compare_conditions

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

Annotations indicate readOnlyHint=false and destructiveHint=true, so the safety profile is declared. The description adds context by specifying DESeq2 and pseudobulk aggregation, and the schema mentions 'Requires 2+ samples per condition.' However, it does not explain what destructive side effects may occur or what state changes are involved, leaving a transparency gap despite annotations.

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 short and front-loaded with the core purpose, followed by a concise Args block. The 'etc.' and redundant parameter list slightly reduce precision, but there is no filler or unnecessary elaboration.

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 complexity of the tool, the rich input schema and output schema carry most of the burden. The nested schema includes thresholds, defaults, and usage differentiation. The top-level description is minimal but sufficient for basic selection; a bit more context about prerequisites or side effects would make it more complete.

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 description lists required parameter names (condition_key, condition1, condition2, sample_key) but adds no semantics beyond the names. The input schema provides rich descriptions for every parameter, so the description adds minimal value beyond what the schema already covers.

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: 'Compare experimental conditions using pseudobulk differential expression (DESeq2).' This provides a specific verb, resource, and method. It does not explicitly name sibling tools, but the scope ('conditions' vs 'cell types') distinguishes it from tools like find_markers.

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 top-level description lacks usage guidance, but the input schema's nested ConditionComparisonParameters description explicitly contrasts compare_conditions with find_markers ('compares conditions ACROSS samples' vs 'cell types/clusters WITHIN a dataset'). This is useful but limited to one alternative and does not provide exclusions or other sibling comparisons.

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