galaxy-tool-wrapping

A Galaxy tool wrapper is an XML file that integrates CLI tools into Galaxy by defining inputs, outputs, and execution logic. Start with a minimal tool.xml, define command parameters and outputs, then validate with planemo lint and planemo test to ensure the wrapper executes correctly.

Planemo is a command-line toolkit for developing and testing Galaxy tools. Use planemo lint to validate XML syntax and best practices, then planemo test to run functional tests against your wrapper in a local Galaxy instance, catching integration issues before submission.

Validate wrappers by running planemo lint for structural checks and planemo test for functional validation. Debug common issues like missing dependencies, incorrect parameter mappings, or malformed XML by checking test output logs and comparing expected vs. actual tool behavior.

Yes. After creating and testing your XML wrapper with Planemo, ensure all tests pass and dependencies are pinned, then submit to the Galaxy Tool Shed using shed metadata workflows. This makes your wrapped tool discoverable and installable by other Galaxy instances.

Include explicit tool dependencies (via conda or other package managers) to ensure reproducibility. Add shed metadata such as categories, descriptions, and authors. Pinning versions and enforcing dependencies prevents compatibility issues and ensures consistent tool behavior across Galaxy instances.

Galaxy tool wrappers define individual tool behavior; for multi-step automation, combine wrappers into Galaxy workflows that chain tool outputs and inputs. Each wrapper must be independently testable with Planemo before integration into larger workflow logic.