{
    "params": {
        "fasta_list": {
            "type": "file[]",
            "description": "FASTA files containing protein sequences",
            "default": [],
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.fasta_list",
            "examples": [
                ["/omic/olamide/examples/prot1.fasta", "/omic/olamide/examples/prot2.fasta"]
            ],
            "pattern": ".*\\.fasta$",
            "validation": {},
            "notes": "Select one or more FASTA files with protein sequences"
        },
        "outdir": {
            "type": "folder",
            "description": "Output Directory",
            "default": "/omic/olamide/output",
            "required": true,
            "pipeline_io": "output",
            "var_name": "params.outdir",
            "examples": [
                "/omic/olamide/output"
            ],
            "pattern": ".*",
            "validation": {},
            "notes": "Select where to save your analysis results"
        },
        "num_samples": {
            "type": "integer",
            "description": "Number of protein structure samples",
            "default": 10,
            "required": true,
            "pipeline_io": "parameter",
            "var_name": "params.num_samples",
            "examples": [
                "10"
            ],
            "pattern": "^\\d+$",
            "validation": {
                "min": 1
            },
            "notes": "More samples provide better coverage of conformational space"
        },
        "batch_size_100": {
            "type": "integer",
            "description": "Batch size parameter",
            "default": 10,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.batch_size_100",
            "hidden": true,
            "examples": [
                "10"
            ],
            "pattern": "^\\d+$"
        },
        "temperature": {
            "type": "integer",
            "description": "Temperature (K) for free energy",
            "default": 300,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.temperature",
            "examples": [
                "300"
            ],
            "pattern": "^\\d+$",
            "validation": {
                "min": 200,
                "max": 500
            },
            "notes": "Temperature in Kelvin for free energy calculations"
        },
        "n_clusters": {
            "type": "integer",
            "description": "Number of conformational clusters",
            "default": 5,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.n_clusters",
            "examples": [
                "5"
            ],
            "pattern": "^\\d+$",
            "validation": {
                "min": 2
            },
            "notes": "Number of clusters for free energy analysis"
        },
        "cache_dir": {
            "type": "folder",
            "description": "Embeddings cache directory",
            "default": "/tmp/bioemu_cache",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.cache_dir",
            "hidden": true,
            "examples": [
                "/tmp/bioemu_cache"
            ]
        }
    }
}