{
  "$schema": "https://dnncha.github.io/dotmatch/agent-tools.schema.json",
  "schema_version": "1.0",
  "tool_contract_version": "1.0",
  "generated_for_version": "0.4.0",
  "transport": {
    "input": "one JSON object supplied by file, stdin, or the Python API",
    "output": "one JSON envelope on stdout or as a Python dictionary",
    "diagnostics": "progress and diagnostics on stderr",
    "network": "ordinary invocations make no outbound network requests"
  },
  "safety": {
    "structured_parameters_only": true,
    "shell_commands_accepted": false,
    "refuses_non_empty_output_directories": true,
    "overwrites_existing_outputs": false,
    "uploads_research_data": false,
    "ambiguity_is_never_forced_into_counts": true,
    "maximum_automatic_revisions": 3,
    "allowed_evidence_backed_changes": [
      "extract.start",
      "extract.length",
      "extract.orientation",
      "assignment.metric",
      "assignment.k",
      "backend.mode=cpu"
    ],
    "forbidden_automatic_changes": [
      "target sequences or target identities",
      "ambiguity counting policy",
      "reliability thresholds or profile",
      "scientific scope",
      "CPU authority without workload-specific GPU validation"
    ]
  },
  "intents": [
    {
      "id": "crispr-guide-counting",
      "boundary": "Known-guide fixed-window counting and MAGeCK-compatible counts; no downstream screen statistics."
    },
    {
      "id": "perturb-seq-guide-capture",
      "boundary": "Direct-guide fixed-window per-read assignment; no cell barcode, UMI, guide-per-cell, expression, or perturbation-effect inference."
    }
  ],
  "envelope": {
    "$ref": "https://dnncha.github.io/dotmatch/agent-tools.schema.json#/$defs/envelope"
  },
  "tools": [
    {
      "name": "discover",
      "purpose": "Discover installed capabilities, evidence boundaries, and next local tools.",
      "input_schema": {
        "type": "object",
        "additionalProperties": false,
        "properties": {
          "intent": {"enum": ["crispr-guide-counting", "perturb-seq-guide-capture"]}
        }
      }
    },
    {
      "name": "prepare_assay",
      "purpose": "Infer and scaffold an immutable local AssaySpec project from a target table and FASTQs.",
      "input_schema": {
        "type": "object",
        "additionalProperties": false,
        "required": ["intent", "targets", "reads_dir", "output_dir"],
        "properties": {
          "intent": {"enum": ["crispr-guide-counting", "perturb-seq-guide-capture"]},
          "targets": {"type": "string", "minLength": 1},
          "reads_dir": {"type": "string", "minLength": 1},
          "output_dir": {"type": "string", "minLength": 1},
          "link_reads": {"type": "boolean", "default": false},
          "threads": {"type": "integer", "minimum": 1, "default": 1},
          "max_reads": {"type": "integer", "minimum": 1, "default": 50000},
          "max_start": {"type": "integer", "minimum": 0, "default": 32},
          "minimum_free_bytes": {"type": "integer", "minimum": 0, "default": 1073741824}
        }
      }
    },
    {
      "name": "inspect_assay",
      "purpose": "Compile a deterministic plan and write target, resource, and reliability preflight evidence.",
      "input_schema": {
        "type": "object",
        "additionalProperties": false,
        "required": ["spec"],
        "properties": {
          "spec": {"type": "string", "minLength": 1},
          "minimum_free_bytes": {"type": "integer", "minimum": 0, "default": 1073741824}
        }
      }
    },
    {
      "name": "run_assay",
      "purpose": "Run locally, inspect reliability, write numbered candidate specs for permitted remediations, and stop safely.",
      "input_schema": {
        "type": "object",
        "additionalProperties": false,
        "required": ["spec"],
        "properties": {
          "spec": {"type": "string", "minLength": 1},
          "max_revisions": {"type": "integer", "minimum": 0, "maximum": 3, "default": 3},
          "minimum_free_bytes": {"type": "integer", "minimum": 0, "default": 1073741824}
        }
      }
    },
    {
      "name": "review_assay",
      "purpose": "Normalize reliability findings, artifacts, scientific boundaries, and next actions.",
      "input_schema": {
        "type": "object",
        "additionalProperties": false,
        "required": ["spec"],
        "properties": {
          "spec": {"type": "string", "minLength": 1},
          "minimum_free_bytes": {"type": "integer", "minimum": 0, "default": 1073741824}
        }
      }
    },
    {
      "name": "handoff_assay",
      "purpose": "Create a hashed, review-sized handoff that excludes raw FASTQ and target tables.",
      "input_schema": {
        "type": "object",
        "additionalProperties": false,
        "required": ["spec", "output_dir"],
        "properties": {
          "spec": {"type": "string", "minLength": 1},
          "output_dir": {"type": "string", "minLength": 1},
          "minimum_free_bytes": {"type": "integer", "minimum": 0, "default": 1073741824}
        }
      }
    }
  ]
}