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file is a top level plop command used to specify the path to various files/directories.

outdirectory     - output directory
datadirectory    - data directory
tempdirectory    - template directory
usrtempdirectory - user template directory
protempdirectory - protein template directory
hettempdirectory - het group template directory
nbfile           - 
covfile          - 
gluefile         - 
logfile          - specify the logfile
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