FileMerger

Merges several MS files into one file.

Web Documentation for FileMerger

Options

version
Version of the tool that generated this parameters file.
in_type
Input file type (default: determined from file extension or content)
annotate_file_origin
Store the original filename in each feature using meta value "file_origin" (for featureXML and consensusXML only).
append_method
(ConsensusXML-only) Append quantitative information about features row-wise or column-wise. - 'append_rows' is usually used when the inputs come from the same MS run (e.g. caused by manual splitting or multiple algorithms on the same file) - 'append_cols' when you want to combine consensusXMLs from e.g. different fractions to be summarized in ProteinQuantifier or jointly exported with MzTabExporter.
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)
gap
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.
rt_auto
Assign retention times automatically (integers starting at 1)
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 input files.
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_rt2795.15.dta'
ms_level
If 1 or higher, this number is assigned to spectra as the MS level. This option is useful for DTA files which do not contain MS level information.

Input Ports

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Input files separated by blank [mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML,fasta]

Output Ports

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Output file [mzML,featureXML,consensusXML,traML,fasta]
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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. [trafoXML]

Views

FileMerger Std Output
The text sent to standard out during the execution of FileMerger.
FileMerger Error Output
The text sent to standard error during the execution of FileMerger. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

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Further Links

Developers

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