---
license: cc-by-4.0
language:
- en
---

# Galaxy Tool Shed Vector Store

This dataset is part of the [Knime2Galaxy](https://github.com/rmassei/imaging_KNIME_to_Galaxy.git) project, which aims to build a 
Retrieval-Augmented Generation (RAG) pipeline for translating KNIME workflows into Galaxy workflows.

## Overview

This dataset enables semantic search over Galaxy tools to support automated workflow translation. 
Galaxy tools are embedded into a vector space, allowing retrieval of the most relevant tools corresponding to KNIME workflow nodes.

## Method

- All available Galaxy tools are embedded using the Qwen/Qwen3-Embedding-4B model  
- Given a KNIME node, similar Galaxy tools are retrieved via vector similarity search  
- Retrieved tools are assembled into a valid Galaxy workflow JSON  
- The workflow is exported as a `.ga` file  

## Contents

- Vector embeddings of Galaxy Tool Shed tools  

## Use Cases

- Automated KNIME to Galaxy workflow translation  
- Semantic search over Galaxy tools  
- RAG-based tool recommendation systems  

## Notes
- Workflow generation logic is implemented in the main project repository