galaxy-tool-wrapping
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
More from delphine-l/claude_global
token-efficiency
Token optimization best practices for cost-effective Claude Code usage. Automatically applies efficient file reading, command execution, and output handling strategies. Includes model selection guidance (Opus for learning, Sonnet for development/debugging). Prefers bash commands over reading files.
1.2Kbioinformatics-fundamentals
Core bioinformatics concepts including SAM/BAM format, AGP genome assembly format, sequencing technologies (Hi-C, HiFi, Illumina), quality metrics, and common data processing patterns. Essential for debugging alignment, filtering, pairing issues, and AGP coordinate validation.
217folder-organization
Best practices for organizing project folders, file naming conventions, and directory structure standards for research and development projects
117obsidian
Integration with Obsidian vault for managing notes, tasks, and knowledge when working with Claude. Supports adding notes, creating tasks, and organizing project documentation. Updated with 2025-2026 best practices including MOCs, properties, practical organization patterns, and Obsidian CLI (1.12+).
72jupyter-notebook-analysis
Best practices for creating comprehensive Jupyter notebook data analyses with statistical rigor, outlier handling, and publication-quality visualizations. Includes Claude API image size helpers.
63managing-environments
Best practices for managing development environments including Python venv and conda. Always check environment status before installations and confirm with user before proceeding.
55