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I am currently using this diagram package (https://github.com/francoislaberge/diagrams) to create a sequence diagram.

It fits my work flow because I want to be able to generate a sequence diagram by running a command.

 diagrams sequence <my file>

However it misses a few features such as supporting loop.

Is there any good cli tool to generate sequence diagram?

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You simply can't beat MSC generator. It is cross-platform, full featured and well supported (Zoltan generally replies very quickly to emails requesting support or new features).

It takes its input from a plain text file:

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Read the excellent user mnaual and search for "loop".

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