annotate test-data/mysettings_galaxy.ini @ 1:c1a9c990d4b0 draft

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author recetox
date Thu, 12 Oct 2023 13:31:44 +0000
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1 # Sample configuration file for RMassBank.
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2 # Adapt this file to your needs.
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3 # NOTE: Do not indent with TAB characters! Use only spaces.
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4 # (If your editor converts TAB to a certain number of spaces, it's OK.)
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5 # Use a space after the colon.
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7 # Deprofile input data?
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8 # Leave empty if input data is already in "centroid" mode.
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9 # Use values deprofile.spline, deprofile.fwhm or deprofile.localMax to convert the input data with the
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10 # corresponding algorithm. See ?deprofile
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11 deprofile:
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13 # Deviation (in minutes) allowed the for retention time
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14 rtMargin: 0.4
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15 # Systematic retention time shift
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16 rtShift: 0.0
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18 # Directory to OpenBabel. Required for creating molfiles for MassBank export.
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19 # If no OpenBabel directory is given, RMassBank will attempt to use the CACTUS webservice
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20 # for SDF generation. You really should install OpenBabel though; the CACTUS structures
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21 # have explicit hydrogen atoms...
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22 # Points to the directory where babel.exe (or the Linux "babel" equivalent) lies.
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23 babeldir: '/home/debian/galaxy/database/dependencies/_conda/envs/mulled-v1-43859fe15e1521a7d623c43fc3f4525ebe6dbf17b1890fad8281284c7ee7581a/bin/'
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24
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25 # Which MassBank record version to use; version 2 is advised.
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26 use_version: 2
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27
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28 # Include reanalyzed peaks?
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29 use_rean_peaks: TRUE
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30
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31 # annotate the spectra files with (putative) molecular formulas for fragments?
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32 add_annotation: TRUE
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33
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34 # Annotations for the spectrum:
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35 annotations:
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36 # Author etc. annotation
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37 authors: Nomen Nescio, The Unseen University
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38 copyright: Copyright (C) XXX
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39 publication:
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40 license: CC BY
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41 instrument: LTQ Orbitrap XL Thermo Scientific
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42 instrument_type: LC-ESI-ITFT
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43 confidence_comment: standard compound
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44 compound_class: N/A; Environmental Standard
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45 internal_id_fieldname: INTERNAL_ID
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46 #
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47 # HPLC annotations:
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48 #
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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
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50 lc_gradient:
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51 # example: lc_flow: 200 uL/min
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52 lc_flow:
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53 # example: lc_solvent_a: water with 0.1% formic acid
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54 lc_solvent_a:
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55 lc_solvent_b:
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56 # example: lc_column: XBridge C18 3.5um, 2.1x50mm, Waters
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57 lc_column:
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58 # Prefix for MassBank accession IDs
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59 entry_prefix: XX
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60 ms_type: MS2
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61 ionization: ESI
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62 ms_dataprocessing:
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63 RECALIBRATE: loess on assigned fragments and MS1
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64
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65 include_sp_tags: FALSE
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66
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67 # Annotator:
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68 # by default, "annotator.default" is used.
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69 # If you want to build your custom annotator (check ?annotator.default and the source code),
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70 # select it here by using e.g.
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71 # annotator: annotator.myown
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72 # for a function annotator.myown(annotation)
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73
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74 # List of data-dependent scans in their order (relative to the parent scan), for annotation of the MassBank records
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75 # For every data-dependent scan event, specify an element with:
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76 # mode: fragmentation mode, e.g. CID
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77 # ces: "short" format collision energy (for record title)
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78 # ce: "long" format collision energy (for annotation field)
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79 # res: FT resolution
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80 spectraList:
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81 # First scan: CID 35% NCE, resolution 7500
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82 - mode: CID
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83 ces: 35%
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84 ce: 35 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
85 res: 7500
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
86 # Second scan: HCD 15% NCE, resolution 7500
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
87 - mode: HCD
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
88 ces: 15%
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
89 ce: 15 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
90 res: 7500
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
91 # Third scan, etc.
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
92 - mode: HCD
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
93 ces: 30%
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
94 ce: 30 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
95 res: 7500
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
96 - mode: HCD
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
97 ces: 45%
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
98 ce: 45 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
99 res: 7500
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
100 - mode: HCD
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
101 ces: 60%
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
102 ce: 60 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
103 res: 7500
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
104 - mode: HCD
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
105 ces: 75%
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
106 ce: 75 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
107 res: 7500
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
108 - mode: HCD
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
109 ces: 90%
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
110 ce: 90 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
111 res: 7500
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
112 - mode: HCD
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
113 ces: 15%
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
114 ce: 15 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
115 res: 15000
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
116 - mode: HCD
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
117 ces: 30%
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
118 ce: 30 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
119 res: 15000
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
120 - mode: HCD
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
121 ces: 45%
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
122 ce: 45 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
123 res: 15000
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
124 - mode: HCD
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
125 ces: 60%
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
126 ce: 60 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
127 res: 15000
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
128 - mode: HCD
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
129 ces: 75%
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
130 ce: 75 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
131 res: 15000
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
132 - mode: HCD
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
133 ces: 90%
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
134 ce: 90 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
135 res: 15000
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
136 - mode: CID
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
137 ces: 35%
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
138 ce: 35 % (nominal)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
139 res: 15000
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
140
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
141 # Shifts of the starting points for RMassBank accession numbers.
