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sirius-ms / sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
GNU Affero General Public License v3.0
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Specifying enforced elements in .ms file #31

Closed pleeferguson closed 3 years ago

pleeferguson commented 3 years ago

Hi, I would like to run the Sirius CLI in batch mode so that I can avoid having to call a new JVM for every formula calculation I am doing, but I need to be able to set different enforced elements for each individual spectrum input. I cannot seem to make this work within the .ms file format. I can of course use the -E flag within the CLI arguments, but then the same elemental alphabet will be applied across all calculations. However, when I specify >elementswithin the .ms files, the elemental alphabet seems to be treated analogous to the CLI argument -e (elements considered).

Perhaps I'm missing a feature? Please let me know if this is possible or if it could be implemented.

kaibioinfo commented 3 years ago

Hi Lee,

you can specify the enforced elements with >FormulaSettings.enforced C,H,N,O,P,S,Cl,Br,I

In fact, you can set all kind of config options this way. A list of all available config options can be found in /.sirius-4.7/custom.config

pleeferguson commented 3 years ago

This works perfectly. Thanks for the quick reply, Kai!

mfleisch commented 3 years ago

Just for completion:

sirius config -h

should give you the list of possible parameters from the command line.