Galaxy |

matchms convert (version 0.27.0+galaxy0)

Spectra file:

Mass spectral library file to convert.

Harmonization metadata:

Apply metadata harmonization, parsing certain keys required by additional filters or initializing other attributes. The default is True.

Spectral library format:

Output format to convert the spectral library into.

Export peak comments:

Retain peak comments from individual peaks after the respective mz and intensity pairs when selected.

Export style:

Converts the keys to a specific style - see [1] for details.. One of ['matchms', 'massbank', 'nist', 'riken', 'gnps']. Default is 'matchms'.

Description

Mass spectral libraries are often stored in various formats, such as msp, mgf or json. This tool can be used to convert from one library format to another. Some of the metadata keywords might change during the conversion process, as they are harmonized internally with matchms.

Footnotes

[1] Export styles - see this table for supported key conversions and detailed description of the export styles.

Documentation

The Python library matchms provides functions to convert, filter and compare mass spectrometry data. For an overview of the different galaxy modules, see the figure below. For detailed documentation on the tool, see https://github.com/matchms/matchms/blob/master/README.rst and https://matchms.readthedocs.io/en/latest/ for the Python API.

Overview