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
142 # Change these if you measure different adducts
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
143 accessionNumberShifts:
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
144 pH: 0 # [M+H]+: Accession numbers 1-14
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
145 pM: 16 # [M]+: 17-30
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
146 pNa: 32 # [M+Na]+: 33-46
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
147 mH: 50 # [M-H]-: 51-64
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
148 mFA: 66 # [M+FA]-: 67-80
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
149
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
150 # A list of known electronic noise peaks
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
151 electronicNoise:
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
152 - 189.825
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
153 - 201.725
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
154 - 196.875
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
155 # Exclusion width of electronic noise peaks (from unmatched peaks, prior to
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
156 # reanalysis)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
157 electronicNoiseWidth: 0.3
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
158
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
159 # recalibration settings:
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
160 # recalibrate by: dppm or dmz
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
161 recalibrateBy: dppm
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
162
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
163 # recalibrate MS1:
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
164 # separately (separate)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
165 # with common curve (common)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
166 # do not recalibrate (none)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
167 recalibrateMS1: common
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
168 # Window width to look for MS1 peaks to recalibrate (in ppm)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
169 recalibrateMS1Window: 15
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
170
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
171 # Custom recalibration function: You can overwrite the recal function by
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
diff changeset
172 # making any function which takes rcdata$recalfield ~ rcdata$mzFound.
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
parents:
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173 # The settings define which recal function is used.
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174 # Note: if recalibrateMS1 is "common", the setting "recalibrator: MS1" is meaningless
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175 # because the MS1 points will be recalibrated together with the MS2 points with
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176 # the MS2 recalibration function.
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177 recalibrator:
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178 MS1: recalibrate.loess
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179 MS2: recalibrate.loess
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180
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181 # Define the multiplicity filtering level
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182 # Default is 2 (peak occurs at least twice)
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183 # Set this to 1 if you want to turn this option off.
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184 # Set this to anything > 2 if you want harder filtering
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185 multiplicityFilter: 2
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186
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187 # Define the title format.
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188 # You can use all entries from MassBank records as tokens
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189 # plus the additional token RECORD_TITLE_CE, which is a shortened
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190 # version of the collision energy specifically for use in the title.
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191 # Every line is one entry and must have one token in curly brackets
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192 # e.g. {CH$NAME} or {AC$MASS_SPECTROMETRY: MS_TYPE} plus optionally
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193 # additional text in front or behind e.g.
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194 # R={AC$MASS_SPECTROMETRY: RESOLUTION}
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195 # If this is not specified, it defaults to a title of the format
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196 # "Dinotefuran; LC-ESI-QFT; MS2; CE: 35%; R=35000; [M+H]+"
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197 # Note how everything must be in "" here because otherwise the : are getting mangled!
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198 titleFormat:
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199 - "{CH$NAME}"
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200 - "{AC$INSTRUMENT_TYPE}"
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201 - "{AC$MASS_SPECTROMETRY: MS_TYPE}"
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202 - "CE: {RECORD_TITLE_CE}"
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203 - "R={AC$MASS_SPECTROMETRY: RESOLUTION}"
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204 - "{MS$FOCUSED_ION: PRECURSOR_TYPE}"
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205
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206 # Define filter settings.
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207 # For Orbitrap, settings of 15 ppm in low mass range, 10 ppm in high
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208 # mass range, m/z = 120 as mass range division and 5 ppm for recalibrated
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209 # data overall are recommended.
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210 filterSettings:
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211 ppmHighMass: 10
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212 ppmLowMass: 15
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213 massRangeDivision: 120
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214 ppmFine: 5
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215 prelimCut: 1000
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216 prelimCutRatio: 0.0
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217 fineCut: 0.0
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218 fineCutRatio: 0.0
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219 specOkLimit: 1000
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220 dbeMinLimit: -0.5
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221 satelliteMzLimit: 0.5
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222 satelliteIntLimit: 0.05
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223
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224 # Define raw MS retrieval settings.
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225 findMsMsRawSettings:
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226 ppmFine: 5
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227 mzCoarse: 0.5
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228 # fillPrecursorScan is FALSE for "good" mzML files which have all the info needed.
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229 # However, for example AB Sciex files will have missing precursor scan information,
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230 # in which case fillPrecursorScan = TRUE is needed. Try it out.
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231 fillPrecursorScan: FALSE
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232
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233 # Select how to treat unknown compound masses:
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234 # "charged" (the default, also if no option set) treats unknown (level 5) compound masses as the m/z,
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235 # "neutral" treats unknown (level 5) compound masses as the neutral mass and applies [M+H]+ and [M-H]- calculations accordingly.
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236 unknownMass: charged