--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annotationRmn2DWrapper.R	Tue Feb 04 10:59:26 2020 -0500
@@ -0,0 +1,227 @@
+#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
+
+## 201919016 2DNmrAnnotation_1.0.0.R
+## Marie Tremblay-Franco
+## MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics
+## www.metabohub.fr/en
+## marie.tremblay-franco@toulouse.inra.fr
+
+runExampleL <- FALSE
+
+if(runExampleL) {
+##------------------------------
+## Example of arguments
+##------------------------------
+}
+
+
+##------------------------------
+## Options
+##------------------------------
+strAsFacL <- options()$stringsAsFactors
+options(stringsAsFactors = FALSE)
+
+##------------------------------
+## Constants
+##------------------------------
+topEnvC <- environment()
+flagC <- "\n"
+
+
+##-------------------------
+## Input parameters reading
+##-------------------------
+
+##------------------------------
+## R libraries laoding
+##------------------------------
+library(batch)
+library(dplyr)
+library(ggplot2)
+library(openxlsx)
+library(stringr)
+library(tidyr)
+
+if(!runExampleL)
+    argLs <- parseCommandArgs(evaluate=FALSE)
+logFile <- argLs[["logOut"]]
+sink(logFile)
+
+cat("\tPACKAGE INFO\n")
+sessionInfo()
+
+##------------------------------
+## Functions
+##------------------------------
+source_local <- function(fname)
+{
+	argv <- commandArgs(trailingOnly = FALSE)
+	base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+	source(paste(base_dir, fname, sep="/"))
+}
+#Import the different functions
+source_local("annotationRmn2D.R")
+source_local("annotationRmn2DGlobale.R")
+source_local("viridis.R")
+
+## Input parameter values
+fileToAnnotate <- argLs[[1]]
+  # Chosen sequence(s)
+cosy <- 0
+hmbc <- 0
+hsqc <- 0
+jres <- 0
+tocsy <- 0
+## sequences <- str_split(argLs[[2]], ",")[[1]]
+## for (s in 1:length(sequences))
+## {
+##   argv <- commandArgs(trailingOnly = FALSE)
+##   currentDir <- dirname(substring(argv[grep("--file=", argv)], 8))
+##   if (sequences[s]=="cosy"){
+##         cosy <- 1
+##         load(paste(currentDir, "BdDReference_COSY.RData", sep="/"))
+##   }else if(sequences[s]=="hmbc"){
+##         hmbc <- 1
+##         load(paste(currentDir, "BdDReference_HMBC.RData", sep="/"))
+##   }else if(sequences[s]=="hsqc"){
+##         hsqc <- 1
+##         load(paste(currentDir, "BdDReference_HSQC.RData", sep="/"))
+##   }else if(sequences[s]=="jres"){
+##         jres <- 1
+##         load(paste(currentDir, "BdDReference_JRES.RData", sep="/"))
+##   }else if(sequences[s]=="tocsy"){
+##         tocsy <- 1
+##         load(paste(currentDir, "BdDReference_TOCSY.RData", sep="/"))
+##   }else
+##     stop("No chosen sequence", call.=FALSE)
+## }
+
+if (argLs[[2]]=='yes')
+{
+  argv <- commandArgs(trailingOnly = FALSE)
+  currentDir <- dirname(substring(argv[grep("--file=", argv)], 8))
+  cosy <- 1
+  load(paste(currentDir, "BdDReference_COSY.RData", sep="/"))
+}
+
+if (argLs[[3]]=='yes')
+{
+  argv <- commandArgs(trailingOnly = FALSE)
+  currentDir <- dirname(substring(argv[grep("--file=", argv)], 8))
+  jres <- 1
+  load(paste(currentDir, "BdDReference_JRES.RData", sep="/"))
+}
+
+if (argLs[[4]]=='yes')
+{
+  argv <- commandArgs(trailingOnly = FALSE)
+  currentDir <- dirname(substring(argv[grep("--file=", argv)], 8))
+  hmbc <- 1
+  load(paste(currentDir, "BdDReference_HMBC.RData", sep="/"))
+}
+
+if (argLs[[5]]=='yes')
+{
+  argv <- commandArgs(trailingOnly = FALSE)
+  currentDir <- dirname(substring(argv[grep("--file=", argv)], 8))
+  hsqc <- 1
+  load(paste(currentDir, "BdDReference_HSQC.RData", sep="/"))
+}
+
+if (argLs[[6]]=='yes')
+{
+  argv <- commandArgs(trailingOnly = FALSE)
+  currentDir <- dirname(substring(argv[grep("--file=", argv)], 8))
+  tocsy <- 1
+  load(paste(currentDir, "BdDReference_TOCSY.RData", sep="/"))
+}
+
+if (argLs[[2]]=='no' & argLs[[3]]=='no' & argLs[[4]]=='no' & argLs[[5]]=='no' & argLs[[6]]=='no')
+  stop("No chosen sequence", call.=FALSE)
+
+
+  # User database
+
+
+  # Allowed chemical shifts
+tolPpm1 <- argLs$tolppm1
+tolPpm2HJRes <- argLs$tolppmJRES
+tolPpm2C <- argLs$tolppm2
+  # Threshold to remove metabolites (probability score < threshold)
+seuil <- argLs$threshold
+# Remove metabolites when multiple assignations?
