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Conversion between OpenMS XML formats and text formats

Export of OpenMS XML formats

As TOPP offers no functionality for statistical analysis, this step is normally done using external statistics packages.
@n In order to export the %OpenMS XML formats into an appropriate format for these packages the
TOPP @b TextExporter can be used.

It converts the the following %OpenMS XML formats to text files:
- FeatureXML
- IdXML
- ConsensusXML

The use of the @b TextExporter is very simple:
TextExporter -in infile.idXML -out outfile.txt

Import of feature data to OpenMS

%OpenMS offers a lot of visualization and analysis functionality for feature data.
@n Feature data in text format, e.g. from other analysis tools, can be imported using the @b TextImporter. The default mode accepts comma separated values
containing the following columns: RT, m/z, intensity. Additionally meta data columns may follow. If meta data is used, meta data column names have to be specified in a header line.
Without headers:
1201  503.123 1435000
1201  1006.246  1235200

Or with headers:

RT  m/z Int isHeavy myMeta
1201  503.123 1435000 true  2
1201  1006.246  1235200 maybe 1

Example invocation:

TextImporter -in infile.txt -out outfile.featureXML

The tool also supports data from msInspect,SpecArray and Kroenik(Hardkloer sibling), just specify the -mode option accordingly.

Import of protein/peptide identification data to OpenMS

Peptide/protein identification data from several identification engines can be converted to idXML format using the @b IDFileConverter tool.

It can currently read the following formats:
- Sequest output folder
- pepXML file
- idXML file

It can currently write the folling formats:
- pepXML
- idXML

This example shows how to convert pepXML to idXML:
IDFileConverter -in infile.pepXML -out outfile.idXML

OpenMS / TOPP release 1.9.0 Documentation generated on Tue May 28 2013 12:41:58 using doxygen 1.8.3.1