validate_tree

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

With no annotations, the description carries the full burden and does reasonably well: it discloses the read-only nature ('no persistent artifact is written'), the shape of the result ('structured errors, warnings, format and counts'), and the constraint that tree_file must live 'inside an allowed read root'. It omits what happens when both content inputs are missing or how errors are categorized.

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?

Front-loaded with the one-line purpose, then returns, then a compact Args block with one line per parameter. Slightly redundant that it repeats the return summary already covered by the output schema, but no sentence is wasted.

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 four-parameter, zero-schema-coverage, zero-annotation tool, this covers purpose, outputs, and each argument. An output schema exists so return values need no further detail; the remaining gap is the mutual-exclusivity/inference rule between tree_content and tree_file.

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 0%, so the description must compensate, and it documents all four parameters: tree_content as direct paste, tree_file as a path under an allowed read root, mol_type with an inline enum (DNA|RNA|protein) not present in the schema, and skip_length_check tied to the FASTA alignment-length check. It still leaves the content-vs-file precedence rule unstated.

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 ('Deep-validate') and resource ('Newick/Nexus tree or FASTA/FASTQ sequence file'), and distinguishes itself from run_figtreekit_cli by noting it writes no persistent artifact. It does not, however, differentiate itself from the closely named sibling check_figtree, which is the most likely source of misselection.

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 note that semantics match ``figtreekit --validate`` with no artifact written implies when this is preferable to the CLI tool, but it never states when to choose validate_tree over check_figtree or cross_validate, or what to do if no input is supplied. Usage is implied rather than explicit.

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