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cafferychen777

ChatSpatial

by cafferychen777
OverviewSchemaRelated ServersScoreDiscussions
Python
Hybrid

find_spatial_genes

DestructiveIdempotent

Detect spatially variable genes with statistical tests, identify genes whose expression patterns correlate to spatial coordinates.

Instructions

Identify spatially variable genes.

Args:
    data_id: Dataset ID
    params: Spatial variable gene parameters (method, n_top_genes, etc.)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
paramsNo
data_idYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
methodYes
data_idYes
warningsNoNon-fatal conditions that may affect result interpretation.
results_keyYes
spatial_genesYes
n_genes_analyzedYes
n_significant_genesYes

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. Changed2 schema fields changedv1.5.3
    • addedInput schema / $defs / SpatialVariableGenesParameters / properties / max_genes_tested
      Added value: +{
+  "anyOf": [
+    {
+      "exclusiveMinimum": 0,
+      "maximum": 50000,
+      "type": "integer"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Cap on how many genes are tested, applied after the mitochondrial/ribosomal/HVG filters by keeping the highest-expressed genes. None = test everything that passes the filters. Use to bound runtime on slow backends (SpatialDE benchmarks at ~10 min per 14,000 genes). This limits the input; n_top_genes limits the output.",
+  "title": "Max Genes Tested"
+}
    • changedInput schema / $defs / SpatialVariableGenesParameters / properties / n_top_genes / description
      Previous value: -"Top spatial variable genes to return. None = all significant."New value: +"Top spatial variable genes to return, ranked by effect size where the backend reports one. None = all significant. This limits the output; use max_genes_tested to limit how many genes are tested."
  2. Changed10 schema fields changedv1.3.2
    • addedInput schema / $defs / SpatialVariableGenesParameters / additionalProperties
      Added value: +false
    • addedInput schema / additionalProperties
      Added value: +false
    • addedOutput schema / additionalProperties
      Added value: +false
    • removedOutput schema / properties / flashs_results
      Removed value: -{
-  "anyOf": [
-    {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    {
-      "type": "null"
-    }
-  ],
-  "default": null,
-  "title": "Flashs Results"
-}
    • removedOutput schema / properties / gene_statistics
      Removed value: -{
-  "additionalProperties": {
-    "type": "number"
-  },
-  "title": "Gene Statistics",
-  "type": "object"
-}
    • removedOutput schema / properties / p_values
      Removed value: -{
-  "additionalProperties": {
-    "type": "number"
-  },
-  "title": "P Values",
-  "type": "object"
-}
    • removedOutput schema / properties / q_values
      Removed value: -{
-  "additionalProperties": {
-    "type": "number"
-  },
-  "title": "Q Values",
-  "type": "object"
-}
    • removedOutput schema / properties / sparkx_results
      Removed value: -{
-  "anyOf": [
-    {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    {
-      "type": "null"
-    }
-  ],
-  "default": null,
-  "title": "Sparkx Results"
-}
    • removedOutput schema / properties / spatialde_results
      Removed value: -{
-  "anyOf": [
-    {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    {
-      "type": "null"
-    }
-  ],
-  "default": null,
-  "title": "Spatialde Results"
-}
    • addedOutput schema / properties / warnings
      Added value: +{
+  "description": "Non-fatal conditions that may affect result interpretation.",
+  "items": {
+    "type": "string"
+  },
+  "title": "Warnings",
+  "type": "array"
+}
  3. First observedv1.2.7

TDQS

C2.9/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already indicate destructiveHint: true and idempotentHint: true, but the description adds no behavioral detail such as side effects (e.g., modifying the dataset, storing results), runtime implications, or auth requirements. It merely states the action without any disclosure beyond the annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is extremely concise with no wasted words, and the Args section provides a clear structure. However, it is almost too terse, borderline under-specified. It earns a high score for lack of fluff but loses a point for being overly minimalist.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Despite having an output schema, the description is incomplete for a tool with 18 parameters and destructive behavior. It does not mention expected outputs, potential runtime (e.g., SpatialDE slow), or side effects. Given the complexity, the description is far from sufficient for an agent to fully understand when and how to use it effectively.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0% because the description only mentions 'params' generically with examples like 'method, n_top_genes, etc.' It does not clarify parameter formats, defaults, or relationships. The schema itself has rich descriptions, but the description fails to add high-level guidance or summary beyond listing a couple of examples.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the verb 'Identify' and the resource 'spatially variable genes', which is specific and distinguishable from siblings like find_markers and analyze_spatial_statistics. It concisely captures the tool's primary function.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

No guidance is provided on when to use this tool versus alternatives. It does not mention conditions like needing spatial transcriptomics data, nor does it differentiate from related analysis tools. The description lacks any contextual hints for selection.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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