OpenMS
2.4.0
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Merges several files. Multiple output format supported, depending on input format.
pot. predecessor tools | FileMerger | 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: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06 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: 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', 'FASTA') -in_type <type> Input file type (default: determined from file extension or content) (valid: 'mzData', 'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXML', 'consensusXML ', 'fid', 'traML', 'FASTA') -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). Options for concatenating files in the retention time (RT) dimension. The RT ranges of inputs are adjusted so they don't overlap in the merged file (traML input not supported): -rt_concat:gap <sec> The amount of gap (in seconds) to insert between the RT ranges of different input files. RT concatenation is enabled if a value > 0 is set. (default: '0') -rt_concat:trafo_out <files> Output of retention time transformations that were applied to the input files to produce non-overlapping RT ranges. If used, one output file per input file is required. (valid formats: 'trafoXML') Options for raw data input/output (primarily for DTA files): -raw:rt_auto Assign retention times automatically (integers starting at 1) -raw:rt_custom <rts> List of custom retention times that are assigned to the files. The number of given retention times must be equal to the number of input files. -raw:rt_filename Try to guess the retention time of a file based on the filename. This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number, e.g. 'my_spectrum_rt2795.1 5.dta' -raw:ms_level <num> If 1 or higher, this number is assigned to spectra as the MS level. This opti on is useful for DTA files which do not contain MS level information. (defaul t: '0') 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: