Note that this reference documentation is identical to the help that is displayed in MATLAB when you type “help ft_analysispipeline”.

  FT_ANALYSIPIPELINE reconstructs the complete analysis pipeline that was used to create
  the input FieldTrip data structure. The pipeline will be visualized as a flowchart.
  In the future it will be possible to output the complete pipeline as a MATLAB script
  or in a specialized pipeline format (e.g. PSOM, JIST, LONI, Taverna).
  Use as
    output = ft_analysispipeline(cfg, data)
  The first cfg input contains the settings that apply to the behaviour of this
  particular function and the second data input argument can be the output of any
  FT_FREQSTATISTICS or whatever you like.
  Alternatively, for the second input argument you can also only give the configuration
  of the processed data (i.e. "data.cfg") instead of the full data.
  The configuration options that apply to the behaviour of this function are
    cfg.filename   = string, filename without the extension
    cfg.filetype   = string, can be 'matlab', 'html' or 'dot'   = string, 'no', 'text', 'gui' or 'yes', whether text and/or
                     graphical feedback should be presented (default = 'yes')
    cfg.showinfo   = string or cell array of strings, information to display
                     in the gui boxes, can be any combination of
                     'functionname', 'revision', 'matlabversion',
                     'computername', 'username', 'calltime', 'timeused',
                     'memused', 'workingdir', 'scriptpath' (default =
                     'functionname', only display function name). Can also
                     be 'all', show all pipeline. Please note that if you want
                     to show a lot of information, this will require a lot
                     of screen real estate.
    cfg.remove     = cell-array with strings, determines which objects will
                     be removed from the configuration prior to writing it to
                     file. For readibility of the script, you may want to
                     remove the large objectssuch as event structure, trial
                     definition, source positions
   cfg.keepremoved = 'yes' or 'no', determines whether removed fields are
                     completely removed, or only replaced by a short textual
                     description (default = 'no')
  This function uses the nested cfg and cfg.previous that are present in
  the data structure. It will use the configuration and the nested previous
  configurations to climb all the way back into the tree. This funtction
  will print a complete MATLAB script to screen (and optionally to file).
  Furthermore, it will show an interactive graphical flowchart
  representation of the steps taken during the pipeline(i). In the flowchart
  you can click on one of the steps to see the configuration details of
  that pipeline(i).
  Note that the nested cfg and cfg.previous in your data might not contain
  all details that are required to reconstruct a complete and valid
  analysis script.
  To facilitate data-handling and distributed computing you can use
    cfg.inputfile   =  ...
  If you specify this, the input data will be read from a *.mat file on disk. The
  file should contain only a single variable, corresponding with the input structure.