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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. The same carry runs in the other direction, so the trim window, the hand-corrected calls and the annotations come back with it rather than being left on indices the file does not have. Not the same as clearing the read's edits, which also discards the trim and the manual calls.

Input Schema

TableJSON 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

TableJSON 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

A4.1/5.0
Behavior4/5

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

Annotations establish the operation is a non-read-only, non-destructive, closed-world mutation. The description adds meaningful behavior beyond that: it discloses that the same carry runs in both directions and that the trim window, hand-corrected calls and annotations are restored rather than orphaned on indices the file does not have. This is substantive state-change detail the annotations cannot convey.

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?

Three sentences, front-loaded with the core action and followed by the semantic consequence and the sibling distinction. Fairly dense and slightly convoluted in the middle clause, but no sentence is wasted.

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 not be explained, and parameters are fully covered by the schema. The description supplies the mutation semantics and the inverse-relationship context an agent needs. Only the unnamed sibling reference keeps it short of complete.

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% for both _files and _subject, with nested field meanings already documented (record_index picks one record of several, etc.). The description adds no parameter syntax or format detail beyond the schema, so the baseline 3 applies.

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?

States a specific verb and resource ('put an open Sanger read back on the base calls its FILE carries') and immediately names the action it reverses ('undoing an adopted re-call'). It further distinguishes itself from a related-but-different operation ('clearing the read's edits'), so an agent can tell it apart from siblings without opening the schema.

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

Usage Guidelines4/5

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

The description gives clear context for use ('undoing an adopted re-call') and warns against confusing it with clearing edits, which is a form of when-not guidance. It does not name the exact sibling tool (adopt_trace_calls) that produces the state being undone, leaving a small inference gap.

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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