diff utils.R @ 0:82737757f3d5 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.R	Mon Feb 13 10:27:56 2023 +0000
@@ -0,0 +1,125 @@
+library(recetox.aplcms)
+
+get_env_sample_name <- function() {
+    sample_name <- Sys.getenv("SAMPLE_NAME", unset = NA)
+    if (nchar(sample_name) == 0) {
+        sample_name <- NA
+    }
+    if (is.na(sample_name)) {
+        message("The mzML file does not contain run ID.")
+    }
+    return(sample_name)
+}
+
+save_sample_name <- function(df, sample_name) {
+    attr(df, "sample_name") <- sample_name
+    return(df)
+}
+
+load_sample_name <- function(df) {
+    sample_name <- attr(df, "sample_name")
+    if (is.null(sample_name)) {
+        return(NA)
+    } else {
+        return(sample_name)
+    }
+}
+
+save_data_as_parquet_file <- function(data, filename) {
+    arrow::write_parquet(data, filename)
+}
+
+load_data_from_parquet_file <- function(filename) {
+    return(arrow::read_parquet(filename))
+}
+
+load_parquet_collection <- function(files) {
+    features <- lapply(files, arrow::read_parquet)
+    features <- lapply(features, tibble::as_tibble)
+    return(features)
+}
+
+save_parquet_collection <- function(table, sample_names, subdir) {
+    dir.create(subdir)
+    for (i in seq_len(length(table$feature_tables))) {
+      filename <- file.path(subdir, paste0(subdir, "_", sample_names[i], ".parquet"))
+      feature_table <- as.data.frame(table$feature_tables[[i]])
+      feature_table <- save_sample_name(feature_table, sample_names[i])
+      arrow::write_parquet(feature_table, filename)
+    }
+}
+
+sort_by_sample_name <- function(tables, sample_names) {
+    return(tables[order(sample_names)])
+}
+
+save_tolerances <- function(table, tol_file) {
+    mz_tolerance <- c(table$mz_tol_relative)
+    rt_tolerance <- c(table$rt_tol_relative)
+    arrow::write_parquet(data.frame(mz_tolerance, rt_tolerance), tol_file)
+}
+
+get_mz_tol <- function(tolerances) {
+    return(tolerances$mz_tolerance)
+}
+
+get_rt_tol <- function(tolerances) {
+    return(tolerances$rt_tolerance)
+}
+
+save_aligned_features <- function(aligned_features, metadata_file, rt_file, intensity_file) {
+    save_data_as_parquet_file(aligned_features$metadata, metadata_file)
+    save_data_as_parquet_file(aligned_features$rt, rt_file)
+    save_data_as_parquet_file(aligned_features$intensity, intensity_file)
+}
+
+select_table_with_sample_name <- function(tables, sample_name) {
+    sample_names <- lapply(tables, load_sample_name)
+    index <- which(sample_names == sample_name)
+    if (length(index) > 0) {
+        return(tables[[index]])
+    } else {
+        stop(sprintf("Mismatch - sample name '%s' not present in %s",
+                     sample_name, paste(sample_names, collapse = ", ")))
+    }
+}
+
+select_adjusted <- function(recovered_features) {
+    return(recovered_features$adjusted_features)
+}
+
+known_table_columns <- function() {
+  c("chemical_formula", "HMDB_ID", "KEGG_compound_ID", "mass", "ion.type",
+    "m.z", "Number_profiles_processed", "Percent_found", "mz_min", "mz_max",
+    "RT_mean", "RT_sd", "RT_min", "RT_max", "int_mean(log)", "int_sd(log)",
+    "int_min(log)", "int_max(log)")
+}
+
+save_known_table <- function(table, filename) {
+  columns <- known_table_columns()
+  arrow::write_parquet(table$known_table[columns], filename)
+}
+
+read_known_table <- function(filename) {
+  arrow::read_parquet(filename, col_select = known_table_columns())
+}
+
+save_pairing <- function(table, filename) {
+  df <- table$pairing %>% as_tibble() %>% setNames(c("new", "old"))
+  arrow::write_parquet(df, filename)
+}
+
+join_tables_to_list <- function(metadata, rt_table, intensity_table) {
+  features <- new("list")
+  features$metadata <- metadata
+  features$intensity <- intensity_table
+  features$rt <- rt_table
+  return(features)
+}
+
+validate_sample_names <- function(sample_names) {
+    if ((any(is.na(sample_names))) || (length(unique(sample_names)) != length(sample_names))) {
+        stop(sprintf("Sample names absent or not unique - provided sample names: %s",
+                     paste(sample_names, collapse = ", ")))
+    }
+}