nf-process-to-galaxy-tool

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Convert a single Nextflow process to a Galaxy tool XML

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[Developer Tools]

When & Why to Use This Skill

This Claude skill automates the conversion of Nextflow processes into Galaxy tool XML wrappers, streamlining the integration of bioinformatics pipelines into the Galaxy ecosystem. It intelligently handles the mapping of container images to Bioconda packages, translates file patterns into Galaxy datatypes, and generates structured XML components including requirements, commands, inputs, and outputs, ensuring compliance with Planemo validation standards.

Use Cases

  • Bioinformatics Pipeline Migration: Efficiently porting individual processes from Nextflow workflows into the Galaxy platform to increase tool accessibility.
  • Automated Tool Wrapping: Rapidly generating standardized Galaxy XML wrappers for command-line tools by extracting metadata and logic from existing Nextflow scripts.
  • Workflow Interoperability: Bridging the gap between different workflow management systems by automating the translation of execution logic and environment requirements.
  • Development Standardization: Ensuring newly created Galaxy tools follow best practices for XML structure and dependency management through automated mapping.
namenf-process-to-galaxy-tool
descriptionConvert a single Nextflow process to a Galaxy tool XML

Nextflow Process to Galaxy Tool

When to Use

Use this skill when:

  • Converting a single Nextflow process to a Galaxy tool
  • Creating a Galaxy tool wrapper for a specific bioinformatics tool
  • You've identified a missing tool during pipeline conversion

Don't use this skill if:

  • The tool already exists in Galaxy (check first with ../check-tool-availability.md)
  • You're converting a whole workflow (use nf-subworkflow-to-galaxy-workflow instead)

Step-by-Step Process

Step 1: Check if Tool Already Exists

CRITICAL: Always check first.

Use: ../check-tool-availability.md and ../scripts/check_tool.sh

cd ../
./scripts/check_tool.sh TOOL_NAME

If tool exists: Stop here, use existing tool. You don't need this skill.

If tool doesn't exist: Continue to Step 2.

Step 2: Decide Where to Create Tool

Use: ../tool-sources.md for decision guidance

Options:

  1. tools-iuc (if community-useful and you have access)
  2. Custom tool (if project-specific)

Present decision to user and wait for approval.

If targeting tools-iuc, follow the higher-level tool creation guidance in:

  • ../../tool-dev/creation/SKILL.md

Step 3: Extract Process Information

Identify from Nextflow process:

  • Container image
  • Input files/parameters
  • Output files
  • Command/script

See: ../process-to-tool.md for detailed extraction guide

Step 4: Map to Galaxy Tool XML

Use these references:

  • ../container-mapping.md - Container → bioconda package
  • ../datatype-mapping.md - File patterns → Galaxy datatypes
  • ../process-to-tool.md - Complete mapping guide

Step 5: Create Tool XML

Follow Galaxy tool XML structure:

  • <tool> wrapper
  • <requirements> (from container)
  • <command> (from script)
  • <inputs> (from process inputs)
  • <outputs> (from process outputs)
  • <tests> (create test cases)
  • <help> (documentation)

See: ../process-to-tool.md for complete examples

Step 6: Validate

planemo lint tool.xml
planemo test tool.xml

Quick Reference

One Nextflow process = One Galaxy tool XML

Key mappings:

  • container → <requirements> (bioconda package)
  • input: path(file) → <param type="data" format="..."/>
  • output: path("*.ext") → <data format="..." name="output"/>
  • script: """...""" → <command><![CDATA[...]]></command>

Resources

These docs live in the parent directory (../):

  • process-to-tool.md - Complete process-to-tool conversion guide
  • check-tool-availability.md - Tool availability checking
  • tool-sources.md - Where to create tools
  • container-mapping.md - Container to bioconda mapping
  • datatype-mapping.md - File patterns to Galaxy datatypes
  • testing-and-validation.md - Routing page to canonical testing docs
  • ../../tool-dev/shared/testing.md - Tool testing with Planemo

Example

See ../examples/capheine-mapping.md for real-world examples of process analysis.

Note: CAPHEINE shows a case where all tools already existed, so no tool creation was needed. This is common - always check first!