diff mysettings.ini @ 0:0b28816c1c2c draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8

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+# Sample configuration file for RMassBank.
+# Adapt this file to your needs.
+# NOTE: Do not indent with TAB characters! Use only spaces.
+# (If your editor converts TAB to a certain number of spaces, it's OK.)
+# Use a space after the colon.
+
+# Deprofile input data?
+# Leave empty if input data is already in "centroid" mode.
+# Use values deprofile.spline, deprofile.fwhm or deprofile.localMax to convert the input data with the
+# corresponding algorithm. See ?deprofile
+deprofile: 
+
+# Deviation (in minutes) allowed the for retention time
+rtMargin: 0.4
+# Systematic retention time shift
+rtShift: 0.0
+
+# Directory to OpenBabel. Required for creating molfiles for MassBank export.
+# If no OpenBabel directory is given, RMassBank will attempt to use the CACTUS webservice
+# for SDF generation. You really should install OpenBabel though; the CACTUS structures
+# have explicit hydrogen atoms...
+# Points to the directory where babel.exe (or the Linux "babel" equivalent) lies.
+babeldir:
+
+# Which MassBank record version to use; version 2 is advised.
+use_version: 2
+
+# Include reanalyzed peaks?
+use_rean_peaks: TRUE
+
+# annotate the spectra files with (putative) molecular formulas for fragments?
+add_annotation: TRUE
+
+# Annotations for the spectrum:
+annotations:
+    # Author etc. annotation
+    authors: Nomen Nescio, The Unseen University
+    copyright: Copyright (C) XXX
+    publication: 
+    license: CC BY
+    instrument: LTQ Orbitrap XL Thermo Scientific
+    instrument_type: LC-ESI-ITFT
+    confidence_comment: standard compound
+    compound_class: N/A; Environmental Standard
+    internal_id_fieldname: INTERNAL_ID
+    #
+    # HPLC annotations:
+    #
+    # example: lc_gradient: 90/10 at 0 min, 50/50 at 4 min, 5/95 at 17 min, 5/95 at 25 min, 90/10 at 25.1 min, 90/10 at 30 min
+    lc_gradient: 
+    # example: lc_flow: 200 uL/min
+    lc_flow: 
+    # example: lc_solvent_a: water with 0.1% formic acid
+    lc_solvent_a: 
+    lc_solvent_b: 
+    # example: lc_column: XBridge C18 3.5um, 2.1x50mm, Waters
+    lc_column: 
+    # Prefix for MassBank accession IDs
+    entry_prefix: XX
+    ms_type: MS2
+    ionization: ESI
+    ms_dataprocessing:
+        RECALIBRATE: loess on assigned fragments and MS1
+
+include_sp_tags: FALSE
+
+# Annotator:
+# by default, "annotator.default" is used.
+# If you want to build your custom annotator (check ?annotator.default and the source code),
+# select it here by using e.g.
+# annotator: annotator.myown
+# for a function annotator.myown(annotation)
+
+# List of data-dependent scans in their order (relative to the parent scan), for annotation of the MassBank records
+# For every data-dependent scan event, specify an element with:
+# mode: fragmentation mode, e.g. CID
+# ces: "short" format collision energy (for record title)
+# ce: "long" format collision energy (for annotation field)
+# res: FT resolution
+spectraList:
+ # First scan: CID 35% NCE, resolution 7500 
+- mode: CID
+  ces: 35%
+  ce: 35 % (nominal)
+  res: 7500
+ # Second scan: HCD 15% NCE, resolution 7500
+- mode: HCD
+  ces: 15%
+  ce: 15 % (nominal)
+  res: 7500
+ # Third scan, etc.
+- mode: HCD
+  ces: 30%
+  ce: 30 % (nominal)
+  res: 7500
+- mode: HCD
+  ces: 45%
+  ce: 45 % (nominal)
+  res: 7500
+- mode: HCD
+  ces: 60%
+  ce: 60 % (nominal)
+  res: 7500
+- mode: HCD
+  ces: 75%
+  ce: 75 % (nominal)
+  res: 7500
+- mode: HCD
+  ces: 90%
+  ce: 90 % (nominal)
+  res: 7500
+- mode: HCD
+  ces: 15%
+  ce: 15 % (nominal)
+  res: 15000
+- mode: HCD
+  ces: 30%
+  ce: 30 % (nominal)
+  res: 15000
+- mode: HCD
+  ces: 45%
+  ce: 45 % (nominal)
+  res: 15000
+- mode: HCD
+  ces: 60%
+  ce: 60 % (nominal)
+  res: 15000
+- mode: HCD
+  ces: 75%
+  ce: 75 % (nominal)
+  res: 15000
+- mode: HCD
+  ces: 90%
+  ce: 90 % (nominal)
+  res: 15000
+- mode: CID
+  ces: 35%
+  ce: 35 % (nominal)
+  res: 15000
+
+# Shifts of the starting points for RMassBank accession numbers.
