# Command Line Interface#

TOPP tools are designed to be called from the command line. OpenMS provides a Command Line Interface (CLI) called TOPP shell to easily execute TOPP tools on mass spectrometry data. However, you can configure the CLI of your choice to run TOPP tools.

Command line calls will depend on the TOPP tools used, as each TOPP tool has its own set of parameters. However, the following arguments are typically used:

• -in

Specify an input file in the command line using the -in argument. The input file should be in a supported format. If not, use the file converter to convert the file to one of the supported formats. For more information, view the file handling documentation.

• -out

Specify an output file in the command line using the -out argument.

• -ini

Specify an INI file in the command line using the -ini argument. TOPP uses INI files to set parameters specific to the command line tool being called.

• -write_ini

Create an INI file using the -write_ini file argument. Create an INI file with this call: <insert TOPP tool> -write_ini <insert output INI File> If you want a visual tool to assist setting parameters, use INIFileEditor, an application provided when you download OpenMS. Otherwise, you can set the parameters from the command line.

• -help

Get information about basic options related to the tool using the -help parameter. For more advanced options (algorithmic parameters), use --help.

• --help

Get detailed information about algorithmic parameters using the --help parameter.

Many (but not all) command line calls will have the following structure:

<insert TOPP tool> -in <insert input mzML file> -out <insert output mzML file> -ini <insert INI file>


The following command line call uses the FileFilter tool to extract data from an mzML file. Note, that this call directly specifies the tool-specific parameters and doesn’t rely on an INI file: