Positional Argument Matching and Parameter Defaults

[DarioS]

Is it possible to specify the value of tol without explicitly specifying all of the parameters preceding it (i.e. StartOrEnd, numProcessors, instrumentType) when they have suitable defaults? It might be more robust to have options specified like --numProcessors 8 instead of depending on the position in the command.

There also doesn't appear to be any option to change the retention time window, which, according to the journal article, "... can be omitted or adjusted by the user." - at least not that I can see in the user guide.

[rpeckner-broad]

At this point the only way to change the retention time window would be to directly modify the code, but I will work on getting that to be an optional parameter, as well as including other optional flags as you suggest.