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Creation

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SKILL.md

Galaxy Tool Creation Skill

Purpose: Guide for creating new Galaxy tool wrappers from scratch or from existing CLI tools.

When to Use This Skill

Use this skill when you need to:

  • •Create a new Galaxy tool wrapper for a CLI tool
  • •Wrap a tool that doesn't have a Galaxy wrapper yet
  • •Create a tool from Nextflow process (see also: ../../nf-to-galaxy)
  • •Build a custom tool for a specific workflow

Not for: Updating existing tools (see ../updates/)

Prerequisites

  • •Understanding of the CLI tool you're wrapping
  • •Access to tool documentation
  • •Basic XML knowledge
  • •Planemo installed (pip install planemo)

Quick Decision Tree

code
What's your starting point?

├─ Converting arcane Nextflow process?
│  └─ See: ../../nf-to-galaxy/nf-process-to-galaxy-tool/SKILL.md
│
├─ Have CLI tool to wrap?
│  └─ Use: from-scratch.md
│
└─ Need to understand tool placement?
   └─ Use: tool-placement.md

Core Workflow

  1. •Understand the tool - Read CLI docs, test locally
  2. •Decide placement - tools-iuc vs custom (see tool-placement.md)
  3. •Create XML structure - Use templates (see ../shared/xml-structure.md)
  4. •Map inputs/outputs - CLI flags → Galaxy params
  5. •Write command template - Cheetah templating
  6. •Add tests - Required for validation (see ../shared/testing.md)
  7. •Write help - RST format (see ../shared/help-sections.md)
  8. •Validate - planemo lint and planemo test

tools-iuc / IUC Targeting Guidance

If you decide the tool should be contributed to tools-iuc:

  1. •

    Have a local tools-iuc clone available

    • •Follow the established directory structure and macros patterns.
    • •Run planemo lint/tests locally before opening a PR.
  2. •

    Prefer Bioconda for dependencies

    • •Use <requirements> with a Bioconda package whenever possible.
    • •If no suitable Bioconda package exists, coordinate with the user about whether to add one.
      • •In that case, having a local clone of bioconda/bioconda-recipes may be helpful for preparing a recipe PR.
  3. •

    Scope the wrapper UI intentionally

    • •Prefer exposing the commonly used options needed for typical workflows.
    • •Avoid mirroring every upstream flag; keep the Galaxy form usable.
    • •Add advanced options only when they are widely used or necessary for correctness.

Key Files

  • •create-tool.md - Main guide for creating tools
  • •from-scratch.md - Creating tool from CLI documentation
  • •from-nextflow.md - Pointer to conversion skill
  • •tool-placement.md - Where to create your tool (tools-iuc vs custom)
  • •examples/ - Concrete examples

Shared References

These are shared with tool-updates/:

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

Related Skills

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

Examples

See examples/ directory for:

  • •Simple single-input/output tool
  • •Multi-output tool with collections
  • •Tool with conditional parameters