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QCImporter

This application is used embed tables or pictures generated externally as attachments to existing quality parameters in the targeted run/set meant to have attachments. If no quality parameter is present an empty value one will be generated with the name of "default set name"/"default mzML file".

pot. predecessor tools $ \longrightarrow $ QCEmbedder $ \longrightarrow $ pot. successor tools
QCExporter QCMerger
XTandemAdapter QCShrinker

If there is additional data from external tools in tabular format containing additional quality control parameter (qp) to runs or sets, or even new runs, in the qcml file at in it can be imported to complete the qcml file, written subsequently to out.

The command line parameters of this tool are:

QCImporter -- Imports tables with quality control parameters into qcml files.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  QCImporter <options>

Options (mandatory options marked with '*'):
  -in <file>         Input qcml file (valid formats: 'qcML')
  -table <file>*     The table containing the additional qp values in the columns. First row is considered 
                     containing the header. The target run or set names/ids are indicated by column "raw data
                     file", so each row after the header will contain the values of qps for that run. (valid
                     formats: 'csv')
  -mapping <file>*   The mapping of the table header to the according qp cvs, also in csv format. The first 
                     row is considered containing the headers as in the table. The second row is considered
                     the according qp cv accessions. (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
+QCImporterImports tables with quality control parameters into qcml files.
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'QCImporter'
in Input qcml fileinput file*.qcML
table The table containing the additional qp values in the columns. First row is considered containing the header. The target run or set names/ids are indicated by column "raw data file", so each row after the header will contain the values of qps for that run.input file*.csv
mapping The mapping of the table header to the according qp cvs, also in csv format. The first row is considered containing the headers as in the table. The second row is considered the according qp cv accessions.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
testfalse Enables the test mode (needed for internal use only)true,false

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5