guide_assignment.json

{
  "tool_id": "guide_assignment",
  "name": "CRISPR Guide Assignment",
  "category": "perturbation",
  "framework": "scagent",
  "function": "scagent.tools.perturbation.assign_guides",
  "valid_after": ["clustering", "annotation"],
  "valid_before": ["perturbation_de"],
  "paradigms": ["perturbation_screen"],
  "parameters": {
    "guide_calls_key": {
      "type": "string",
      "default": "guide_ids",
      "guidance": "Column in adata.obs with guide IDs from Cell Ranger multi."
    },
    "max_guides_per_cell": {
      "type": "int",
      "default": 1,
      "guidance": "Max guides per cell. Cells with more are marked 'multi-guide'."
    }
  },
  "outputs": {
    "perturbation": "adata.obs['perturbation']",
    "guide": "adata.obs['guide']",
    "n_guides": "adata.obs['n_guides']"
  },
  "notes": "Assigns CRISPR guide identities to cells from Cell Ranger multi output or feature barcode matrix. Handles multi-guide cells and unassigned cells.",
  "provenance_captures": ["guide_calls_key", "n_assigned", "n_perturbations"]
}