CLI_List.md

+[[_TOC_]]   
+# Introduction
+This page describes all the process plugins you can run using the command line.   
+The specific options related to the plugins
+# ICA
+Specifics options:   
+````bash
+anywave --run ica --modality <meg|ieeg|eeg> --comp <number of IC>  --input_file <path to data>
+````
+Optionals:   
+````bash
+--skip_bad <true=default|false> 
+````
+skip_bad: avoid channels marked as bad.
+
+# h2/r2
+Specifics options:   
+````bash
+anywave --run h2 --algorithm <r2|h2=default> --input_file <path to data> --time_window <seconds> --max_lag <seconds> --step <seconds>
+````
+
+# Write values from marker file to 4DNI MEG trigger channel
+````bash
+anywave --run trigger_writer --meg_file <path to data> --marker_file <mrk file path>
+````
+Optionals:   
+````bash
+--duration <ms>  specify the duration in ms of the trigger value.  Default is 20ms.
+````