--- 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: - `` wrapper - `` (from container) - `` (from script) - `` (from process inputs) - `` (from process outputs) - `` (create test cases) - `` (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` → `` (bioconda package) - `input: path(file)` → `` - `output: path("*.ext")` → `` - `script: """..."""` → `<\/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!