annotate macros.xml @ 1:c1a9c990d4b0 draft

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author recetox
date Thu, 12 Oct 2023 13:31:44 +0000
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1 <macros>
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2 <token name="@TOOL_VERSION@">3.0.0</token>
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3
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4 <xml name="creator">
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5 <creator>
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6 <person
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7 givenName="KarolĂ­na"
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8 familyName="Trachtová"
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9 url="https://github.com/trachtok" />
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10 <organization
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11 url="https://www.recetox.muni.cz/"
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12 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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13 name="RECETOX MUNI" />
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14 </creator>
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15 </xml>
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17 <token name="@HELP@">
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18 <![CDATA[
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19 RMassBank workflow - part I and II
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20 This is implementation of RMassBank workflow (Bioconductor R package) based on publication by Stravs et al. 2013.
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21
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22 Original RMassBank package is used to process tandem MS files and build MassBank records. Functions include
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23 automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem
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24 MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet
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25 databases, and export to MassBank records.
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26
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27 This script is a full pipeline of RmassBank that loads settings file, compounds list, infolist and input .mzML
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28 files (one or multiple) and goes through all 8 steps of data-preprocessing referenced in RMassBank's
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29 Bioconductor manual (Mass spectrometry workflow, function msmsWorkflow()) and all steps of MassBank record
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30 generation (MassBank record workflow, function mbWorkflow()). To make it easier for user, based on template
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31 of settings required by RMassBank package the corresponding settings file is created as well
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32 (see section Settings file).
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33
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34 User's inputs:
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35 - *compounds list* **(must have suffix .csv)** - separator must be ',', required columns: ID, Name_deu, Name_Eng, Name, SMILES, RT, CAS
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36 - *mode* - either **pH** (positive H) specifies [M+H]+ OR **pNa** specifies [M+Na]+ OR **pM** specifies [M]+ OR **mFA** specify [M-H]- and [M+FA]-
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37 - *input mzML files* - files for RMassBank package must have specific naming, each filename should be in format: xxxxxxxx_1234_xxx.mzXML where the xxx denotes anything and 1234 is compound ID (must be stated in ID column of compound csv file).
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38 - *infolist* **(must have suffix .csv)** - separator must be ',', columns (required columns are **bold**): '' (column name empty, values are numbers from 1 to n=number of chemicals), OK, id, dbcas, dbname_d, dbname_e, dataused, COMMENT.CONFIDENCE, COMMENT.EAWAG_UCHEM_ID, **CH$NAME1**, CH$NAME2, CH$NAME3, CH$COMPOUND_CLASS, **CH$FORMULA**, **CH$EXACT_MASS**, **CH$SMILES**, **CH$IUPAC**, CH$LINK.CAS, CH$LINK.CHEBI, CH$LINK.HMDB, CH$LINK.KEGG, CH$LINK.LIPIDMAPS, CH$LINK.PUBCHEM, **CH$LINK.INCHIKEY**, CH$LINK.CHEMSPIDER
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39 - *settings parameters* - either filled in Galaxy or the whole settings file can be uploaded and used to run the RMassBank workflow
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40
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41 Galaxy outputs:
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42 - CSV file with failed peaks (empty if there were no failed peaks)
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43 - PDF plot showing performance of the recalibration
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44 - Full R environment (.RData) that should be used as an input for RMassBank workflow - part II
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45 - R environment with re-analyzed spectra (_RA.RData, see RMassBank manual for more information)
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46 - R environment with refiltered spectra (_RF.RData, see RMassBank manual for more information)
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47 - *zipped folder* with records ready to be uploaded to MassBank database
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48 - *settings file* used to run the RMassBank
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49
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50 For more information about the data-preprocessing and record generation of the RMassBank pipeline, please refer
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51 to `Bioconductor manual <https://www.bioconductor.org/packages/release/bioc/html/RMassBank.html>`_ for RMassBank.
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52
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53 Settings file
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54 In the original RMassBank R package, user has to specify multiple parameters via the settings file. To make
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55 life easier for users of this tool, most of the parameters can be specified in the Galaxy intrface for this
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56 tool and are automatically filled in the settings template that can is then used for RMassBank workflow.
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57 If the user wants to supply his/her own settings files, that is also possible. Path to OpenBabel will be
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58 automatically filled no matter what is the original specification in the supplied settings file.
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59
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60 For all parameters, please refer to the manual for RMassBank at `Bioconductor website
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61 <https://www.bioconductor.org/packages/release/bioc/html/RMassBank.html>`_ .
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62
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63 Parameters that can only be changed manually are:
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64 - *deprofile:* leave empty if input data are already in centroid mode (usuall case), otherwise use one of the values from deprofile.spline, deprofile.fwhm or deprofile.localMax to convert the input $
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65 - *babeldir:* do not change this if the settings file is to be further used in Galaxy
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66 - *annotations:* several fields containg information about author, used instrument etc.
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67 - *spectraList:* list of data-dependent scans in their order (relative to the parent scan), for annotation of the MassBank records
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68 - *electronicNoise:* list of known electronic noise peaks
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69 - *recalibrator:* custom recalibration function
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70 - *titleFormat:* defines the title format
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71
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72 **All parameters are more thoroughly described in the created settings file, which can be edited in any simple
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73 text editor.**
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74
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75 **NOTE:** In case of manual editing of the settings file, do not indent with TAB characters! Use only spaces.
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76
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77 Authors of RMassBank: Michael Stravs, Emma Schymanski, Steffen Neumann, Erik Mueller, with contributions
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78 from Tobias Schulze.
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79
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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80 RMassBank maintainer: at Eawag (massbank@eawag.ch)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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81 ]]>
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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82 </token>
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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83 </macros>