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jean — Molecular Biology & Genomics

history_protocol

Read-only

Render a construct's build history into a numbered bench-recipe protocol.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
rootYesa history-node tree.
_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.
_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

TableJSON Schema
NameRequiredDescriptionDefault
protocolYesnumbered bench-recipe protocol text

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

B3.2/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, and openWorldHint=false, so the safety profile is covered without the description's help. The description only adds that the output is a "numbered bench-recipe protocol," a light framing detail; it says nothing about permissions, input tree requirements, or failure behavior.

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

Conciseness4/5

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

A single sentence with no filler, and the key action and output are front-loaded. It is efficient, though its brevity borders on under-specification for a tool with nested object inputs.

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?

An output schema exists, so return values need not be explained. However, the tool takes a nested "history-node tree" and record references, and the description offers no help on obtaining that tree or relating the tool to its history-oriented siblings, leaving a meaningful gap for a fairly complex tool.

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

Parameters3/5

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

Schema description coverage is 100%, so the schema already documents root, _files, and _subject in detail. The description contributes no additional parameter meaning, so the baseline 3 applies.

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?

The description gives a specific verb ("Render"), a resource ("a construct's build history"), and a concrete output form ("numbered bench-recipe protocol"), so the transformation is clear. It does not, however, distinguish itself from close siblings like get_construction_history or build_assembly_report, which an agent could easily confuse it with.

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?

There is no when-to-use, when-not-to-use, or alternative named. Given that get_construction_history and build_assembly_report exist in the sibling set, the absence of any routing guidance leaves the agent to guess which history-related tool to pick.

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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