annotate rmassbank.r @ 2:5a6bb93ec656 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit bc3445f7c41271b0062c7674108f57708d08dd28
author recetox
date Thu, 30 May 2024 14:53:55 +0000
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1 #!/usr/bin/env Rscript
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2 # Script for running RMassBank pipeline:
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3 # - part1 (all 8 steps at once)
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4 # - part2 (generation of MassBank records)
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5 #
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6 # Author: Karolina Trachtova (k.trachtova@gmail.com)
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7 # Original authors of RMassBank: Michael Stravs, Emma Schymanski,
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8 # Steffen Neumann, Erik Mueller, with contributions from Tobias Schulze.
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9 #
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10 # INPUT1: settings list
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11 # INPUT2: compounds csv list
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12 # INPUT3: mode
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13 # INPUT4: folder with infolists
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14 # INPUT5: one or more mzML files
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15 #
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16 # RUN:
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17 # Rscript rmassbank_galaxy_part1.r mysettings.ini Compoundlist.csv pH \
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18 # /path/to/files/1_3_Chlorophenyl_piperazin_2818_pos.mzML \
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19 # /path/to/files/1_3_Trifluoromethylphenyl_piperazin_2819_pos.mzML
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20 #############################################################
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21 # Load libraries
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22 rm(list = ls(all = TRUE))
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24 suppressMessages(library("RMassBank", warn.conflicts = TRUE, quietly = TRUE))
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26 #############################################################
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27 # Read arguments
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28 args <- commandArgs(trailingOnly = TRUE)
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29
2
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30 stt <- args[1] # file with settings
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31 cmp <- args[2] # csv file with compounds
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32 md <- args[3] # mode
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33 inf <- args[4] # folder with csv infolist
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34 files <- (args[5:length(args)]) # one or multiple mzML files
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36 print(paste0("Used settings file: ", stt))
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37 print(paste0("Used compound list: ", cmp))
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38 print(paste0("RMassBank pipeline will be run in mode: ", md))
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39 print(paste0("Input files: ", files))
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41 #############################################################
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42 ## PART I
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43 #
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44 # Preparing environment for running RMassBank
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45 print("Preparing environment for part I ...")
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47 ## Load file with settings
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48 loadRmbSettings(stt)
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49
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50 ## create a workspace
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51 w <- newMsmsWorkspace()
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52
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53 ## Load compound list
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54 loadList(cmp)
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56 ## Load input files
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57 w@files <- files
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59 # Running RMassBank pipeline part I
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60 print("Running RMassBank pipeline part 1 - all 8 steps...")
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61
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62 prf <- c("results")
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63 w <- msmsWorkflow(w, mode = md, steps = c(1:8), archivename = prf)
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65 ## Part II
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66 #
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67 # Preparing environment for running RMassBank
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68 print("Preparing environment for part II ...")
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70 mb <- newMbWorkspace(w)
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72 loadList(cmp)
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74 loadRmbSettings(stt)
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76 print("Loading infolist...")
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78 mb <- resetInfolists(mb)
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80 mb <- loadInfolists(mb, inf)
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82 print("Running RMassBank pipeline for generation of MassBank records...")
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84 mb <- mbWorkflow(mb)