diff frag4feature.R @ 0:4b417094bf71 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/frag4feature.R	Wed May 02 13:09:23 2018 -0400
@@ -0,0 +1,139 @@
+library(optparse)
+library(msPurity)
+library(xcms)
+print(sessionInfo())
+
+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)])
+  }
+ print(pa@fileList)
+ print(xset@filepaths)
+
+ 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)
+    }
+  }
+
+
+  return(list(pa, xset))
+}
+
+
+option_list <- list(
+  make_option(c("-o", "--out_dir"), type="character"),
+  make_option("--pa", type="character"),
+  make_option("--xset", type="character"),
+  make_option("--ppm", default=10),
+  make_option("--plim", default=0.0),
+  make_option("--convert2RawRT", action="store_true"),
+  make_option("--mostIntense", action="store_true"),
+  make_option("--createDB", action="store_true"),
+  make_option("--cores", default=4),
+  make_option("--mzML_files", type="character"),
+  make_option("--galaxy_names", type="character"),
+  make_option("--grp_peaklist", type="character")
+)
+
+# store options
+opt<- parse_args(OptionParser(option_list=option_list))
+
+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() %in% name]))
+}
+
+# This function retrieve a xset like object
+#@author Gildas Le Corguille [e-mail]
+getxcmsSetObject <- function(xobject) {
+    # XCMS 1.x
+    if (class(xobject) == "xcmsSet")
+        return (xobject)
+    # XCMS 3.x
+    if (class(xobject) == "XCMSnExp") {
+        # Get the legacy xcmsSet object
+        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
+        sampclass(xset) <- xset@phenoData$sample_group
+        return (xset)
+    }
+}
+
+# Requires
+pa <- loadRData(opt$pa, 'pa')
+xset <- loadRData(opt$xset, c('xset','xdata'))
+xset <- getxcmsSetObject(xset)
+
+pa@cores <- opt$cores
+
+print(pa@fileList)
+print(xset@filepaths)
+
+if(is.null(opt$mostIntense)){
+    mostIntense = FALSE
+}else{
+    mostIntense = TRUE
+}
+
+if(is.null(opt$convert2RawRT)){
+    convert2RawRT = FALSE
+}else{
+    convert2RawRT= TRUE
+}
+
+if(is.null(opt$createDB)){
+    createDB = FALSE
+}else{
+    createDB = TRUE
+}
+
+
+fix <- xset_pa_filename_fix(opt, pa, xset)
+pa <- fix[[1]]
+xset <- fix[[2]]
+
+if(is.null(opt$grp_peaklist)){
+    grp_peaklist = NA
+}else{
+    grp_peaklist = opt$grp_peaklist
+}
+
+print('heck')
+print(pa@fileList)
+print(names(pa@fileList))
+print(xset@filepaths)
+saveRDS(pa, 'test_pa.rds')
+
+pa <- msPurity::frag4feature(pa=pa, xset=xset, ppm=opt$ppm, plim=opt$plim,
+                            intense=opt$mostIntense, convert2RawRT=convert2RawRT,
+                            db_name='alldata.sqlite', out_dir=opt$out_dir, grp_peaklist=grp_peaklist,
+                             create_db=createDB)
+
+save(pa, file=file.path(opt$out_dir, 'frag4feature.RData'))
+
+print(head(pa@grped_df))
+write.table(pa@grped_df, file.path(opt$out_dir, 'frag4feature.tsv'), row.names=FALSE, sep='\t')