ExecutePipeline

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: 3.5.0-pre-nightly-2025-10-23 Oct 24 2025, 02:40:49, Revision: a0cf6d9
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

+ExecutePipelineExecutes workflows created by TOPPAS.

version3.5.0-pre-nightly-2025-10-23 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