QCImporter

Will import several quality parameter from a tabular (text) format into a qcML file - counterpart to QCExporter.

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 parameter (qp) to runs or sets, or even new runs, these can be imported into the qcML file. For an example see the examples in the share directory.

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.
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.

The command line parameters of this tool are:

QCImporter -- Imports tables with quality control parameters into qcml files.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

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. (csv
                     without "!) (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. (csv without "!) (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.

version2.3.0 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. (csv without "!)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. (csv without "!)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 Overwrite tool specific checks.true,false

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