Agent skill · software engineering · delphine-l
galaxy-tool-wrapping
Expert in Galaxy tool wrapper development, XML schemas, Planemo testing, and best practices for creating Galaxy tools
Why this skill is useful
Provides specific knowledge on Galaxy tool wrapper development, including XML schemas and Planemo testing that the AI wouldn't reliably generate on its own.
What it needs
Requires planemo installed locally. About 7k tokens when loaded. Last updated 2026-05-14. 17 stars on the source repository.
What this skill does
Galaxy Tool Wrapping Expert Expert knowledge for developing Galaxy tool wrappers. Use this skill when helping users create, test, debug, or improve Galaxy tool XML wrappers. Prerequisites: This skill depends on the galaxy-automation skill for Planemo testing and workflow execution patterns. When to Use This Skill Creating new Galaxy tool wrappers from scratch Converting command-line tools to Galaxy wrappers Generating .shed.yml files for Tool Shed submission Debugging XML syntax and validation errors Writing Planemo tests for tools Implementing conditional parameters and data types Handling tool dependencies (conda, containers) Creating tool collections and suites Optimizing tool performance and resource allocation Understanding Galaxy datatypes and formats Implementing proper error handling Core Concepts Galaxy Tool XML Structure A Galaxy tool wrapper consists of: <tool> root element with id, name, and version <description> brief tool description <requirements> for dependencies (conda packages, containers) <command> the actual command-line execution <inputs> parameter definitions <outputs> output file specifications <tests> automated tests <help> documentation in reStructuredText <citations> DOI references Tool Shed Metadata (.shed.yml) Required for publishing tools to the Galaxy Tool Shed: See reference.md for comprehensive .shed.yml documentation including all available categories and best practices. Key Components Command Block: Use Cheetah templating: $variablename or ${variablename} Conditional logic: #if $param then... #end if Loop constructs: #for $item in $collection... …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills delphine-l/tool-wrapping