OpenMS
2.6.0
|
This application is used to remove extra verbose table attachments from a qcML file that are not needed anymore, e.g. for a final report.
pot. predecessor tools | QCShrinker | pot. successor tools |
QCMerger | ||
... |
If there is a lot of verbose or deprecated information in the given qcml file at in
that can be purged.
qp_accessions
A list of cv accessions that should be removed. If empty, the usual suspects will be removed.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;Output is in qcML format (see parameter out
) which can be viewed directly in a modern browser (chromium, firefox, safari).
The command line parameters of this tool are:
QCShrinker -- This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report. Full documentation: http://www.openms.de/documentation/UTILS_QCShrinker.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 QCShrinker: 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: QCShrinker <options> Options (mandatory options marked with '*'): -in <file>* Input qcml file (valid formats: 'qcML') -qp_accessions <names> A list of cv accessions that should be removed. If empty, the usual suspects will be removed! -name <string> The name of the target run or set that contains the requested quality parameter. -run <file> The file from which the name of the target run that contains the requested quality parameter is taken. This overrides the name parameter! (valid formats: 'mzML') -out <file>* Output extended/reduced qcML file (valid formats: 'qcML') 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: