MCP Server: Galaxy Tool Utilities

@goeckslab

About MCP Server: Galaxy Tool Utilities

MCP server for Generating Galaxy Tools

Config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "mcp-server-galaxy-tool": {
      "command": "uv",
      "args": [
        "sync"
      ]
    }
  }
}

Tools

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Overview

What is MCP Server: Galaxy Tool Utilities?

MCP Server: Galaxy Tool Utilities is an MCP server that exposes utilities for working with Galaxy tool XML files. It allows users to validate Galaxy tool XML against the official schema and generate boilerplate templates. It is intended for use with MCP-compatible agents such as Cline.

How to use MCP Server: Galaxy Tool Utilities?

Clone the repository, install dependencies with uv sync, then add the server to your Cline MCP configuration (using uv as the command and pointing to the repository directory). Once configured, you can invoke it via Cline with prompts like "Create a Galaxy tool that uses PyCaret to perform regression on tabular data."

Key features of MCP Server: Galaxy Tool Utilities

Validate Galaxy tool XML files against the official schema.
Generate a basic boilerplate Galaxy tool XML template.
Easy integration with Cline and other MCP-compatible agents.
Uses the standard stdio transport.

Use cases of MCP Server: Galaxy Tool Utilities

Quickly bootstrap a new Galaxy tool by generating a valid XML template.
Check an existing Galaxy tool XML file for schema compliance.
Automate Galaxy tool creation within an MCP agent workflow.

FAQ from MCP Server: Galaxy Tool Utilities

What does MCP Server: Galaxy Tool Utilities do?

It provides two utilities: validate a Galaxy tool XML file against the official schema and generate a basic boilerplate Galaxy tool XML template.

What are the requirements to run this server?

Python 3.8+, uv for execution, and an MCP-compatible agent like Cline.

How do I configure the server in Cline?

Add the server entry to your Cline MCP configuration file with the command pointing to your uv binary and the arguments --directory <path-to-repo> run main.py. The transport type is stdio.

What transport does the server use?

The server is configured to use stdio transport, as shown in the example MCP configuration.

What are the current limitations of this server?

Only two features are currently implemented: validation and template generation. The README notes "More Coming Soon."

Frequently asked questions

What does MCP Server: Galaxy Tool Utilities do?

It provides two utilities: validate a Galaxy tool XML file against the official schema and generate a basic boilerplate Galaxy tool XML template.

What are the requirements to run this server?

Python 3.8+, [uv](https://github.com/astral-sh/uv) for execution, and an MCP-compatible agent like Cline.

How do I configure the server in Cline?

Add the server entry to your Cline MCP configuration file with the command pointing to your `uv` binary and the arguments `--directory <path-to-repo> run main.py`. The transport type is `stdio`.