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DBExporter

Extracts MS data from a OpenMS database.

Deprecated:
Deprecated in OpenMS 1.9

[Tool is no longer supported and will be removed in OpenMS 2.0]

Extracts arbitrary MS data (MS, LC-MS, MS/MS) from a OpenMS database. A single dataset can be exported by giving one id contained in the 'MSExperiment' table. A query that returns several ids of the 'MSExperiment' table can be used to export several datasets at a time.

If only one dataset is exported, it is stored with the given name. If several datasets are exported, the given name is prefixed with the DB id and an underscore.

In order to create a new OpenMS database, use the DBImporter.

The command line parameters of this tool are:

DBExporter -- Exports data from an OpenMS database to a file.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  DBExporter <options>

Options (mandatory options marked with '*'):
  -user <user>*          User/login of the DB
  -host <host>           Host name of the DB server (default: 'localhost')
  -password <password>*  Password for the user
  -port <port>           Port the DB server is running on (default: '3306')
  -db <name>*            DB name
  -id <DB id>            Id of the the map to export (default: '0')
  -query <query>         A SQL query that returns one or several DB ids of the MSExperiment table
  -out <file>*           Output file in mzML format (prefixed with DB id and '_' if several files are exporte
                         d)
                         
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
+DBExporterExports data from an OpenMS database to a file.
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'DBExporter'
user user/login of the DB
hostlocalhost host name of the DB server
password password for the user
port3306 port the DB server is running on
db DB name
id0 id of the the map to export
query a SQL query that returns one or several DB ids of the MSExperiment table
out output file in mzML format (prefixed with DB id and '_' if several files are exported)
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