AgentSkillsCN

nf-process-to-galaxy-tool

将单个Nextflow流程转换为Galaxy工具的XML格式。

SKILL.md
--- frontmatter
name: nf-process-to-galaxy-tool
description: Convert 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

bash
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

bash
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!