Calculates basic quality parameters from MS experiments and compiles data for subsequent QC into a qcML file.

pot. predecessor tools	$\longrightarrow$ QCCalculator $\longrightarrow$	pot. successor tools
FeatureFinderCentroided		QCMerger
XTandemAdapter		QCExporter

The calculated quality parameters or data compiled as attachments for easy plotting input include file origin, spectra distribution, aquisition details, ion current stability ( & TIC ), id accuracy statistics and feature statistics. The MS experiments base name is used as name to the qcML element that is comprising all quality parameter values for the given run (including the given downstream analysis data).

id produces quality parameter values for the identification file; this file should contain either only the final psm to each spectrum (1 PeptideHit per identified spectrum) or have the PeptideHits sorted to 'best' first, where 'best' depends on the use case.
feature produces quality parameter values for the feature file; this file can be either mapped or unmapped, the latter reulting in less metrics available.
consensus produces quality parameter values for the consensus file; some quality parameter calculation are only available if both feature and ids are given.
remove_duplicate_features only needed when you work with a set of merged features. Then considers duplicate features only once.

Output is in qcML format (see parameter out) which can be viewed directly in a modern browser (chromium, firefox, safari).

Note: Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

QCCalculator -- Calculates basic quality parameters from MS experiments and subsequent analysis data as ident
ification or feature detection.
Full documentation: http://www.openms.de/documentation/UTILS_QCCalculator.html
Version: 2.5.0-nightly-2020-03-06 Mar  7 2020, 01:22:16, Revision: 84b1398
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.
To cite QCCalculator:
  Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P,  Martens, L. qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments. Molecular & Cellular Proteomics 2014; 13(8). doi:10.1074/mcp.M113.035907.

Usage:
  QCCalculator <options>

Options (mandatory options marked with '*'):
  -in <file>*                  Raw data input file (this is relevant if you want to look at MS1, MS2 and prec
                               ursor peak information) (valid formats: 'mzML')
  -out <file>*                 Your qcML file. (valid formats: 'qcML')
  -id <file>                   Input idXML file containing the identifications. Your identifications will be 
                               exported in an easy-to-read format (valid formats: 'idXML')
  -feature <file>              Feature input file (this is relevant for most QC issues) (valid formats: 'feat
                               ureXML')
  -consensus <file>            Consensus input file (this is only used for charge state deconvoluted output. 
                               Use the consensusXML output form the DeCharger) (valid formats: 'consensusXML'
                               )
  -remove_duplicate_features   This flag should be set, if you work with a set of merged features.
                               
Common UTIL 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

+QCCalculatorCalculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.

version2.5.0-nightly-2020-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'QCCalculator'

in raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)input file*.mzML

out Your qcML file.output file*.qcML

id Input idXML file containing the identifications. Your identifications will be exported in an easy-to-read formatinput file*.idXML

feature feature input file (this is relevant for most QC issues)input file*.featureXML

consensus consensus input file (this is only used for charge state deconvoluted output. Use the consensusXML output form the DeCharger)input file*.consensusXML

remove_duplicate_featuresfalse This flag should be set, if you work with a set of merged features.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