What does an IO compatibility check involve?

It compares the input parameters, data types, and output formats between tools to ensure a user could swap them without changing the semantics of the analysis task.

How does this improve AI-driven tool discovery?

By providing a larger, more accurate set of 'correct' answers (ground truth), it allows AI models to be better trained and evaluated on their ability to suggest relevant tools to researchers.

Why is the expansion manual instead of automated?

Automated expansions often introduce false positives; manual review ensures that alternative tools are truly interchangeable for a specific user intent and workflow step.

Which Galaxy instances are supported?

The skill is optimized for usegalaxy.org but can be configured to work with any Galaxy server catalog that provides tool details via API.

Galaxy Benchmark Ground-Truth Expander

Name: Galaxy Benchmark Ground-Truth Expander
Author: goeckslab

bygoeckslab

0•

Data Science & ML

Refines and expands acceptable ground-truth tools for Galaxy tool recommendation benchmarks through manual validation and IO compatibility analysis.

This skill is designed for maintaining high-quality benchmarks within the Galaxy Project ecosystem. It enables developers to manually expand the list of 'correct' tool recommendations for specific user queries by analyzing tool catalogs, input/output structures, and tutorial contexts. By enforcing strict manual review rules and preventing bulk automated updates, it ensures that benchmarks for tool recommendation agents remain precise, reliable, and functionally accurate for researchers and data scientists using the Galaxy platform.

Key Features

010 GitHub stars

02Manual validation of alternative tool recommendations

03Synchronization between JSONL data and readable Markdown exports

04Automated IO structure and parameter compatibility checking

05Integration with usegalaxy.org tool catalogs

06Semantic matching via tool help text and tutorial analysis

Use Cases

01Improving the precision of Galaxy tool recommendation agent benchmarks

02Maintaining synchronized benchmark datasets and human-readable documentation

03Identifying functionally equivalent tools for specific bioinformatics workflows

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add goeckslab/galaxy-tool-recommendation-agent-benchmark galaxy-ground-truth-expansion

For use in Claude.ai and ChatGPT

Download Skill

Key Features

010 GitHub stars

02Manual validation of alternative tool recommendations

03Synchronization between JSONL data and readable Markdown exports

04Automated IO structure and parameter compatibility checking

05Integration with usegalaxy.org tool catalogs

06Semantic matching via tool help text and tutorial analysis

Use Cases

01Improving the precision of Galaxy tool recommendation agent benchmarks

02Maintaining synchronized benchmark datasets and human-readable documentation

03Identifying functionally equivalent tools for specific bioinformatics workflows

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add goeckslab/galaxy-tool-recommendation-agent-benchmark galaxy-ground-truth-expansion

For use in Claude.ai and ChatGPT

Download Skill