AgentSkillsCN

Tool Dev

工具开发

SKILL.md

Galaxy Tool Development Skill

Purpose: Router for Galaxy tool development tasks - creating new tools or updating existing tools.

When to Use This Skill

Use this skill family when you need to:

  • •Create a new Galaxy tool wrapper
  • •Update an existing Galaxy tool to a new version
  • •Fix bugs in Galaxy tools
  • •Improve tool documentation or tests
  • •Work with Galaxy tool XML structure

Decision Tree

Creating New Tools?

If you need to:

  • •Wrap a CLI tool that doesn't have a Galaxy wrapper yet
  • •Create a tool from scratch
  • •Convert a Nextflow process to a Galaxy tool
  • •Decide where to place a new tool (tools-iuc vs custom)

→ Use: creation/SKILL.md

Updating Existing Tools?

If you need to:

  • •Update a Galaxy tool to a new version
  • •Fix bugs in existing tool wrappers
  • •Debug failing planemo tests
  • •Improve help sections or documentation
  • •Research upstream changes

→ Use: updates/SKILL.md

Need Reference Material?

If you need to understand:

  • •Galaxy XML structure and syntax
  • •How to write planemo tests
  • •RST help section formatting

→ See: shared/ directory

  • •shared/xml-structure.md - Galaxy XML anatomy
  • •shared/testing.md - Planemo testing guide
  • •shared/help-sections.md - RST help formatting

Skill Structure

code
tool-dev/
├── SKILL.md              # This router file
├── creation/             # Creating new Galaxy tools
│   ├── SKILL.md
│   ├── create-tool.md
│   ├── from-scratch.md
│   ├── from-nextflow.md
│   ├── tool-placement.md
│   └── examples/
├── updates/              # Updating existing Galaxy tools
│   ├── SKILL.md
│   ├── update-tool.md
│   ├── research-upstream.md
│   ├── common-bugs.md
│   └── commit-template.md
└── shared/               # Shared references
    ├── xml-structure.md
    ├── testing.md
    └── help-sections.md

Related Skills

  • •../nf-to-galaxy/ - Converting Nextflow to Galaxy (includes process-to-tool conversion)
  • •../galaxy-integration/ - Testing tools on Galaxy instances

Quick Start

New tool? → creation/SKILL.md

Update tool? → updates/SKILL.md

Need XML help? → shared/xml-structure.md

Need testing help? → shared/testing.md