Developing a Galaxy tool

Galaxy is mostly a very advanced workflow engine with an easy-to-use interface. Concrete work is delegated to tools. Here, we will learn how to develop a basic tool. The fundamental objective of this chapter is to demonstrate how easy it is to develop a tool; it might seem daunting, but really it is not. The Galaxy developers made sure that all the boilerplate work is done by a tool called Planemo (https://planemo.readthedocs.io). Planemo is very well-documented, and this recipe should be seen as a starting point; Planemo's documentation is the end point. Again, our main objective here is to gain confidence that tool development is accessible for all who want to do it.

Getting ready

Strictly speaking, tool development is language-agnostic. Many tools are actually just wrappers for existing applications; no Python code involved. But Python is well-suited to tool development, especially because Galaxy is implemented in Python, so it's the best choice for tool development...