comparison test-data/mysettings_galaxy.ini @ 0:0b28816c1c2c draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
author recetox
date Thu, 18 May 2023 13:01:04 +0000
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1 # Sample configuration file for RMassBank.
2 # Adapt this file to your needs.
3 # NOTE: Do not indent with TAB characters! Use only spaces.
4 # (If your editor converts TAB to a certain number of spaces, it's OK.)
5 # Use a space after the colon.
6
7 # Deprofile input data?
8 # Leave empty if input data is already in "centroid" mode.
9 # Use values deprofile.spline, deprofile.fwhm or deprofile.localMax to convert the input data with the
10 # corresponding algorithm. See ?deprofile
11 deprofile:
12
13 # Deviation (in minutes) allowed the for retention time
14 rtMargin: 0.4
15 # Systematic retention time shift
16 rtShift: 0.0
17
18 # Directory to OpenBabel. Required for creating molfiles for MassBank export.
19 # If no OpenBabel directory is given, RMassBank will attempt to use the CACTUS webservice
20 # for SDF generation. You really should install OpenBabel though; the CACTUS structures
21 # have explicit hydrogen atoms...
22 # Points to the directory where babel.exe (or the Linux "babel" equivalent) lies.
23 babeldir: '/home/debian/galaxy/database/dependencies/_conda/envs/mulled-v1-43859fe15e1521a7d623c43fc3f4525ebe6dbf17b1890fad8281284c7ee7581a/bin/'
24
25 # Which MassBank record version to use; version 2 is advised.
26 use_version: 2
27
28 # Include reanalyzed peaks?
29 use_rean_peaks: TRUE
30
31 # annotate the spectra files with (putative) molecular formulas for fragments?
32 add_annotation: TRUE
33
34 # Annotations for the spectrum:
35 annotations:
36 # Author etc. annotation
37 authors: Nomen Nescio, The Unseen University
38 copyright: Copyright (C) XXX
39 publication:
40 license: CC BY
41 instrument: LTQ Orbitrap XL Thermo Scientific
42 instrument_type: LC-ESI-ITFT
43 confidence_comment: standard compound
44 compound_class: N/A; Environmental Standard
45 internal_id_fieldname: INTERNAL_ID
46 #
47 # HPLC annotations:
48 #
49 # 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
50 lc_gradient:
51 # example: lc_flow: 200 uL/min
52 lc_flow:
53 # example: lc_solvent_a: water with 0.1% formic acid
54 lc_solvent_a:
55 lc_solvent_b:
56 # example: lc_column: XBridge C18 3.5um, 2.1x50mm, Waters
57 lc_column:
58 # Prefix for MassBank accession IDs
59 entry_prefix: XX
60 ms_type: MS2
61 ionization: ESI
62 ms_dataprocessing:
63 RECALIBRATE: loess on assigned fragments and MS1
64
65 include_sp_tags: FALSE
66
67 # Annotator:
68 # by default, "annotator.default" is used.
69 # If you want to build your custom annotator (check ?annotator.default and the source code),
70 # select it here by using e.g.
71 # annotator: annotator.myown
72 # for a function annotator.myown(annotation)
73
74 # List of data-dependent scans in their order (relative to the parent scan), for annotation of the MassBank records
75 # For every data-dependent scan event, specify an element with:
76 # mode: fragmentation mode, e.g. CID
77 # ces: "short" format collision energy (for record title)
78 # ce: "long" format collision energy (for annotation field)
79 # res: FT resolution
80 spectraList:
81 # First scan: CID 35% NCE, resolution 7500
82 - mode: CID
83 ces: 35%
84 ce: 35 % (nominal)
85 res: 7500
86 # Second scan: HCD 15% NCE, resolution 7500
87 - mode: HCD
88 ces: 15%
89 ce: 15 % (nominal)
90 res: 7500
91 # Third scan, etc.
92 - mode: HCD
93 ces: 30%
94 ce: 30 % (nominal)
95 res: 7500
96 - mode: HCD
97 ces: 45%
98 ce: 45 % (nominal)
99 res: 7500
100 - mode: HCD
101 ces: 60%
102 ce: 60 % (nominal)
103 res: 7500
104 - mode: HCD
105 ces: 75%
106 ce: 75 % (nominal)
107 res: 7500
108 - mode: HCD
109 ces: 90%
110 ce: 90 % (nominal)
111 res: 7500
112 - mode: HCD
113 ces: 15%
114 ce: 15 % (nominal)
115 res: 15000
116 - mode: HCD
117 ces: 30%
118 ce: 30 % (nominal)
119 res: 15000
120 - mode: HCD
121 ces: 45%
122 ce: 45 % (nominal)
123 res: 15000
124 - mode: HCD
125 ces: 60%
126 ce: 60 % (nominal)
127 res: 15000
128 - mode: HCD
129 ces: 75%
130 ce: 75 % (nominal)
131 res: 15000
132 - mode: HCD
133 ces: 90%
134 ce: 90 % (nominal)
135 res: 15000
136 - mode: CID
137 ces: 35%
138 ce: 35 % (nominal)
139 res: 15000
140
141 # Shifts of the starting points for RMassBank accession numbers.
