calculate_pca

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

With no annotations, the description carries full burden but only states input type and optional output path. It does not disclose output format, computational demands, or side effects, leaving significant behavioral gaps.

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?

Two concise, front-loaded sentences with no redundant information. Every word provides value.

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?

For a simple computation tool with fully documented parameters, the description is adequate but lacks details on output values and behavioral notes. Could be more complete given the absence of output schema.

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?

Input schema covers 100% of parameters with descriptions, so baseline is 3. The description adds minimal additional meaning beyond reiterating PLINK files and PCA context.

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 performs Principal Component Analysis for population stratification using PLINK files. It distinguishes from sibling tools like 'create_pca_plot' (plotting) and 'run_gwas' (association 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 implies when to use (PCA for stratification) and specifies input format, but lacks explicit guidance on when not to use or comparison to alternatives like 'create_pca_plot'.

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