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.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
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:
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |