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 |