Executes workflows created by TOPPAS.

This tool is the non-GUI, i.e. command line version for non-interactive execution of TOPPAS pipelines. In order to really use this tool in batch-mode, you can provide a TOPPAS resource file (.trf) which specifies the input files for the input nodes in your pipeline.

*.trf files

A TOPPAS resource file (*.trf) specifies the locations of input files for a pipeline. It is an XML file following the normal TOPP INI file schema, i.e. it can be edited using the INIFileEditor or filled using a script (we do NOT provide one - sorry). It can be exported from TOPPAS (File -> Save TOPPAS resource file). For two input nodes 1 and 2 with files (dataA.mzML, dataB.mzML) and (dataC.mzML) respectively it has the following format.

<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.3" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_3.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="1" description="">
    <ITEMLIST name="url_list" type="string" description="">
      <LISTITEM value="file:///Users/jeff/dataA.mzML"/>
      <LISTITEM value="file:///Users/jeff/dataB.mzML"/>
    </ITEMLIST>
  </NODE>
  <NODE name="2" description="">
    <ITEMLIST name="url_list" type="string" description="">
      <LISTITEM value="file:///Users/jeff/dataC.mzML"/>
    </ITEMLIST>
  </NODE>
</PARAMETERS>

The command line parameters of this tool are:

ExecutePipeline -- Executes workflows created by TOPPAS.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_ExecutePipeline.html
Version: 3.6.0-pre-nightly-2026-03-06 Mar  7 2026, 01:46:19, Revision: c92c980
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  ExecutePipeline <options>

Options (mandatory options marked with '*'):
  -in <file>*            The workflow to be executed. (valid formats: 'toppas')
  -out_dir <directory>   Directory for output files (default: user's home directory)
  -resource_file <file>  A TOPPAS resource file (*.trf) specifying the files this workflow is to be applied 
                         to
  -num_jobs <integer>    Maximum number of jobs running in parallel (default: '1') (min: '1')
                         
Common TOPP options:
  -ini <file>            Use the given TOPP INI file
  -threads <n>           Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>      Writes the default configuration file
  --help                 Shows options
  --helphelp             Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.

Each parameter entry contains the following information:

Name The identifier used in configuration files and on the command line.
Default value The value used if the parameter is not explicitly specified.
Description A short explanation describing the purpose and behavior of the parameter.
Tags Additional metadata associated with the parameter.
Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.

Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.

+ExecutePipelineExecutes workflows created by TOPPAS.

version3.6.0-pre-nightly-2026-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'ExecutePipeline'

in The workflow to be executed.input file*.toppas

out_dir Directory for output files (default: user's home directory)

resource_file A TOPPAS resource file (*.trf) specifying the files this workflow is to be applied to

num_jobs1 Maximum number of jobs running in parallel1:∞

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false