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Jean — Molecular Biology & Genomics

restore_trace_file_calls

Put an open Sanger read back on the base calls its FILE carries, undoing an adopted re-call.

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
basesYeshow many bases the file's own reading carries
sequenceYesthe read the document now carries

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.8/5.0
Behavior3/5

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

Annotations already declare this is not read-only, not destructive, and closed-world, while the description adds that the operation reverses an adopted re-call. However, it does not explain side effects such as whether the adopted call data is discarded, retained, or how conflicts are handled.

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 definition is a single front-loaded sentence with no filler. It immediately states the operation and its undo semantics.

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 two-parameter tool with full schema coverage, annotations, and an output schema, the description covers the core operation and its reversal purpose. It could be slightly more complete about prerequisites or effects, but the remaining structured data carries most of that burden.

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 nested _files and _subject parameters are fully documented in the schema. The description adds no parameter-specific meaning beyond hinting that the FILE carries the base calls.

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 states a specific action: restoring an open Sanger read to the base calls carried by its FILE, explicitly framed as undoing an adopted re-call. That distinguishes it from the adoption path and from generic base-calling tools.

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 phrase 'undoing an adopted re-call' implies the scenario for use, but it does not explicitly name the alternative (adopt_trace_calls) or state when not to use this tool. Usage is inferable rather than directly guided.

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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