diff utils.R @ 0:cfd2e19f00a9 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.R	Mon Jun 26 13:55:56 2023 +0000
@@ -0,0 +1,37 @@
+library(recetox.xmsannotator)
+library(dplyr)
+
+load_table <- function(filename, filetype) {
+    if (filename == "None") {
+        return(NULL)
+    }
+    if (filetype == "csv") {
+        return(as.data.frame(read.csv(filename)))
+    } else {
+        return(as.data.frame(arrow::read_parquet(filename)))
+    }
+}
+
+save_table <- function(table, filename, filetype) {
+    if (filetype == "csv") {
+        write.csv(table, filename, row.names = FALSE)
+    } else {
+        arrow::write_parquet(table, filename)
+    }
+}
+
+create_filter_by_adducts <- function(comma_separated_values) {
+    if (comma_separated_values == "None") {
+        return(NA)
+    }
+    filter_by <- strsplit(trimws(comma_separated_values), ",")[[1]]
+    return(filter_by)
+}
+
+create_peak_table <- function(metadata_table, intensity_table) {
+    metadata_table <- select(metadata_table, id, mz, rt)
+    peak_table <- inner_join(metadata_table, intensity_table, by = "id")
+    peak_table <- rename(peak_table, peak = id)
+    peak_table$peak <- as.integer(peak_table$peak)
+    return(peak_table)
+}