Hi Rahel,
There is a command-line version, it's called iotbx.reflection_file_editor. It's a bit complicated to use because you have to define filenames for each input array. We recommend that you use the GUI.
If you want to batch process a bunch of reflection files, you might try using the GUI first and looking at the .eff file that is generated to get a sense of how to structure your parameters. To do so,
1) Set up your inputs in the GUI
2) In the menu bar, under "File", select "Save parameter file"
The saved parameter file will illustrate how the parameter names are set.