Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
FileFilter

Extracts portions of the data from an mzML, featureXML or consensusXML file.

pot. predecessor tools $ \longrightarrow $ FileFilter $ \longrightarrow $ pot. successor tools
any tool yielding output
in mzML, featureXML
or consensusXML format

any tool that profits on reduced input

With this tool it is possible to extract m/z, retention time and intensity ranges from an input file and to write all data that lies within the given ranges to an output file.

Depending on the input file type, additional specific operations are possible:

The priority of the id-flags is (decreasing order): remove_annotated_features / remove_unannotated_features -> remove_clashes -> keep_best_score_id -> sequences_whitelist / accessions_whitelist

MS2 and higher spectra can be filtered according to precursor m/z (see 'pc_mz'). This flag can be combined with 'rt' range to filter precursors by RT and m/z. If you want to extract an MS1 region with untouched MS2 spectra included, you will need to split the dataset by MS level and use 'mz' option for MS1 and 'pc_mz' for MS2 data. Then merge them again. RT can be filtered at any step.

The command line parameters of this tool are:

INI file documentation of this tool:

For the parameters of the S/N algorithm section see the class documentation there:
peak_options:sn

Todo:
add tests for selecting modes (port remove modes) (Andreas)

OpenMS / TOPP release 1.11.1 Documentation generated on Mon Dec 23 2013 22:47:51 using doxygen 1.8.5