": {},
            "notes": "Can be a single PDB file or a pattern to match multiple PDB files."
        },
        "outdir": {
            "type": "folder",
            "description": "Directory for PROPKA prediction results",
            "default": "/mnt/OmicNAS/private/old/olamide/propka/output",
            "required": true,
            "pipeline_io": "output",
            "var_name": "params.outdir",
            "examples": [
                "/mnt/OmicNAS/private/old/olamide/propka/output",
                "/path/to/custom/output"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Directory where pKa prediction results will be stored. Will be created if it doesn't exist."
        },
        "ph": {
            "type": "number",
            "description": "pH value for titration calculations",
            "default": 7.0,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.ph",
            "examples": [
                7.0,
                5.5
            ],
            "validation": {
                "min": 0.0,
                "max": 14.0
            },
            "notes": "The pH value used for calculating residue protonation states."
        },
        "options": {
            "type": "string",
            "description": "Additional command-line options for PROPKA",
            "default": "",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.options",
            "examples": [
                "--titrate_only Asp,Glu",
                "--window 1.0"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Additional command-line options to pass to propka3. See propka3 --help for available options."
        }
    }
}