Mercurial > repos > recetox > rmassbank
diff rmassbank.r @ 0:0b28816c1c2c draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
author | recetox |
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date | Thu, 18 May 2023 13:01:04 +0000 |
parents | |
children | 5a6bb93ec656 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmassbank.r Thu May 18 13:01:04 2023 +0000 @@ -0,0 +1,84 @@ +#!/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)