compare_conditions

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

Annotations indicate idempotent and not read-only, which is consistent. The description mentions the DESeq2 method and pseudobulk aggregation, but does not detail potential side effects or prerequisites beyond what parameters imply. No contradictions.

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 very concise with a single sentence and a simple list of required args. No unnecessary words; it is well 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 complexity (many parameters, output schema exists, annotations present), the description plus schema object description are mostly complete. However, the main description could briefly mention the output (top DEGs) and the requirement for multiple samples, which is currently only in parameter defaults.

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 0%, but the schema itself includes parameter descriptions. The main description lists required params but adds little beyond the schema. The schema's object description provides some parameter context, but the tool description does not compensate for low coverage.

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 compares experimental conditions using pseudobulk differential expression (DESeq2), with explicit differentiation from find_markers in the schema's ConditionComparisonParameters description, serving as a specific verb+resource+method combination.

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 schema's object description explicitly contrasts with find_markers, explaining when to use this tool (conditions across samples) versus find_markers (cell types within a dataset), providing clear usage guidance.

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