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rewire-bio

genomics-mcp

Official
by rewire-bio

list_files

Read-only

Retrieve files from a genomic study or dataset with details on format, size, checksums, index, and readiness. Filter results by format or lower the record limit.

Instructions

List files of a study/dataset with format, size, checksums, index and readiness. Not implemented in this build: returns error code 'unsupported' (E2, E6, E7).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cursorNo
sourceYes
formatsNo
accessionYes
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

B3.3/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the safety profile is covered. The description adds a critical behavioral fact beyond annotations: the tool is not implemented and returns error code 'unsupported' (E2, E6, E7). This is valuable transparency, though it does not elaborate on pagination or other runtime behavior.

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 description is two sentences with no filler. The primary purpose is front-loaded, and the unsupported-status caveat is placed second. 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?

The description adequately discloses that the tool is non-functional in this build, which is essential context. However, it leaves parameter semantics unexplained and the error codes (E2, E6, E7) undefined. Since an output schema exists, return-value details are less critical, but the overall guidance is still incomplete for a 5-parameter tool.

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%, with only max_records having a description. The tool description does not explain source, accession, cursor, or formats, and only vaguely implies that accession refers to a study/dataset. It fails to compensate for the low schema coverage.

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 states a specific verb and resource ('List files of a study/dataset') and enumerates the returned fields (format, size, checksums, index, readiness), which distinguishes it from sibling tools like list_samples or fetch_file. However, the 'Not implemented in this build' caveat muddies what the tool actually does in practice, so it is not a perfect 5.

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

Usage Guidelines2/5

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

There is no guidance on when to use this tool versus alternatives such as fetch_file, list_samples, or describe_dataset. The only usage-related information is that it is unsupported in this build, which tells the agent not to use it but does not explain what to use instead or under what conditions it would be appropriate.

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