+# Change these if you measure different adducts 
+accessionNumberShifts:
+    pH: 0 # [M+H]+: Accession numbers 1-14
+    pM: 16 # [M]+: 17-30
+    pNa: 32 # [M+Na]+: 33-46
+    mH: 50 # [M-H]-: 51-64
+    mFA: 66 # [M+FA]-: 67-80
+
+# A list of known electronic noise peaks
+electronicNoise:
+- 189.825
+- 201.725
+- 196.875
+# Exclusion width of electronic noise peaks (from unmatched peaks, prior to
+# reanalysis)
+electronicNoiseWidth: 0.3
+
+# recalibration settings:
+# recalibrate by: dppm or dmz
+recalibrateBy: dppm
+
+# recalibrate MS1:
+# separately (separate)
+# with common curve (common)
+# do not recalibrate (none)
+recalibrateMS1: common
+# Window width to look for MS1 peaks to recalibrate (in ppm)
+recalibrateMS1Window: 15
+
+# Custom recalibration function: You can overwrite the recal function by
+# making any function which takes rcdata$recalfield ~ rcdata$mzFound.
+# The settings define which recal function is used.
+# Note: if recalibrateMS1 is "common", the setting "recalibrator: MS1" is meaningless
+# because the MS1 points will be recalibrated together with the MS2 points with 
+# the MS2 recalibration function.
+recalibrator:
+    MS1: recalibrate.loess
+    MS2: recalibrate.loess
+
+# Define the multiplicity filtering level
+# Default is 2 (peak occurs at least twice)
+# Set this to 1 if you want to turn this option off.
+# Set this to anything > 2 if you want harder filtering
+multiplicityFilter: 2
+
+# Define the title format.
+# You can use all entries from MassBank records as tokens
+# plus the additional token RECORD_TITLE_CE, which is a shortened
+# version of the collision energy specifically for use in the title.
+# Every line is one entry and must have one token in curly brackets
+# e.g. {CH$NAME} or {AC$MASS_SPECTROMETRY: MS_TYPE} plus optionally
+# additional text in front or behind e.g.
+# R={AC$MASS_SPECTROMETRY: RESOLUTION}
+# If this is not specified, it defaults to a title of the format
+# "Dinotefuran; LC-ESI-QFT; MS2; CE: 35%; R=35000; [M+H]+"
+# Note how everything must be in "" here because otherwise the : are getting mangled!
+titleFormat:
+- "{CH$NAME}"
+- "{AC$INSTRUMENT_TYPE}"
+- "{AC$MASS_SPECTROMETRY: MS_TYPE}"
+- "CE: {RECORD_TITLE_CE}"
+- "R={AC$MASS_SPECTROMETRY: RESOLUTION}"
+- "{MS$FOCUSED_ION: PRECURSOR_TYPE}"
+
+# Define filter settings.
+# For Orbitrap, settings of 15 ppm in low mass range, 10 ppm in high
+# mass range, m/z = 120 as mass range division and 5 ppm for recalibrated
+# data overall are recommended. 
+filterSettings:
+    ppmHighMass: 10
+    ppmLowMass: 15
+    massRangeDivision: 120
+    ppmFine: 5
+    prelimCut: 1000
+    prelimCutRatio: 0
+    fineCut: 0
+    fineCutRatio: 0
+    specOkLimit: 1000
+    dbeMinLimit: -0.5
+    satelliteMzLimit: 0.5
+    satelliteIntLimit: 0.05
+    
+ # Define raw MS retrieval settings.
+findMsMsRawSettings:
+    ppmFine: 10
+    mzCoarse: 0.5
+    # fillPrecursorScan is FALSE for "good" mzML files which have all the info needed.
+    # However, for example AB Sciex files will have missing precursor scan information,
+    # in which case fillPrecursorScan = TRUE is needed. Try it out.
+    fillPrecursorScan: FALSE
+    
+# Select how to treat unknown compound masses: 
+# "charged" (the default, also if no option set) treats unknown (level 5) compound masses as the m/z,
+# "neutral" treats unknown (level 5) compound masses as the neutral mass and applies [M+H]+ and [M-H]- calculations accordingly.
+unknownMass: charged