This application is used to embed tables or plots generated externally as attachments to existing quality parameters in qcML files.

pot. predecessor tools	→ QCEmbedder →	pot. successor tools
QCExporter		QCMerger
XTandemAdapter		QCShrinker

If there is additional data from external tools to a certain quality parameter (qp) in the qcML file at in, it can be attached in tabluar (csv) format or as png image file. If no corresponding quality parameter is present an empty value one will be generated with the name of "default set name"/"default mzML file".

qp_att_acc defines the qp cv accession of the qp to which the table/image is attached.
cv_acc defines the cv accession of the attachment.
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.
plot if a plot image is to be attached to a qp, this has to be specified here.
table if a table is to be attached to a qp, this has to be specified here.

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:

stty: 'standard input': Inappropriate ioctl for device

QCEmbedder -- Attaches a table or an image to a given qc parameter.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_QCEmbedder.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
To cite QCEmbedder:
 + 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:
  QCEmbedder <options>

Options (mandatory options marked with '*'):
  -in <file>            Input qcml file (valid formats: 'qcML')
  -qp_att_acc <string>  Defines the qp cv accession of the qp to which the table/image is attached.
  -cv_acc <string>*     Defines the cv accession of the attachment.
  -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 formats: '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.
  -plot <file>          If a plot image is to be attached to a qp, this has to be specified here. (valid formats: 'PNG')
  -table <file>         If a table is to be attached to a qp, this has to be specified here. (valid formats: 'csv')
  -out <file>*          Output extended qcML file (valid formats: 'qcML')
                        
Common TOPP 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

+QCEmbedderAttaches a table or an image to a given qc parameter.

version3.4.0-pre-nightly-2024-12-16 Version of the tool that generated this parameters file.

++1Instance '1' section for 'QCEmbedder'

in Input qcml fileinput file*.qcML

qp_att_acc Defines the qp cv accession of the qp to which the table/image is attached.

cv_acc Defines the cv accession of the attachment.

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.input file*.mzML

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.

plot If a plot image is to be attached to a qp, this has to be specified here.input file*.PNG

table If a table is to be attached to a qp, this has to be specified here.input file*.csv

out Output extended qcML fileoutput file*.qcML

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 Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false