+unicite <- str_to_upper(argLs$unicity)
+
+## Output paramater values
+AnnotationGraph <- argLs[["AnnotationGraph"]]
+
+print(argLs)
+
+## ANNOTATION
+st0=Sys.time()
+pdf(AnnotationGraph,onefile=TRUE)
+annotationMelange <- annotationRmn2DGlobale(fileToAnnotate, tolPpm1=tolPpm1, tolPpm2HJRes=tolPpm2HJRes, 
+                                             tolPpm2C=tolPpm2C, cosy=cosy, hmbc=hmbc, hsqc=hsqc, 
+                                             jres=jres, tocsy=tocsy, seuil=seuil, unicite=unicite)
+dev.off()
+
+if (cosy==1)
+{
+  write.table(annotationMelange$COSY$liste_resultat, file=argLs[["annotationCOSY"]], quote=FALSE, 
+              row.names=FALSE,sep="\t")
+  if (nrow(annotationMelange$COSY$listing_ppm_commun) != 0)
+      write.table(annotationMelange$COSY$listing_ppm_commun, file=argLs[["ppmCommunCOSY"]], quote=FALSE, 
+                  row.names=FALSE,sep="\t")
+}
+
+if (hmbc==1)
+{
+  write.table(annotationMelange$HMBC$liste_resultat, file=argLs[["annotationHMBC"]], quote=FALSE, 
+              row.names=FALSE,sep="\t")
+  if (nrow(annotationMelange$HMBC$listing_ppm_commun) != 0)
+    write.table(annotationMelange$HMBC$listing_ppm_commun, file=argLs[["ppmCommunHMBC"]], quote=FALSE, 
+                row.names=FALSE,sep="\t")
+}
+
+if (hsqc==1)
+{
+  write.table(annotationMelange$HSQC$liste_resultat, file=argLs[["annotationHSQC"]], quote=FALSE, 
+              row.names=FALSE,sep="\t")
+  if (nrow(annotationMelange$HSQC$listing_ppm_commun) != 0)
+    write.table(annotationMelange$HSQC$listing_ppm_commun, file=argLs[["ppmCommunHSQC"]], quote=FALSE, 
+                row.names=FALSE,sep="\t")
+}
+
+if (jres==1)
+{
+  write.table(annotationMelange$JRES$liste_resultat, file=argLs[["annotationJRES"]], quote=FALSE, 
+              row.names=FALSE,sep="\t")
+  if (nrow(annotationMelange$JRES$listing_ppm_commun) != 0)
+    write.table(annotationMelange$JRES$listing_ppm_commun, file=argLs[["ppmCommunJRES"]], quote=FALSE, 
+                row.names=FALSE,sep="\t")
+}
+
+if (tocsy==1)
+{
+  write.table(annotationMelange$TOCSY$liste_resultat, file=argLs[["annotationTOCSY"]], quote=FALSE, 
+              row.names=FALSE,sep="\t")
+  if (nrow(annotationMelange$TOCSY$listing_ppm_commun) != 0)
+    write.table(annotationMelange$TOCSY$listing_ppm_commun, file=argLs[["ppmCommunTOCSY"]], quote=FALSE, 
+                row.names=FALSE,sep="\t")
+}
+
+## Combinaison de sequences
+if (cosy + jres + hmbc + hsqc + tocsy > 1)
+{
+  write.table(annotationMelange$combination, file=argLs[["annotationCombination"]], quote=FALSE, 
+              row.names=FALSE,sep="\t")
+}
+st1=Sys.time()
+print(st1-st0)
+
+## Ending
+##--------
+cat("\nEnd of '2D NMR annotation' Galaxy module call: ", as.character(Sys.time()), sep = "")
+sink()
+options(stringsAsFactors = strAsFacL)
+rm(list = ls())