Types of QIIME 2 Actions

A QIIME 2 plugin action is any operation that accepts parameters and files (:term:artifact or metadata) as input, and generates some type of output. Actions are interpreted as “commands” by QIIME 2 interfaces and come in three flavors:

1. A Method accepts some combination of QIIME 2 Artifacts and Parameters as input, and produces one or more QIIME 2 artifacts as output. These output artifacts could subsequently be used as input to other QIIME 2 Methods or Visualizers. Methods can produce intermediate or terminal outputs in a QIIME 2 analysis. For example, the rarefy method defined in the q2-feature-table plugin accepts a feature table artifact and sampling depth as input and produces a rarefied feature table artifact as output. This rarefied feature table artifact could then be used in another analysis, such as alpha diversity calculations provided by the alpha method in q2-diversity.

A Visualizer is similar to a Method in that it accepts some combination of QIIME 2 Artifacts and Parameters as input. In contrast to a method, a visualizer produces exactly one Visualization as output. Visualizations, by definition, cannot be used as input to other QIIME 2 methods or visualizers. Thus, visualizers can only produce terminal output in a QIIME 2 analysis.

A Pipeline accepts some combination of QIIME 2 Artifacts and Parameters as input and produces one or more artifacts and/or visualizations as output. It does so by incorporating one or more methods and/or visualizers into a single registered action.