find_markers

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

Annotations indicate readOnlyHint=false and idempotentHint=true, but the description adds no behavioral context (e.g., whether it modifies the dataset, requires specific permissions, or stores results). The description's 'Find' implies read-only, contradicting the readOnlyHint, but idempotentHint suggests safe retries. Overall, the description fails to clarify the actual side effects or state changes.

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

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

The description is concise: two sentences covering purpose and a parameter summary. It is front-loaded with the main action. However, the parameter list could be more structured or formatted for easier parsing, but it remains efficient with minimal waste.

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

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 does not mention what the tool returns (e.g., a table of genes with scores) or any prerequisites (e.g., preprocessed data with cluster annotations). The complex parameter structure and lack of outcome description leave gaps for an agent to correctly interpret the tool's full behavior.

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

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

The input schema provides detailed descriptions for all sub-parameters via $defs, so the schema coverage is high. The main description adds a brief summary of required and optional parameters ('Required - group_key and optional method...'), which provides a quick overview but adds limited value beyond the schema.

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

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

The description clearly states the tool's purpose: 'Find differentially expressed genes between groups.' This is a specific verb and resource, and it effectively distinguishes the tool from siblings like analyze_enrichment or compare_conditions by focusing on differential expression analysis.

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

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

The description provides no guidance on when to use this tool versus alternatives like analyze_enrichment or compare_conditions. It only lists required and optional parameters without explaining context or exclusions. This leaves the agent without direction for selecting the right tool among siblings.

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