# MCP Server: Galaxy Tool Utilities

This project provides an MCP (Model Context Protocol) server that exposes utilities for working with [Galaxy](https://galaxyproject.org/) tool XML files.

## Features (More Coming Soon)

- **Validate Galaxy Tool XML**: Check if a Galaxy tool XML file is valid according to the official schema.
- **Generate Basic Template**: Instantly create a boilerplate Galaxy tool XML file.

## Requirements

- Python 3.8+
- [uv](https://github.com/astral-sh/uv) (for running the server, or use your preferred Python environment)
- Cline (or any MCP-compatible agent)

## Installation

1. Clone this repository:
   ```bash
   git clone https://github.com/yourusername/mcp-server-galaxy-tool.git
   cd mcp-server-galaxy-tool
   ```

2. Install dependencies:
   ```bash
   uv sync
   ```

## Configuring the MCP Server in Cline

To use this MCP server with Cline in VSCode, add it to your Cline MCP configuration. Here’s how:

1. Install Cline in VSCode by searching for it in the Extensions marketplace and installing it.

2. Follow the Cline [documentation](https://docs.cline.bot/mcp-servers/configuring-mcp-servers) to add a new server entry. Here is an example MCP servers config:

   ```json
   {
     "mcpServers": {
       "Galaxy Tools": {
         "disabled": false,
         "timeout": 60,
         "command": "<path to your uv>",
         "args": [
           "--directory",
           "</path/to/this/repo/mcp-server-galaxy-tool>",
           "run",
           "main.py"
         ],
         "transportType": "stdio"
       }
     }
   }
   ```

- Make sure the `command` and `workingDirectory` match your local setup.
- Save the file and restart Cline if necessary.

## Usage

Once the server is running and configured in Cline, you can try this example in Cline:
```
Create a Galaxy tool that uses PyCaret to perform regression on tabular data.
```

## Project Structure

- `main.py` — MCP server entry point
- `galaxy.xsd` — Official Galaxy tool XML schema
- `pyproject.toml` — Python project configuration
- `README.md` — This documentation

## License

MIT License

## Acknowledgments

- [Galaxy Project](https://galaxyproject.org/)
- [Model Context Protocol (MCP)](https://github.com/modelcontextprotocol)
- [Cline](https://github.com/saoudrizwan/cline)