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

Annotations already declare readOnlyHint=false and destructiveHint=false; the description adds that the result is emitted as a NEW record (so inputs are not mutated in place) and that features are carried across. It does not say what happens when homology is below the limit or that pydna may fail on incompatible ends, which keeps it short of 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?

A single front-loaded sentence plus one clause; the mechanism and output semantics come first with no filler, and the pydna attribution is compact.

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 an output schema present, return values need not be described, and the schema documents all five parameters richly. The description is nonetheless complete on the mechanism and its non-destructive output; only failure/validation behavior is unstated.

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%, including the `limit` homology threshold and the 'in order' constraint on `fragments`, so the schema carries the burden. The description adds no parameter detail beyond noting features carry across, making the baseline 3 appropriate.

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 mechanism (overlap-extension/fusion PCR) plus the resource and the criterion that selects it: fragments must share terminal homology. This distinguishes it from sibling assembly tools like ligate_fragments or golden_gate_assemble, which do not rely on terminal homology, without needing to open any schema.

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 homology requirement implies when this tool applies, but no alternative is named and no when-not condition is given. An agent must infer that homolog-free joining should route to gibson_assemble/ligate_fragments instead.

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