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

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit bc3445f7c41271b0062c7674108f57708d08dd28

#!/usr/bin/env Rscript
# Script for running RMassBank pipeline:
#   - part1 (all 8 steps at once)
#   - part2 (generation of MassBank records)
#
# Author: Karolina Trachtova ([e-mail])
# 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)