Galaxy Tool Update Skill

Purpose: Update existing Galaxy tool wrappers when underlying CLI tools release new versions.

When to Use This Skill

Use this skill when you need to:

• •Update a Galaxy tool to a new version
• •Fix bugs in existing Galaxy tools
• •Improve tool documentation
• •Debug failing planemo tests

Not for: Creating new tools (see ../creation/)

Prerequisites

• •Existing Galaxy tool XML
• •Knowledge of new upstream version
• •Planemo installed (pip install planemo)

Quick Workflow

1. •Research upstream - Check for breaking changes (see research-upstream.md)
2. •Update version - Modify @TOOL_VERSION@ token
3. •Review code - Check command section, outputs, filters
4. •Fix bugs - Common issues (see common-bugs.md)
5. •Update docs - Expand help section if minimal (see ../shared/help-sections.md)
6. •Test - Run planemo test, analyze failures (see ../shared/testing.md)
7. •Commit - Use standard message format (see commit-template.md)

Key Files

• •update-tool.md - Main workflow, step-by-step process
• •research-upstream.md - How to check for breaking changes
• •common-bugs.md - Frequent bug patterns and fixes
• •commit-template.md - Standard commit message formats

Shared References

These are shared with tool-creation/:

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

Common Patterns

Repeat Element Access

#for item in $section.repeat_name:
    --flag '$item.param_name'
#end for

Flexible Test Assertions

<has_n_lines min="100"/>
<output_collection min="5">

Related Skills

• •../creation/ - Creating new tools
• •../../nf-to-galaxy/ - Converting Nextflow to Galaxy
• •../../galaxy-integration/ - Testing tools on Galaxy instances

Origin

Created from ncbi-datasets-cli 18.5.1 → 18.13.0 update session.