| OpenMS 2.5.0

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/documentation/UTILS_QCEmbedder.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    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 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 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
+QCEmbedder Attaches a table or an image to a given qc parameter.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'QCEmbedder'
in Input qcml file input 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 file output file*.qcML
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false