diff createMSP.R @ 0:df2efceff4cd 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/createMSP.R	Fri May 24 09:06:56 2019 -0400
@@ -0,0 +1,60 @@
+library(optparse)
+library(msPurity)
+print(sessionInfo())
+
+# Get the parameter
+option_list <- list(
+  make_option(c("-i","--rdata_input"),type="character"),
+  make_option(c("-m","--method"),type="character"),
+  make_option(c("-meta","--metadata"),type="character"),
+  make_option(c("-metac","--metadata_cols"),type="character"),
+  make_option(c("-a","--adduct_split"),type="character"),
+  make_option(c("-x","--xcms_groupids"),type="character"),
+  make_option(c("-f","--filter"),action="store_true"),
+  make_option("--intensity_ra",type="character"),
+  make_option("--msp_schema",type="character"),
+  make_option(c("-o","--out_dir"),type="character", default=".")
+)
+opt <- parse_args(OptionParser(option_list=option_list))
+
+print(opt)
+
+load(opt$rdata_input)
+
+if (is.null(opt$metadata)){
+  metadata <- NULL
+}else{
+  metadata <- read.table(opt$metadata,  header = TRUE, sep='\t', stringsAsFactors = FALSE, check.names = FALSE)
+  print(head(metadata))
+}
+
+if(is.null(opt$adduct_split)){
+  adduct_split <- FALSE
+}else{
+  adduct_split <- TRUE
+}
+
+if (is.null(opt$xcms_groupids)){
+  xcms_groupids <- NULL
+}else{
+  xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]])
+}
+
+if(is.null(opt$filter)){
+  filter <- FALSE
+}else{
+  filter <- TRUE
+}
+
+msPurity::createMSP(pa,
+                    msp_file_pth = file.path(opt$out_dir, 'lcmsms_spectra.msp'),
+                    metadata = metadata,
+                    metadata_cols = opt$metadata_cols,
+                    method = opt$method,
+                    adduct_split = adduct_split,
+                    xcms_groupids = xcms_groupids,
+                    filter = filter,
+                    intensity_ra=opt$intensity_ra,
+                    msp_schema=opt$msp_schema)
+
+print('msp created')