galaxy-skills

Use when authoring a Galaxy User-Defined Tool (UDT) -- a `class: GalaxyUserTool` YAML definition that wraps a container and command into a tool a non-admin user creates and runs (e.g. via Galaxy MCP create_user_tool / run_user_tool, or POST /api/unprivileged_tools). Not for classic XML/ToolShed tool wrappers.

Use this skill when asked to create, draft, or write a Galaxy workflow report template for the Workflow Editor's Report tab. Triggers on requests like "create a report for this workflow", "draft a workflow report template", "write a Galaxy report for workflow <id/url>".

Galaxy Collection Transformation Command - transform Galaxy dataset collections reproducibly using Galaxy's native tools. Use when asked to filter, sort, relabel, restructure, flatten, nest, merge, or otherwise manipulate Galaxy collections.

Galaxy MCP server tools reference for histories, datasets, tools, and workflows

Router for Galaxy MCP, JupyterLite notebooks, and BioBlend automation

Building UCSC Track Hubs (track hubs and assembly hubs) — bigBed/bigChain/bigMaf format requirements, composite-track rules, hub.txt / genomes.txt / trackDb.txt structure. Use when emitting a UCSC hub from Galaxy outputs, wrapping a hub-publishing tool, or debugging hubCheck failures.

Galaxy tool development reference — creating new tools, testing, IUC review preparation, and updating existing tools. Use when authoring or modifying Galaxy tool wrappers for tools-iuc.

Generate a tool selection flowchart diagram (PNG) for a Galaxy tool suite from a JSON definition. Use when creating visual guides that help users pick the right tool in a multi-tool suite.

Add/update a ToolShed tool revision in usegalaxy-tools repo

This skill should be used when creating Galaxy Hub news posts, writing content for galaxyproject.org/news, or converting content to Galaxy Hub markdown format.

Convert a complete Nextflow pipeline to Galaxy

Convert a single Nextflow process to a Galaxy tool XML

Convert a Nextflow subworkflow to a Galaxy workflow

Router skill for Nextflow to Galaxy conversions - directs to appropriate sub-skill

Write JupyterLite notebooks for Galaxy dataset interaction using gxy package