Match parameters between GUI and peakdetector CLI

[PMSeitzer]

May be as simple as modifying the R pipeline script appropriately.

[Progress109]

Currently I am only able to edit/change the following 22 parameters in the CLI:
slices / peak picking
"-e" = "E", # mz slice determination algorithm (most up-to-date slicing algorithm)
"-r" = 10, # of scans used in RT step size computation for mass slicing.
"-n" = 100, # Maximum number of peak groups to pick out a single EIC.
"-y" = 5, #EIC Smoothing Window size - in # scans
"-7" = 5, # baseline smoothing window size.
"-8" = 60, # percentile of observed intensity values to exclude for baseline calculation
"--peakRtBoundsSlopeThreshold" = 0, # Define edges of peaks based on flattening out of trace, to this slope.
"--peakRtBoundsMaxIntensityFraction" = 0, # Define edges of peaks based on intensity reaching this proportion of max. -1 if unused.

peak grouping
"-f" = "E", # peak grouping algorithm (most up-to-date peak grouping algorithm)
"-g" = 0.25, # Max distance in RT from sample peak to merged EIC peak to include sample peak.
"-b" = 1, # Minimum number of peaks in a group considered "good" to retain peak group
"-i" = 1000, # Minimum raw intensity for tallest peak in peak group to retain peak group.
"-q" = 0.5, # Minimum quality score value for highest-quality peak in peak group to retain peak group.
"-u" = 0.8, # Merge peak group if this proportion of RT range (or more) of two groups is shared.
"-z" = 5, # Minimum Signal:Baseline ratio value for highest Signal:Baseline peak in peak group to retain peak group.
"--mergedPeakRtBoundsSlopeThreshold" = 0, # Merged EIC peak edge detection criteria.
"--mergedPeakRtBoundsMaxIntensityFraction" = 0, # Criteria to determine edge of smoothed bounds.
"--mergedSmoothedMaxToBoundsMinRatio" = 0, # Retain peak group associated with merged EIC peak by sufficient max to bounds ratio.
"--mergedSmoothedMaxToBoundsIntensityPolicy" = "MEDIAN", # Approach for calculating max to bounds ratios. Either "MEDIAN", "MAXIMUM", or "MINIMUM".

searches
"-1" = "", # MSP file for mzkitchen compound search.
"-0" = "", # mzkitchen search type. "metaboliteSearch" or "lipidSearch"
"-9" = "", # mzkitchen search parameters

other
"-a" = 0 # align samples flag.

However, in the GUI I can count at least 34 parameter options that can be modified. It is tricky match the parameters in the command line to those in the GUI since their names/descriptions differ. I think the best first step is maybe to match them by the name they have in the GUI and then this will help identify which are missing?

[PMSeitzer]

Some parameters are not being respected in the GUI.
Some parameters are not being saved properly in the encoded information block.

[PMSeitzer]

Some bugs associated with inconsistencies between the maven gui and peakdetector were added as a result of #606

[PMSeitzer]

Note bug in determination of monisotopes:

#748

[PMSeitzer]

I was finally able to sync the parameters between the GUI and peakdetector, though this required fixing some bugs in the MAVEN GUI, specifically:

1. MAVEN Search was not filtering out peak groups that had 0 MS2s associated with them.
2. Parameters were not displaying correctly in Maven.
3. IDisRequireMatchingAdduct was not being set based on the match adduct check box.
4. Removed malfunctioning 'Require Monoisotopic' option from peaks dialog.
5. Avoid bug Peak Grouping Depends on Order of samples #749, dependence on order of samples in peak grouping, by sorting samples by natural order prior to peak grouping.