Modify the dest.txt

Inform AnyWave your plugin will handle command line options. Add the line:

flags = CanRunFromCommandLine

Note that you can set several flags separating them by ':'

Specify the command line parameters your plugin will handle

The plugin will receive all the default command line options handled by AnyWave but if you need to handle your own options then you must provide a file called args.json and put it along with desc.txt file in the plugin's folder.
Example of a plugin that will handle the options eeg_file (path to a EEG data file) and meg_file (path to a MEG data file):

{
"Parameters" : [ "eeg_file", "meg_file"]
}

Folder contents

Example of plugin folder contents compatible with BIDS pipeline (or command line execution more generally)

Handle options in your code

function main(varargin)
% init function will give you back a struct filled with all you need:
args = anywave('init', varargin);
% test if command line option are set (if not we are running in normal GUI mode)
eeg_file = '';
if isfield(args, 'eeg_file') 
   % we are running in command line mode/bids pipeline
   eeg_file = args.eeg_file;
else
   % open Dialog box to get the file
   eeg_file = uigetfile('...');
end
end

Avoid figure and guis

If you want the plugin to be run as a BIDS pipeline you must not stop the execution asking for a confirmation of by displaying a Dialog Box showing errors.

Tips about logging errors

The command line option output_dir will always be set by AnyWave either by the pipeline itself or by default.
Write a log.txt file for example in that location and report all logs for your plugin in that file.

Call your plugin using the command line

If you want to run your plugin outside of BIDS Pipeline context:

anywave --run my_plugin --eeg_file <path to eeg> --meg_file <path to meg>