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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author | recetox |
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date | Thu, 12 Oct 2023 13:31:44 +0000 |
parents | 0b28816c1c2c |
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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: '/home/debian/galaxy/database/dependencies/_conda/envs/mulled-v1-43859fe15e1521a7d623c43fc3f4525ebe6dbf17b1890fad8281284c7ee7581a/bin/' # 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: 0.0 fineCut: 0.0 fineCutRatio: 0.0 specOkLimit: 1000 dbeMinLimit: -0.5 satelliteMzLimit: 0.5 satelliteIntLimit: 0.05 # Define raw MS retrieval settings. findMsMsRawSettings: ppmFine: 5 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