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@gonzalocasal At this time we do not have a standalone tool or script available that can hash passwords for this purpose, and there isn't any public documentation regarding the methodology used to encode these passwords. The best/easiest option is to take an existing hash from a current configuration file where you know what the password is and use that already hashed password in your script. This option would only really be helpful for deploying the config files with the same username and password though.
If each config file will have a unique user the best alternative would be not to set the password when generating the file. Then after you apply the configuration file you would need to either run the Alteryx System Settings to set the correct password, or if the configuration is for Designer with Scheduler (admin install) or Alteryx Server you could update these credentials using the AlteryxService from a command line.