comparison main.R @ 1:4e6281945270 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5

0:d740352d272a

rcx_aplcms_to_rcx_xmsannotator <- function(peak_table) {
    col_base <- c("feature", "mz", "rt")
    output_table <- peak_table %>% distinct(across(any_of(col_base)))

    for (level in levels(peak_table$sample)) {
        subdata <- peak_table %>%
            filter(sample == level) %>%
            select(any_of(c(col_base, "sample_intensity"))) %>%
            rename(!!level := "sample_intensity")
        output_table <- inner_join(output_table, subdata, by = col_base)

  save_all_corrected_features(res$corrected_features, sample_files)

  save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file)
  save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format)
}

1:4e6281945270

rcx_aplcms_to_rcx_xmsannotator <- function(peak_table) {
    col_base <- c("feature", "mz", "rt")
    output_table <- peak_table %>% distinct(across(any_of(col_base)))

    for (level in levels(factor(peak_table$sample))) {
        subdata <- peak_table %>%
            filter(sample == level) %>%
            select(any_of(c(col_base, "sample_intensity"))) %>%
            rename(!!level := "sample_intensity")
        output_table <- inner_join(output_table, subdata, by = col_base)

  save_all_corrected_features(res$corrected_features, sample_files)

  save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file)
  save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format)
}

two_step_hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, recovered_file, aligned_file, out_format, metadata, ...) {
  sample_files <- sort_samples_by_acquisition_number(sample_files)
  metadata <- read.table(metadata, sep = ",", header = TRUE)

  known_table <- read_known_table(known_table_file)
  res <- two.step.hybrid(filenames = sample_files, known.table = known_table, work_dir = getwd(), metadata = metadata, ...)

  save_known_table(res$known_table, updated_known_table_file)
  save_aligned_feature_table(res$aligned_features, aligned_file)
  save_recovered_feature_table(res$final_features, recovered_file, out_format)
}