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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
.gafile
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
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