OpenMS
QCEmbedder

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:

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: 3.2.0-pre-nightly-2024-07-19 Jul 20 2024, 02:06:43, Revision: f10e72e
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry 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 leas
                        t 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 form
                        ats: '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.
version3.2.0-pre-nightly-2024-07-19 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