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rewire-bio

genomics-mcp

Official
by rewire-bio

get_signal

Read-only

Retrieve signal values or binned summaries from a bigWig file for a specified genomic interval.

Instructions

Signal values or binned summaries over an interval from bigWig. Not implemented in this build: returns error code 'unsupported' (E5).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
binsNo
fileYes
summaryNomean
intervalYes
max_recordsNoLower the record limit.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
dataNo
errorNoSet when status is error.
errorsNoPer-source failures in partial results.
limitsNo
statusYes
warningsNo
operationYes
provenanceNo
truncationNo
source_statusNo
schema_versionNo1

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A3.5/5.0
Behavior4/5

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

Beyond the readOnlyHint and openWorldHint annotations, the description adds critical behavioral information: the tool is not implemented and returns a specific error code (E5). This is exactly the kind of context that prevents an agent from wasting time invoking a non-functional tool.

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, no filler, and the most important operational fact (not implemented) is stated immediately after the purpose. Every word earns its place.

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

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a tool that is not implemented, the description provides the essential fact an agent needs: calling it will fail. However, given the complexity of the input schema (nested FileRef and Interval) and the low parameter coverage, the description would be insufficient if the tool were functional.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is only 20%, and the description does not explain the parameters (file, interval, bins, summary, max_records). The phrase 'signal values or binned summaries' hints at bins and summary, but it does not compensate for the low schema coverage or clarify how the parameters interact.

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?

The description clearly identifies the operation: retrieving signal values or binned summaries over an interval from bigWig files. It distinguishes itself from sibling tools by naming the data type (bigWig) and the concept of signal, though it does not explicitly contrast with get_coverage or other genomic retrieval 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 description explicitly warns that the tool is not implemented in this build and will return an 'unsupported' error, which tells the agent not to rely on it. However, it does not suggest an alternative tool or explain when this tool would be preferred if it were implemented.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.