{
    "params": {
        "query": {
            "type": "file",
            "description": "Path to input protein structure files (PDB/mmCIF format)",
            "default": "s3://omic/eureka/foldseek/input/1CRN.pdb",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.query",
            "examples": [
                "s3://omic/eureka/foldseek/input/1CRN.pdb",
                "s3://omic/eureka/foldseek/input/*.pdb"
            ],
            "pattern": ".*\\.(pdb|cif|mmcif)(\\.gz)?$",
            "enum": [],
            "validation": {},
            "notes": "Can be a single PDB/mmCIF file or a pattern to match multiple files. Supports gzipped files."
        },
        "target": {
            "type": "file",
            "description": "Path to target database or directory for structure search",
            "default": "s3://omic/eureka/foldseek/input/",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.target",
            "examples": [
                "s3://omic/eureka/foldseek/input/",
                "s3://omic/eureka/foldseek/databases/"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Can be a Foldseek database or a directory containing structure files."
        },
        "outdir": {
            "type": "folder",
            "description": "Directory for Foldseek output results",
            "default": "s3://omic/eureka/foldseek/output",
            "required": true,
            "pipeline_io": "output",
            "var_name": "params.outdir",
            "examples": [
                "s3://omic/eureka/foldseek/output"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Directory where all output files will be stored. Will be created if it doesn't exist."
        },
        "mode": {
            "type": "string",
            "description": "Operation mode for Foldseek pipeline",
            "default": "search",
            "required": true,
            "pipeline_io": "parameter",
            "var_name": "params.mode",
            "examples": [
                "search",
                "cluster",
                "multimersearch",
                "createdb"
            ],
            "pattern": "^(search|cluster|multimersearch|createdb)$",
            "enum": ["search", "cluster", "multimersearch", "createdb"],
            "validation": {},
            "notes": "search: structure search, cluster: clustering, multimersearch: complex search, createdb: create database"
        },
        "sensitivity": {
            "type": "number",
            "description": "Search sensitivity (higher = more sensitive but slower)",
            "default": 9.5,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.sensitivity",
            "examples": [
                7.5,
                9.5
            ],
            "pattern": "^[0-9]+(\\.[0-9]+)?$",
            "enum": [],
            "validation": {},
            "notes": "Fast: 7.5, Default: 9.5. Range: 1.0 to 15.0"
        },
        "evalue": {
            "type": "number",
            "description": "E-value threshold for reporting matches",
            "default": 0.001,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.evalue",
            "examples": [
                0.001,
                0.01,
                10
            ],
            "pattern": "^[0-9]+(\\.[0-9]+)?([eE][+-]?[0-9]+)?$",
            "enum": [],
            "validation": {},
            "notes": "Lower values are more stringent. Default: 0.001"
        },
        "threads": {
            "type": "integer",
            "description": "Number of CPU threads to use",
            "default": 4,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.threads",
            "examples": [
                4,
                8,
                16
            ],
            "pattern": "^[0-9]+$",
            "enum": [],
            "validation": {},
            "notes": "More threads improve speed for larger searches."
        },
        "alignment_type": {
            "type": "integer",
            "description": "Type of structural alignment algorithm",
            "default": 2,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.alignment_type",
            "examples": [
                0,
                1,
                2
            ],
            "pattern": "^[0-3]$",
            "enum": [0, 1, 2, 3],
            "validation": {},
            "notes": "0: 3Di only, 1: TMalign (global), 2: 3Di+AA (default), 3: LoLalign"
        },
        "coverage": {
            "type": "number",
            "description": "Minimum fraction of aligned residues",
            "default": 0.0,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.coverage",
            "examples": [
                0.0,
                0.5,
                0.8
            ],
            "pattern": "^[0-1](\\.[0-9]+)?$",
            "enum": [],
            "validation": {},
            "notes": "Range: 0.0 to 1.0. Higher values produce more global alignments."
        },
        "format_output": {
            "type": "string",
            "description": "Output format columns (comma-separated)",
            "default": "query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.format_output",
            "examples": [
                "query,target,fident,evalue,bits",
                "query,target,alntmscore,qtmscore,ttmscore"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Available columns: query, target, fident, alnlen, mismatch, gapopen, qstart, qend, tstart, tend, evalue, bits, alntmscore, qtmscore, ttmscore, lddt, prob"
        }
    }
}