output, results

Syntax

The value of this parameter is an ASCII string, with three possible values: all, valid, and stochastic

Notes

1. No error message is generated by an invalid value for this parameter.
2. The default value for this parameter is valid

Description

The value for this parameter determines which results are written to the output file at the end of a modelling session. The three possible values cover the most interesting use cases for X! TANDEM, from a bioinformatics perspective. The exact form of the reported results will depend on the values chosen for other output parameters.

1. all - When this value is set, results are reported for all of the spectra that were used in the modelling session. This value is not recommended for normal use, as most spectra in a large data set will not return useful results. Storing the large volume of purely stochastic matches that can results is a waste of resources, for most users.
2. valid - When this value is set, results that have an expectation value less than output, maximum valid expectation value are reported. This setting is of the most general use.
3. stochastic - When this value is set, results that have an expectation value greater than output, maximum valid expectation value are all reported. This is the compliment to the valid set, and it can be useful for debugging and bioinformatics purposes.