name: wham
version: "0.1.0"
author: D. Bauer <bauer@cbs.tu-darmstadt.de>
about: WHAM analysis
args:
    - metadata:
        short: f
        long: file
        value_name: METADATA
        help: Sets the metadata file
        takes_value: true
        required: true
    - min_hist:
        long: min
        value_name: HIST_MIN 
        takes_value: true
        required: true
        allow_hyphen_values: true
    - max_hist:
        long: max
        value_name: HIST_MAX 
        takes_value: true
        required: true
        allow_hyphen_values: true
    - bins:
        short: b
        long: bins
        value_name: BINS
        takes_value: true
        required: true
    - tolerance:
        short: t
        long: tolerance
        value_name: TOLERANCE
        takes_value: true
        required: false
    - iterations:
        short: i
        long: iterations
        value_name: ITERATIONS
        takes_value: true
        required: false
    - cyclic:
        long: cyclic
        help: For periodic reaction coordinates. If this is set, the first and last coordinate bin will be assumed to be neighbors for the bias calculation.        
    - verbose:
        short: v
        long: verbose
        help: Enables verbose output.
        takes_value: false
    - temperature:
        short: T
        long: temperature
        help: WHAM temperature in Kelvin
        takes_value: true
        required: true
    - output:
        short: o
        long: output
        help: Free energy output file (defaults to "wham.out")
        takes_value: true
        required: false