OpenMS
2.6.0
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Extracts a table attachment of a given quality parameter from a qcML file as tabular (text) format.
pot. predecessor tools | QCExtractor | pot. successor tools |
QCEmbedder | ||
QCShrinker |
If there is a table attached to a given qp that is needed as a single file, e.g. for easy input to plotting software, this can be extracted to a tabular (text) format.
qp
defines the qp name to which the table is attached;run
the file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name.name
if no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given.set/run
if the target qp is contained in a set, this has to be set here;Output is in csv format (see parameter out_csv
) which can be easily parsed by many programs.
The command line parameters of this tool are:
QCExtractor -- Extracts a table attachment to a given qc parameter. Full documentation: http://www.openms.de/documentation/UTILS_QCExtractor.html Version: 2.6.0 Sep 30 2020, 12:54:34, Revision: c26f752 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 QCExtractor: 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: QCExtractor <options> Options (mandatory options marked with '*'): -in <file>* Input qcml file (valid formats: 'qcML') -qp <string>* Target attachment qp. -run <file> The file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name. (valid form ats: 'mzML') -name <string> If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given. -out_csv <file>* Output csv formatted table. (valid formats: 'csv') 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: