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jean — Molecular Biology & Genomics

describe_discovery_corpus

Read-only

The design step's view of a discovery corpus: each record's name, file, length and GC fraction, and how many records each file holds. Runs no test and returns no statistic, so hypotheses proposed from it are proposed before any result is seen (POPPER's metadata-only design step). Use it before run_discovery_programme.

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.
sequencesNothe corpus: library document or file names, or wired records.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
filesYesevery file with its record count and total length
recordsYesevery record: name, file, length, GC fraction

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.4/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so safety is covered. The description adds meaningful epistemic context beyond annotations: it runs no test, returns no statistic, and serves as the pre-registration design step so hypotheses precede results. That is genuine behavioral value, though it does not cover return format or limits.

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?

Front-loaded with the purpose and what is returned, then the behavioral nuance and the ordering instruction. Every sentence earns its place; the parenthetical '(POPPER's metadata-only design step)' is slightly ornamental but conveys the intent compactly.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

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 needn't be explained, and the description fully covers purpose, content, ordering relative to its sibling, and the read-only nature. Nothing an agent needs to call it correctly is missing.

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 _files, _subject, and sequences thoroughly. The description does not add syntax or format detail beyond the schema, so the baseline 3 is correct when the schema does the heavy lifting.

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 (describe) and resource (discovery corpus), then enumerates exactly what the view contains: record name, file, length, GC fraction, and per-file record counts. It clearly distinguishes itself from run_discovery_programme by being the metadata-only view. An agent can tell what it does 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 Guidelines5/5

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

Explicitly positions itself in the workflow: 'Use it before run_discovery_programme.' It also carves out what it does not do ('runs no test and returns no statistic'), naming the sibling and the condition that selects it. Nothing is left to inference about ordering.

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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