find_common_differentially_expressed_genes

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

Despite lacking annotations, the description fully discloses the behavior: it performs inner joins on upregulated and downregulated genes, returns a markdown table with log2fc values, and includes formatting instructions. This covers the tool's non-destructive, read-only nature sufficiently.

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 well-structured with a concise intro and numbered steps. It includes useful formatting instructions, though the capitalization in 'FORMATTING INSTRUCTION' is slightly noisy. Overall, it is efficient and front-loaded.

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?

Given the presence of an output schema (so return details are covered), the description is complete. It explains the entire process, threshold usage, and output format, with no observable gaps for a tool of this complexity.

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?

Schema description coverage is 100%, providing definitions for each parameter. The description adds value by explaining how thresholds are used in the algorithm (filtering genes) but does not significantly extend beyond the schema's parameter descriptions.

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 states 'Find common differentially expressed genes across multiple assays' and explains the step-by-step process, clearly distinguishing it from sibling tools like 'find_differentially_expressed_genes' which likely handle single assays.

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 specifies that the tool requires 2 or more assay IDs and explains the algorithm, implicitly indicating when to use. It does not explicitly contrast with alternatives or provide 'when not to use' guidance, but the context is clear.

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