annotate utils.R @ 1:2c6fa447f6a0 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 8547c5323747595eabbeed29039a1b2363491243

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)
}