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jean — Molecular Biology & Genomics

get_selection

Read-only

The region selected on the canvas, as its own record. This is what makes a highlighted stretch a pipeline INPUT: wire its record into any node's subject and that step runs on the selection rather than on the whole molecule.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
padNoextend the selection by this many bases on each side, clamped to the molecule (or wrapped, on a circular one). In bp.
_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.
reverse_complementNoemit the bottom strand of the selection (what a feature on the minus strand actually reads).

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
endYesend on the parent, exclusive
startYes0-based start on the parent molecule
lengthYeslength in bp
recordYesthe selected region as a linear record (subject for downstream nodes)
sequenceYesthe selected bases 5'→3'

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4/5.0
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 is covered. The description adds conceptual behavior, namely that the selection becomes its own record usable as pipeline input, but it does not disclose prerequisites such as requiring an active canvas selection, error behavior, or return details beyond the output schema.

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?

Two sentences, front-loaded with the core identity of the tool; the second sentence explains the practical purpose without redundancy. No filler or restatement of the name.

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?

With a fully documented input schema, an output schema, and annotations covering safety, the description mainly needs to explain what the selection record is and how it is used. It does that well, though it could mention that an active selection is a prerequisite and what happens when none exists.

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 pad, _subject, _files, and reverse_complement are already documented in the input schema. The description adds no additional meaning for these parameters, which is acceptable given the high coverage baseline.

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 that the tool returns the canvas-selected region as its own record, a specific resource distinct from whole-molecule records. The pipeline-input framing further differentiates it from generic record loaders or browsers. The verb is implicit in the tool name, but the resource and scope are unambiguous.

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?

It explains how to use the result: wire its record into any node's subject so that step runs on the selection rather than the whole molecule. This gives clear context for when to call it, but it does not name explicit alternatives or when-not conditions.

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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