diff combineAnnotations.R @ 4:68c405751ef6 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 14eafbdb65f491713d1314d77c454defd137c392

--- a/combineAnnotations.R	Tue Jun 18 10:08:40 2019 -0400
+++ b/combineAnnotations.R	Tue Jun 18 11:14:17 2019 -0400
@@ -47,32 +47,6 @@
 
 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()