diff frag4feature.R @ 18:49e063070647 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6

--- a/frag4feature.R	Thu Jun 14 09:25:22 2018 -0400
+++ b/frag4feature.R	Tue Jul 17 12:30:24 2018 -0400
@@ -3,7 +3,7 @@
 library(xcms)
 print(sessionInfo())
 
-xset_pa_filename_fix <- function(opt, pa, xset){
+xset_pa_filename_fix <- function(opt, pa, xset=NULL){
 
 
   if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
@@ -26,19 +26,22 @@
     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)
+  print(pa@fileList)
+
+  if(!is.null(xset)){
+
+    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)
-    }
-  }
-
+    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))
 }
@@ -56,12 +59,15 @@
   make_option("--cores", default=4),
   make_option("--mzML_files", type="character"),
   make_option("--galaxy_names", type="character"),
-  make_option("--grp_peaklist", type="character")
+  make_option("--grp_peaklist", type="character"),
+  make_option("--use_group", 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)
@@ -111,10 +117,19 @@
     createDB = TRUE
 }
 
+if(is.null(opt$use_group)){
+    fix <- xset_pa_filename_fix(opt, pa, xset)
+    pa <- fix[[1]]
+    xset <- fix[[2]]
+    use_group=FALSE
+}else{
+    # if are only aligning to the group not eah file we do not need to align the files between the xset and pa object
+    print('use_group')
+    fix <- xset_pa_filename_fix(opt, pa)
+    pa <- fix[[1]]
+    use_group=TRUE
+}
 
-fix <- xset_pa_filename_fix(opt, pa, xset)
-pa <- fix[[1]]
-xset <- fix[[2]]
 
 if(is.null(opt$grp_peaklist)){
     grp_peaklist = NA
@@ -130,7 +145,7 @@
 pa <- msPurity::frag4feature(pa=pa, xset=xset, ppm=opt$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)
+                             create_db=createDB, use_group=use_group)
 
 save(pa, file=file.path(opt$out_dir, 'frag4feature.RData'))