changeset 4:28fb8befb3b2 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e05cb49ba56d359fec34f132d1c9ace582e5b483-dirty

--- a/combineAnnotations.R	Fri Jun 14 08:55:15 2019 -0400
+++ b/combineAnnotations.R	Tue Jun 18 09:50:03 2019 -0400
@@ -13,7 +13,8 @@
   make_option(c("-cw","--sirius_csi_weight"),type="numeric"),
   make_option(c("-pw","--probmetab_weight"),type="numeric"),
   make_option("--create_new_database", action="store_true"),
-  make_option(c("-o","--outdir"),type="character", default=".")
+  make_option(c("-o","--outdir"),type="character", default="."),
+  make_option("--eic", action="store_true")
 )
 opt <- parse_args(OptionParser(option_list=option_list))
 
@@ -45,3 +46,33 @@
                              weights = weights)
 
 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
+
+if (!is.null(opt$eic)){
+
+  if (is.null(xset)){
+    xset <- xa@xcmsSet
+  }
+  # previous check should have matched filelists together
+  xset@filepaths <- unname(pa@fileList)
+
+  convert2Raw <- function(x, xset){
+    sid <- unique(x$sample)
+    # for each file get list of peaks
+    x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])]
+    x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])]
+    x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])]
+    return(x)
+
+  }
+
+  xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset))
+
+  # Saves the EICS into the previously created database
+  px <- msPurity::purityX(xset, saveEIC = TRUE,
+                          cores=1, sqlitePth=db_pth,
+                          rtrawColumns = TRUE)
+
+}
+
+closeAllConnections()
+

--- a/createDatabase.R	Fri Jun 14 08:55:15 2019 -0400
+++ b/createDatabase.R	Tue Jun 18 09:50:03 2019 -0400
@@ -10,7 +10,7 @@
 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 
+    # 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]])
@@ -58,8 +58,7 @@
   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")
+  make_option("--grpPeaklist", type="character")
 )
 
 
@@ -100,17 +99,17 @@
 
 
 if (opt$xcms_camera_option=='xcms'){
-  
+
   xset <- loadRData(opt$xset, c('xset','xdata'))
   xset <- getxcmsSetObject(xset)
-  fix <- xset_pa_filename_fix(opt, pa, 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)  
+  fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
   pa <- fix[[1]]
   xa@xcmsSet <- fix[[2]]
   xset <- NULL
@@ -128,7 +127,7 @@
 
 dbPth <- msPurity::createDatabase(pa,
                                    xset=xset,
-                                   xsa=xa, 
+                                   xsa=xa,
                                    outDir=opt$outDir,
                                    grpPeaklist=grpPeaklist,
                                    dbName='createDatabase_output.sqlite'
@@ -136,22 +135,33 @@
 
 
 
+
+
 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)
 
+  convert2Raw <- function(x, xset){
+    sid <- unique(x$sample)
+    # for each file get list of peaks
+    x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])]
+    x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])]
+    x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])]
+    return(x)
+
+  }
+
+  xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset))
+
   # Saves the EICS into the previously created database
   px <- msPurity::purityX(xset, saveEIC = TRUE,
                            cores=1, sqlitePth=db_pth,
-                           rtrawColumns = rtrawColumns)
+                           rtrawColumns = TRUE)
+
 }
 
-con <- DBI::dbConnect(RSQLite::SQLite(), dbPth)
+closeAllConnections()