README.md

metadata

license: cc-by-4.0
language:
  - en

Galaxy Tool Shed Vector Store

This dataset is part of the Knime2Galaxy 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