Galaxy Tool Creation Skill

Converts CLI tools and Nextflow processes into Galaxy XML wrappers with tests and Planemo validation.

7|12|Updated Dec 17, 2025

Search Tags:#workflow #testing #CLI #galaxy #XML #tool-wrapping #planemo

Ready to run

npx skills add https://github.com/galaxyproject/galaxy-skills --skill galaxy-tool-creation-skill

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: Galaxy Tool Creation Skill
Source: https://github.com/galaxyproject/galaxy-skills/tree/main/tool-dev/creation
Command: npx skills add https://github.com/galaxyproject/galaxy-skills --skill galaxy-tool-creation-skill

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Galaxy tool development can be tedious and error-prone when turning a CLI tool into a reusable Galaxy tool wrapper. This skill provides a structured guide to convert CLI tools (and Nextflow processes) into XML wrappers, tests, and documentation, promoting reproducibility and community reuse.

Core Features & Use Cases

Guided conversion of CLI tools into Galaxy wrappers (XML, tests, help).
Decision guidance on tool placement (tools-iuc vs custom) and workflow integration.
End-to-end workflow covering understanding the tool, mapping inputs/outputs, templating commands, and validation with Planemo.
Use Case: A team wraps a new CLI utility into Galaxy to enable standardized workflows and sharing across projects.

Quick Start

Read this Skill (SKILL.md) for overview and decision points.
Choose your path: from-scratch.md or from-nextflow.md.
Decide placement: tool-placement.md.
Create the tool: create-tool.md.

Frequently Asked Questions about Galaxy Tool Creation Skill

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I convert a CLI tool into a Galaxy wrapper for reproducible workflows?▼

You convert a CLI tool into a Galaxy wrapper by mapping its inputs and outputs to a standard XML structure, applying frontmatter-driven metadata, and validating the result with Planemo for reproducible workflows.

What is the standard process for wrapping Nextflow processes into Galaxy tools?▼

The standard process for wrapping Nextflow processes into Galaxy tools uses a guided conversion path to map process logic into XML wrappers, generate tests, and enforce a help framework for community reuse.

How do I test a Galaxy tool wrapper after creating it from a CLI utility?▼

To test a Galaxy tool wrapper, you use Planemo to validate the XML structure, verify command templating, and ensure mapped inputs and outputs function correctly within reproducible workflows.

Can I use this guided conversion approach for both new and existing CLI tools?▼

Yes, this guided conversion approach applies when wrapping both new and existing CLI tools, providing decision guidance on tool placement and workflow integration from discovery through testing.

What's the best way to decide tool placement when wrapping a CLI utility for Galaxy?▼

The best way to decide tool placement for a Galaxy wrapper is to follow decision guidance evaluating whether the tool belongs in tools-iuc for community reuse or a custom repository for project-specific workflows.