Mercurial > repos > recetox > rmassbank
view rmassbank.r @ 2:5a6bb93ec656 draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit bc3445f7c41271b0062c7674108f57708d08dd28
author | recetox |
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date | Thu, 30 May 2024 14:53:55 +0000 |
parents | 0b28816c1c2c |
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#!/usr/bin/env Rscript # Script for running RMassBank pipeline: # - part1 (all 8 steps at once) # - part2 (generation of MassBank records) # # Author: Karolina Trachtova (k.trachtova@gmail.com) # Original authors of RMassBank: Michael Stravs, Emma Schymanski, # Steffen Neumann, Erik Mueller, with contributions from Tobias Schulze. # # INPUT1: settings list # INPUT2: compounds csv list # INPUT3: mode # INPUT4: folder with infolists # INPUT5: one or more mzML files # # RUN: # Rscript rmassbank_galaxy_part1.r mysettings.ini Compoundlist.csv pH \ # /path/to/files/1_3_Chlorophenyl_piperazin_2818_pos.mzML \ # /path/to/files/1_3_Trifluoromethylphenyl_piperazin_2819_pos.mzML ############################################################# # Load libraries rm(list = ls(all = TRUE)) suppressMessages(library("RMassBank", warn.conflicts = TRUE, quietly = TRUE)) ############################################################# # Read arguments args <- commandArgs(trailingOnly = TRUE) stt <- args[1] # file with settings cmp <- args[2] # csv file with compounds md <- args[3] # mode inf <- args[4] # folder with csv infolist files <- (args[5:length(args)]) # one or multiple mzML files print(paste0("Used settings file: ", stt)) print(paste0("Used compound list: ", cmp)) print(paste0("RMassBank pipeline will be run in mode: ", md)) print(paste0("Input files: ", files)) ############################################################# ## PART I # # Preparing environment for running RMassBank print("Preparing environment for part I ...") ## Load file with settings loadRmbSettings(stt) ## create a workspace w <- newMsmsWorkspace() ## Load compound list loadList(cmp) ## Load input files w@files <- files # Running RMassBank pipeline part I print("Running RMassBank pipeline part 1 - all 8 steps...") prf <- c("results") w <- msmsWorkflow(w, mode = md, steps = c(1:8), archivename = prf) ## Part II # # Preparing environment for running RMassBank print("Preparing environment for part II ...") mb <- newMbWorkspace(w) loadList(cmp) loadRmbSettings(stt) print("Loading infolist...") mb <- resetInfolists(mb) mb <- loadInfolists(mb, inf) print("Running RMassBank pipeline for generation of MassBank records...") mb <- mbWorkflow(mb)