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### Command line usage

 Flow-R can be used in command line mode. Open a shell / command prompt and change the directory to the executable folder (named FlowR). You need to give 2 parameters: paramsfile: a file specific for command line mode (see below) outputdir: the directory where the results will be written For Windows, the command line is for example: app.exe --paramsfile "C:\path\to\FlowR\parameters\scripts\commandline_script.xml" --outputdir "C:\Users\me\Desktop\sometests" For Linux, the command line is for example:FlowR --paramsfile "/home/me/path/to/FlowR/parameters/scripts/commandline_script.xml" --outputdir "/home/me/FlowR/results"Here is an example of the xml file required for the paramsfile option (it is not possible here to define multiple runs):