Publishing a Story in Studio to a custom Publish Channel can be done by using any of the files that are provided in the output file (see Configuring Studio for publishing to a custom Publish Channel).
Recommended is to use the file in PSV (Prism Source Vocabulary) format: a combination of XML (for the metadata, re-use rights, and so on) and HTML5 (for the Story content).
For an overview of how the components of a Digital article are defined as PSV classes, see the components boilerplate.
Note: Properties such as paragraph alignment will be added to the class attribute.
For more information about Digital article components, see Working with the components of a Digital article in Studio.