monocle3.json

{
  "tool_id": "monocle3_pseudotime",
  "name": "Monocle 3 Pseudotime Analysis",
  "category": "trajectory",
  "framework": "monocle3",
  "function": "Monocle 3 (R via subprocess)",
  "valid_after": ["clustering"],
  "valid_before": [],
  "paradigms": ["developmental_trajectory"],
  "parameters": {
    "root_cell_type": {
      "type": "string",
      "default": null,
      "guidance": "Specify the root/progenitor cell type to anchor pseudotime at 0. If not specified, Monocle picks the root interactively or by heuristic."
    },
    "reduction_method": {
      "type": "string",
      "default": "UMAP",
      "options": ["UMAP", "tSNE", "PCA"],
      "guidance": "Dimensionality reduction to use for trajectory graph learning."
    },
    "partition_qval": {
      "type": "float",
      "default": 0.05,
      "guidance": "Q-value threshold for partitioning cells into supergroups."
    },
    "use_partition": {
      "type": "bool",
      "default": true,
      "guidance": "If true, learn separate trajectories per partition. Set false to force a single trajectory."
    }
  },
  "outputs": {
    "pseudotime": "Pseudotime values per cell",
    "trajectory_graph": "Principal graph with nodes and edges",
    "branch_points": "Identified branch points in the trajectory"
  },
  "validation": {
    "check": "Pseudotime values should span a reasonable range. Root cells should have pseudotime near 0. Check that trajectory topology matches known biology."
  },
  "provenance_captures": ["root_cell_type", "reduction_method", "partition_qval", "use_partition", "n_trajectories", "n_branch_points"]
}