OpenMS
2.8.0
|
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.
The command line parameters of this tool are:
ExecutePipeline -- Executes workflows created by TOPPAS. Full documentation: http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ExecutePipeline.html Version: 2.8.0 Feb 22 2022, 11:52:07, Revision: d203985 To cite OpenMS: Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959. 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: