Menu
Convert a single Nextflow process to a Galaxy tool XML
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
Use when authoring a Galaxy User-Defined Tool (UDT) -- a `class: GalaxyUserTool` YAML definition that wraps a container and command into a tool a non-admin user creates and runs (e.g. via Galaxy MCP create_user_tool / run_user_tool, or POST /api/unprivileged_tools). Not for classic XML/ToolShed tool wrappers.
Use this skill when asked to create, draft, or write a Galaxy workflow report template for the Workflow Editor's Report tab. Triggers on requests like "create a report for this workflow", "draft a workflow report template", "write a Galaxy report for workflow <id/url>".
Galaxy Collection Transformation Command - transform Galaxy dataset collections reproducibly using Galaxy's native tools. Use when asked to filter, sort, relabel, restructure, flatten, nest, merge, or otherwise manipulate Galaxy collections.
Galaxy MCP server tools reference for histories, datasets, tools, and workflows
Router for Galaxy MCP, JupyterLite notebooks, and BioBlend automation
Building UCSC Track Hubs (track hubs and assembly hubs) — bigBed/bigChain/bigMaf format requirements, composite-track rules, hub.txt / genomes.txt / trackDb.txt structure. Use when emitting a UCSC hub from Galaxy outputs, wrapping a hub-publishing tool, or debugging hubCheck failures.
| name | nf-process-to-galaxy-tool |
| description | Convert a single Nextflow process to a Galaxy tool XML |
Use this skill when:
Don't use this skill if:
../check-tool-availability.md)nf-subworkflow-to-galaxy-workflow instead)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.
Use: ../tool-sources.md for decision guidance
Options:
Present decision to user and wait for approval.
If targeting tools-iuc, follow the higher-level tool creation guidance in:
../../tool-dev/SKILL.mdIdentify from Nextflow process:
See: ../process-to-tool.md for detailed extraction guide
Use these references:
../container-mapping.md - Container → bioconda package../datatype-mapping.md - File patterns → Galaxy datatypes../process-to-tool.md - Complete mapping guideFollow 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
planemo lint tool.xml
planemo test tool.xml
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>These docs live in the parent directory (../):
process-to-tool.md - Complete process-to-tool conversion guidecheck-tool-availability.md - Tool availability checkingtool-sources.md - Where to create toolscontainer-mapping.md - Container to bioconda mappingdatatype-mapping.md - File patterns to Galaxy datatypestesting-and-validation.md - Routing page to canonical testing docs../../tool-dev/references/testing.md - Tool testing with PlanemoSee ../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!