142 # Change these if you measure different adducts
143 accessionNumberShifts:
144 pH: 0 # [M+H]+: Accession numbers 1-14
145 pM: 16 # [M]+: 17-30
146 pNa: 32 # [M+Na]+: 33-46
147 mH: 50 # [M-H]-: 51-64
148 mFA: 66 # [M+FA]-: 67-80
149
150 # A list of known electronic noise peaks
151 electronicNoise:
152 - 189.825
153 - 201.725
154 - 196.875
155 # Exclusion width of electronic noise peaks (from unmatched peaks, prior to
156 # reanalysis)
157 electronicNoiseWidth: 0.3
158
159 # recalibration settings:
160 # recalibrate by: dppm or dmz
161 recalibrateBy: dppm
162
163 # recalibrate MS1:
164 # separately (separate)
165 # with common curve (common)
166 # do not recalibrate (none)
167 recalibrateMS1: common
168 # Window width to look for MS1 peaks to recalibrate (in ppm)
169 recalibrateMS1Window: 15
170
171 # Custom recalibration function: You can overwrite the recal function by
172 # making any function which takes rcdata$recalfield ~ rcdata$mzFound.
173 # The settings define which recal function is used.
174 # Note: if recalibrateMS1 is "common", the setting "recalibrator: MS1" is meaningless
175 # because the MS1 points will be recalibrated together with the MS2 points with
176 # the MS2 recalibration function.
177 recalibrator:
178 MS1: recalibrate.loess
179 MS2: recalibrate.loess
180
181 # Define the multiplicity filtering level
182 # Default is 2 (peak occurs at least twice)
183 # Set this to 1 if you want to turn this option off.
184 # Set this to anything > 2 if you want harder filtering
185 multiplicityFilter: 2
186
187 # Define the title format.
188 # You can use all entries from MassBank records as tokens
189 # plus the additional token RECORD_TITLE_CE, which is a shortened
190 # version of the collision energy specifically for use in the title.
191 # Every line is one entry and must have one token in curly brackets
192 # e.g. {CH$NAME} or {AC$MASS_SPECTROMETRY: MS_TYPE} plus optionally
193 # additional text in front or behind e.g.
194 # R={AC$MASS_SPECTROMETRY: RESOLUTION}
195 # If this is not specified, it defaults to a title of the format
196 # "Dinotefuran; LC-ESI-QFT; MS2; CE: 35%; R=35000; [M+H]+"
197 # Note how everything must be in "" here because otherwise the : are getting mangled!
198 titleFormat:
199 - "{CH$NAME}"
200 - "{AC$INSTRUMENT_TYPE}"
201 - "{AC$MASS_SPECTROMETRY: MS_TYPE}"
202 - "CE: {RECORD_TITLE_CE}"
203 - "R={AC$MASS_SPECTROMETRY: RESOLUTION}"
204 - "{MS$FOCUSED_ION: PRECURSOR_TYPE}"
205
206 # Define filter settings.
207 # For Orbitrap, settings of 15 ppm in low mass range, 10 ppm in high
208 # mass range, m/z = 120 as mass range division and 5 ppm for recalibrated
209 # data overall are recommended.
210 filterSettings:
211 ppmHighMass: 10
212 ppmLowMass: 15
213 massRangeDivision: 120
214 ppmFine: 5
215 prelimCut: 1000
216 prelimCutRatio: 0.0
217 fineCut: 0.0
218 fineCutRatio: 0.0
219 specOkLimit: 1000
220 dbeMinLimit: -0.5
221 satelliteMzLimit: 0.5
222 satelliteIntLimit: 0.05
223
224 # Define raw MS retrieval settings.
225 findMsMsRawSettings:
226 ppmFine: 5
227 mzCoarse: 0.5
228 # fillPrecursorScan is FALSE for "good" mzML files which have all the info needed.
229 # However, for example AB Sciex files will have missing precursor scan information,
230 # in which case fillPrecursorScan = TRUE is needed. Try it out.
231 fillPrecursorScan: FALSE
232
233 # Select how to treat unknown compound masses:
234 # "charged" (the default, also if no option set) treats unknown (level 5) compound masses as the m/z,
235 # "neutral" treats unknown (level 5) compound masses as the neutral mass and applies [M+H]+ and [M-H]- calculations accordingly.
236 unknownMass: charged