Templating

[AlvaroSmorras]

I changed completely the amber_inputs code to use the templates, which I believe are flexible enough. The templates are also added in the setup.py to be copied to the base folder when installed and adapted the duck_amber and batch_preparation. I added seed specifications for your tests (albeit I still didn't add the parameter in the input). @simonbray do you think we should maybe go back to using a yaml input? Now the input seems to have too many options.

[simonbray]

Thanks for doing this!

I don't think I have a strong opinion about the yaml file. I think personally I prefer typing the commands directly on the command line, but yaml is fine too.