diversity_by_group

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

With no annotations, the description carries the full behavioral disclosure burden. It discloses the exact computed metrics, the rarefaction adjustment based on the smallest group, the two valid group-definition mechanisms, and the output file name. It does not mention computational cost or failure modes, but for a non-destructive analysis tool this is a reasonably complete behavioral picture.

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 compact and front-loaded with the tool's purpose, followed by grouping instructions, the detailed metric list, and the output artifact. Every sentence contributes information, with no filler or repetition of schema fields.

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 tool with nine parameters, the description plus full schema coverage provides enough to use it correctly: required variant set ID is documented in the schema, grouping options are explained, and output is named. It does not explicitly describe what happens when no group definition is supplied, but this is a minor edge case and the output schema likely fills remaining gaps.

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%, so the baseline is 3. The description adds meaningful cross-parameter semantics by explaining that groups_json and metadata_tsv + group_column are alternate ways to define groups, and it clarifies the rarefaction behavior tied to group sizes. This goes beyond what the individual parameter descriptions state.

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 opens with a specific summary—'Per-population diversity: He, Ho, Fis, MAF, % polymorphic, allelic richness'—which clearly identifies the tool's resource and outputs. It does not explicitly contrast this tool with close siblings like diversity_fst, though it references diversity_fst for grouping, so the differentiation is left somewhat implicit.

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 the tool: whenever per-population diversity statistics are needed. It explains how to define groups and points to diversity_fst as a behavioral reference, but it does not state when to choose diversity_by_group over alternatives such as diversity_summary or diversity_fst, nor does it give explicit when-not-to-use conditions.

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