diff createDatabase.R @ 0:fc9bb7e49a3a draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/createDatabase.R	Fri May 24 09:02:25 2019 -0400
@@ -0,0 +1,140 @@
+library(msPurity)
+library(optparse)
+library(xcms)
+library(CAMERA)
+print(sessionInfo())
+print('CREATING DATABASE')
+
+
+
+xset_pa_filename_fix <- function(opt, pa, xset){
+
+  if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
+    # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables 
+    # needs to be done due to Galaxy moving the files around and screwing up any links to files
+
+    filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
+    filepaths <- filepaths[filepaths != ""]
+    new_names <- basename(filepaths)
+
+    galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
+    galaxy_names <- galaxy_names[galaxy_names != ""]
+
+    nsave <- names(pa@fileList)
+    old_filenames  <- basename(pa@fileList)
+    pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
+    names(pa@fileList) <- nsave
+
+    pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
+    pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
+  }
+
+
+ if(!all(basename(pa@fileList)==basename(xset@filepaths))){
+    if(!all(names(pa@fileList)==basename(xset@filepaths))){
+       print('FILELISTS DO NOT MATCH')
+       message('FILELISTS DO NOT MATCH')
+       quit(status = 1)
+    }else{
+      xset@filepaths <- unname(pa@fileList)
+    }
+  }
+
+  print(xset@phenoData)
+  print(xset@filepaths)
+
+  return(list(pa, xset))
+}
+
+
+
+
+option_list <- list(
+  make_option(c("-o", "--outDir"), type="character"),
+  make_option("--pa", type="character"),
+  make_option("--xset_xa", type="character"),
+  make_option("--xcms_camera_option", type="character"),
+  make_option("--eic", action="store_true"),
+  make_option("--cores", default=4),
+  make_option("--mzML_files", type="character"),
+  make_option("--galaxy_names", type="character"),
+  make_option("--grpPeaklist", type="character"),
+  make_option("--raw_rt_columns", action="store_true")
+)
+
+
+# store options
+opt<- parse_args(OptionParser(option_list=option_list))
+print(opt)
+
+loadRData <- function(rdata_path, name){
+  #loads an RData file, and returns the named xset object if it is there
+  load(rdata_path)
+  return(get(ls()[ls() == name]))
+}
+
+print(paste('pa', opt$pa))
+print(opt$xset)
+
+print(opt$xcms_camera_option)
+# Requires
+pa <- loadRData(opt$pa, 'pa')
+
+
+print(pa@fileList)
+
+
+if (opt$xcms_camera_option=='xcms'){
+  xset <- loadRData(opt$xset, 'xset')
+  fix <- xset_pa_filename_fix(opt, pa, xset)  
+  pa <- fix[[1]]
+  xset <- fix[[2]]
+  xa <- NULL
+}else{
+  
+  xa <- loadRData(opt$xset, 'xa')
+  fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)  
+  pa <- fix[[1]]
+  xa@xcmsSet <- fix[[2]]
+  xset <- NULL
+}
+
+
+
+if(is.null(opt$grp_peaklist)){
+  grpPeaklist = NA
+}else{
+  grpPeaklist = opt$grp_peaklist
+}
+
+
+
+dbPth <- msPurity::createDatabase(pa,
+                                   xset=xset,
+#                                   xsa=xa, 
+                                   outDir=opt$outDir,
+#                                   grpPeaklist=grpPeaklist,
+                                   dbName='createDatabase_output.sqlite'
+)
+
+
+
+if (!is.null(opt$eic)){
+  if (is.null(opt$raw_rt_columns)){
+    rtrawColumns <- FALSE
+  }else{
+    rtrawColumns <- TRUE
+  }
+  if (is.null(xset)){
+      xset <- xa@xcmsSet
+  }
+  # previous check should have matched filelists together
+  xset@filepaths <- unname(pa@fileList)
+
+  # Saves the EICS into the previously created database
+  px <- msPurity::purityX(xset, saveEIC = TRUE,
+                           cores=1, sqlitePth=db_pth,
+                           rtrawColumns = rtrawColumns)
+}
+
+con <- DBI::dbConnect(RSQLite::SQLite(), dbPth)