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FileMerger

Merges several files. Multiple output format supported, depending on input format.

pot. predecessor tools $ \longrightarrow $ FileMerger $ \longrightarrow $ pot. successor tools
any tool/instrument producing merge able files any tool operating merged files (e.g. XTandemAdapter)

The meta information that is valid for the whole experiment (e.g. MS instrument and sample) is taken from the first file.

The retention times for the individual scans are taken from either:

The command line parameters of this tool are:

FileMerger -- Merges several MS files into one file.
Version: 2.0.0 May 16 2015, 09:22:21, Revision: GIT-NOTFOUND

Usage:
  FileMerger <options>

Options (mandatory options marked with '*'):
  -in <files>*            Input files separated by blank (valid formats: 'mzData', 'mzXML', 'mzML', 'dta', 
                          'dta2d', 'mgf', 'featureXML', 'consensusXML', 'fid', 'traML')
  -in_type <type>         Input file type (default: determined from file extension or content) (valid: 'mzDat
                          a', 'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXML', 'consensusXML', 'fid',
                          'traML')
  -out <file>*            Output file (valid formats: 'mzML', 'featureXML', 'consensusXML', 'traML')
  -annotate_file_origin   Store the original filename in each feature using meta value "file_origin" (for 
                          featureXML and consensusXML only).
                          

Flags for non-featureXML input/output:
  -raw:rt_auto            Assign retention times automatically (integers starting at 1)
  -raw:rt_custom <rt>     List of custom retention times that are assigned to the files. The number of given 
                          retention times must be equal to the number of given input file.
  -raw:rt_filename        If this flag is set FileMerger tries to guess the rt of the file name.
                          This option is useful for merging DTA file, which should contain the string
                          'rt' directly followed by a floating point number:
                          i.e. my_spectrum_rt2795.15.dta
  -raw:ms_level <num>     This option is useful for use with DTA files which does not contain MS level inform
                          ation. The given level is assigned to the spectra. (default: '2')
  -raw:user_ms_level      If this flag is set, the MS level given above is used

                          
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
+FileMergerMerges several MS files into one file.
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'FileMerger'
in[] Input files separated by blankinput file*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.fid,*.traML
in_type Input file type (default: determined from file extension or content)mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML
out Output fileoutput file*.mzML,*.featureXML,*.consensusXML,*.traML
annotate_file_originfalse Store the original filename in each feature using meta value "file_origin" (for featureXML and consensusXML only).true,false
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 Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false
+++rawFlags for non-featureXML input/output
rt_autofalse Assign retention times automatically (integers starting at 1)true,false
rt_custom[] List of custom retention times that are assigned to the files. The number of given retention times must be equal to the number of given input file.
rt_filenamefalse If this flag is set FileMerger tries to guess the rt of the file name.
This option is useful for merging DTA file, which should contain the string
'rt' directly followed by a floating point number:
i.e. my_spectrum_rt2795.15.dta
true,false
ms_level2 This option is useful for use with DTA files which does not contain MS level information. The given level is assigned to the spectra.
user_ms_levelfalse If this flag is set, the MS level given above is usedtrue,false

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:42 using doxygen 1.8.9.1