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

Annotations already establish read-only, non-destructive, closed-world behavior, and the description adds real substance beyond them: it aligns the two inputs, reports every substitution/indel/uncalled position, maps each onto design features, and ranks by Ensembl's published consequence severity. It does not discuss coverage thresholds, failure modes, or performance limits, keeping it below a 5.

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 sentences, front-loaded with the core comparison and then the consequence-ranking payoff. The second sentence is long and clause-heavy, but every clause carries distinct information, so there is little waste.

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?

With 13 parameters, 100% schema coverage, and an output schema, the definition is nearly self-sufficient — the description explains the comparison logic and the consequence framing that the schema cannot. It leaves the tuning parameters entirely to the schema, which is acceptable given their documented coverage, but a note on when to touch them would round it out.

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 coverage is 100%, so the baseline is 3; every alignment parameter (match, gap_open, word_size, min_coverage, etc.) is already documented in the schema. The description reinforces the semantics of the two required inputs ('the construct you INTENDED' vs 'what actually came back from sequencing') but adds no format or usage detail beyond what the schema states.

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?

States a specific verb and two named resources ('Compare a sequencing RESULT against the construct you designed') and describes the output semantics (substitutions, indels, uncalled positions mapped onto features and ranked by consequence severity). This distinguishes it from adjacent siblings like alignment_agreement, compare_reads_to_reference and verify_read, which the agent can rule out without opening schemas.

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?

It gives a clear use context — a pipeline gating on 'nothing worse than synonymous' rather than a raw difference count — which tells the agent the intended workflow. It stops short of naming alternatives or explicit when-not conditions, so it is clear context without exclusions.

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