Legend:

required parameter

advanced parameter

+FileMergerMerges several MS files into one file.

version1.10.0 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 (MetaValue: file_origin).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

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.dtatrue,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