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. Version: 2.3.0 Jan 9 2018, 17:46:23, Revision: 38ae115 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:
OpenMS / TOPP release 2.3.0 | Documentation generated on Tue Jan 9 2018 18:22:06 using doxygen 1.8.13 |