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jean — Molecular Biology & Genomics

list_library

Read-only

List the project's sequence documents (id, name, length, topology, kind).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
kindNorestrict to one document kind (all kinds when unset). Kind is derived from the record itself — `amplicon` is provenance, not a file property, so documents read from disk are never classified as one.
_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
idsYesjust the entry ids, in the same order — the list to scatter a per-document step over
countYesnumber of entries
itemsYesthe library entries
namesYesjust the entry names, in the same order

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.6/5.0
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 needs no restating. The description adds only the returned field list, which the existing output schema already carries, so it contributes little behavioral context (no filtering semantics, no mention that unset kind returns all kinds).

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 front-loaded sentence with no filler; the resource comes first and the enumerated return fields are compact. Nothing needs trimming.

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?

An output schema exists, so return values need no explanation, and annotations plus a fully documented 3-parameter schema carry the rest. The only gap is the absence of any filtering guidance for the kind parameter in the description, which is minor given the schema's own detailed enum note.

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% and the schema itself explains the kind enum, including the subtle 'amplicon is provenance' nuance and the _files/_subject record shape. The description adds no parameter information at all, so 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?

Specific verb ('List') plus resource ('the project's sequence documents'), with the returned fields enumerated (id, name, length, topology, kind). It implicitly separates itself from list_traces/list_samples by scoping to sequence documents, but never names a sibling explicitly.

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 only implied: the agent can infer this enumerates a project's sequence documents, but there is no statement of when to prefer it over search_records, get_open_record, or load_record, and no exclusions. Minimum-viable guidance.

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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