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rnaseq-mcp

rnaseq-mcp

by sbarbi-gh
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

get_outputs

Retrieve all files from the session's output directory. Per-sample CSV data is blocked for privacy and replaced with an explanatory message; PNG images are returned as base64-encoded strings.

Instructions

Retrieve all files written to /output during this session. CSV files containing per-sample data are blocked and replaced with an explanatory message. Images (PNG) are returned as base64-encoded strings.

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "get_outputs"
  }
}

Input Schema

NameRequiredDescriptionDefault

No arguments

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.2/5.0
Behavior4/5

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

Discloses that CSVs are blocked with a message and PNGs are returned as base64. Could mention other file types or that output is session-specific.

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?

Three concise sentences, front-loaded with main purpose, no waste.

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?

Given no parameters and presence of an output schema, the description is largely complete. Minor gap on handling of non-CSV/non-PNG files.

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

Parameters4/5

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

No parameters, so schema is trivially covered. Description adds value by explaining behavior of the tool beyond schema.

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?

Clearly states the tool retrieves all files from /output during the session. Differentiates from siblings like list_data_files by specifying the output directory and session context.

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?

No explicit guidance on when to use vs alternatives, but the purpose is implied. Could improve by stating not to use for data files outside output.

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

Deploy Server

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