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export_newick

Export a reconstructed phylogenetic tree to a Newick string, with options to include branch lengths and node names.

Instructions

Export a reconstructed tree to a Newick string.

Args: dataset_id: Dataset handle. tree_key: Which tree in tdata.obst to export. record_branch_lengths: Include branch lengths in the Newick. record_node_names: Include internal node names in the Newick.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
tree_keyYes
dataset_idYes
record_node_namesNo
record_branch_lengthsNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
newickYes
tree_keyYes
dataset_idYes
Behavior2/5

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

No annotations are provided, so the description carries the full burden. It does not disclose behavioral traits such as whether the operation is read-only, potentially destructive, or requires specific authentication. The minimal description leaves the agent guessing about side effects.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is extremely concise: a single-sentence summary followed by a clean arg list. Every word is necessary and relevant, with no redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's simplicity and the presence of an output schema, the description covers the basic purpose and parameters. However, it lacks usage context and behavioral transparency, making it only minimally complete for an agent to use confidently.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, but the description adds inline explanations for all 4 parameters (e.g., 'Which tree in tdata.obst to export'). This provides useful context not present in the schema alone, though each explanation is brief.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description uses the specific verb 'Export' and resource 'reconstructed tree to a Newick string', clearly distinguishing it from sibling tools like reconstruct_tree (which builds the tree) and plot_tree (which visualizes it).

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

No guidance on when to use this tool versus alternatives like compare_trees or plot_tree. The description only lists parameters without contextual hints on scenarios or prerequisites.

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

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