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Jean — Molecular Biology & Genomics

list_traces

Read-only

List the Sanger trace files in this project (.ab1 / .abi / .scf / .ztr) — the list a batch runs over.

Input Schema

NameRequiredDescriptionDefault
_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

NameRequiredDescriptionDefault
idsYestheir project file ids, in the same order (unambiguous where two names match)
countYeshow many traces that is
namesYesthe trace file names, in project order — the list to scatter a trace reader over

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, and an output schema covers the return shape, so the description's remaining job is small. It does add that only Sanger formats are returned and that scope is the current project, which is useful but not deep behavioral detail (no ordering, no empty-result behavior).

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, front-loaded with the core action and formats, with the batch-feeding context appended — no wasted wording.

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?

For a simple read-only listing tool with annotations and an output schema, this covers what an agent needs: what is listed, which formats, and what scope. Minor gaps (whether it recurses, what it returns when none match) are not blocking.

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 both parameters (_files, _subject) are documented there, so the baseline applies. The phrase 'in this project' loosely maps to _files but the description adds no meaning about which parameter selects the project or how _subject interacts with a listing operation.

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 and resource (list Sanger trace files), enumerates the four accepted formats (.ab1/.abi/.scf/.ztr) and scopes it to 'this project'. It is clearly distinguishable from siblings like load_trace, trace_raw_signal or export_trace, though it never names them.

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?

The clause 'the list a batch runs over' implies when to reach for it (feed a batch/consensus step), but there is no explicit when-not or named alternative such as load_trace for a single trace.

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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