plugin_h2_cli.md

+# Using the plugin from the command line   
+The plugin will requires the following options:   
+
+| option | type | description/value |   
+| :---    | :---  | :---  |   
+| --run h2 |  **MANDATORY** | name of the plugin |
+| --time_window value | **MANDATORY** | length time window (s) |    
+| --max_lag value | **MANDATORY**     | maximum lag duration (s) |
+| --step value |  **MANDATORY**  | step in seconds |  
+| --algorithm value | optional | h2 r2 (default is h2) |
+| --downsampling_factor value |  optional  | default is 1 (no downsampling). Set to 2 to reduce the sr by 2 |  
+
+This plugin also supports the following common options:   
+
+| option |  type |
+| :---    | :--- |
+| --input_file |  **MANDATORY** |
+| --use_markers | optional |
+| --skip_markers | optional |
+| --output_dir | optional |
+| --output_prefix | optional |
+| --marker_file  | optional |
+| --montage_file | optional |
+
+# Command line examples
+Compute h2 on EEG data using a specific marker file and only on H2 markers.   
+The frequency band is 1-40.   
+```bash
+anywave --run h2 --input_file d:\data\myfile.eeg --time_window 4 --step 1 --max_lag 0.1 --marker_file d:\data\h2markers.mrk --use_markers "H2" --hp 1 --lp 40
+```    
+
+Compute r2 on the same data assuming the data file has markers named H2:   
+```bash
+anywave --run h2 --algorithm r2 --input_file d:\data\myfile.eeg --time_window 4 --step 1 --max_lag 0.1 --use_markers "H2" --hp 1 --lp 40
+```   
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