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Jean — Molecular Biology & Genomics

export_tree

Read-only

Convert a tree between the four formats this workbench reads and writes — Newick, NEXUS, PhyloXML and NeXML — sniffing the input format rather than making the caller declare it.

Input Schema

NameRequiredDescriptionDefault
nameNothe tree's name inside the written file (NEXUS and NeXML carry one). Advanced.tree1
treeYesthe tree, in any of the four formats.
_filesNoThe project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
formatNothe format to write. Values: newick (Newick), nexus (NEXUS), phyloxml (PhyloXML), nexml (NeXML).newick
_subjectNoThe record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

Output Schema

NameRequiredDescriptionDefault
textYesthe tree written in the requested format
sourceFormatYesthe format the input was sniffed as — check this when a conversion surprises you

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.9/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so the safety profile is given; the description adds genuinely new behavior — that input format is sniffed automatically rather than declared, and that only NEXUS/NeXML outputs carry the internal tree name. It stops short of saying where output lands or whether anything is persisted.

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?

A single sentence that front-loads the core action, lists the formats, and closes with the auto-detection detail. No filler and no repetition of schema fields.

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

Completeness4/5

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 no explanation, and the description covers direction, supported formats, and detection behavior. The remaining gap is sibling disambiguation against transform_tree, and a note on where the written output goes.

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 coverage is 100%, so the baseline is 3, but the description earns a bump by clarifying that `tree` accepts any of four formats while `format` describes only the output written. That removes real ambiguity about the direction of conversion, though it says nothing about `_files`, `_subject`, or the default of newick.

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

Purpose4/5

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

States a specific verb (convert) and resource (tree) and enumerates the four target formats, so the operation is unambiguous. However, it never distinguishes itself from the close sibling transform_tree, which an agent could easily pick by mistake.

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

Usage Guidelines3/5

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

Usage is implied: reach for this when you need a tree emitted in a different serialization than it arrived in, and the caller need not pre-declare the input format. There is no explicit when-not guidance and no named alternative (transform_tree, draw_tree) to route against.

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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