MATLAB_BIDS.md

+# 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):    
+````json
+{
+"Parameters" : [ "eeg_file", "meg_file"]
+}
+````  
+
+# Folder contents
+Example of plugin folder contents compatible with BIDS pipeline (or command line execution more generally)
+![image](uploads/b7ab2969759d292e3a89bfc596f71489/image.png)
+
+# Handle options in your code
+````matlab
+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:     
+````bash
+anywave --run my_plugin --eeg_file <path to eeg> --meg_file <path to meg>
+````
+