diff rmassbank.r @ 0:0b28816c1c2c draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8

--- /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 ([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)