--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/main.R	Fri Jun 18 20:51:55 2021 +0000
@@ -0,0 +1,76 @@
+library(recetox.aplcms)
+
+save_extracted_features <- function(df, filename) {
+  df <- as.data.frame(df)
+  columns <- c("mz", "pos", "sd1", "sd2", "area")
+  arrow::write_parquet(df[columns], filename)
+}
+
+save_feature_sample_table <- function(df, filename) {
+  columns <- c("feature", "mz", "rt", "sample", "sample_rt", "sample_intensity")
+  arrow::write_parquet(df[columns], filename)
+}
+
+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(df, filename) {
+  columns <- known_table_columns()
+  arrow::write_parquet(df[columns], filename)
+}
+
+read_known_table <- function(filename) {
+  arrow::read_parquet(filename, col_select = known_table_columns())
+}
+
+save_pairing <- function(df, filename) {
+  write.table(df, filename, row.names = FALSE, col.names = c("new", "old"))
+}
+
+save_all_extracted_features <- function(dfs, filenames) {
+  filenames <- tools::file_path_sans_ext(basename(filenames))
+  filenames <- paste0(filenames, ".parquet")
+  filenames <- file.path("extracted", filenames)
+  dir.create("extracted")
+  mapply(save_extracted_features, dfs, filenames)
+}
+
+save_all_corrected_features <- function(dfs, filenames) {
+  filenames <- tools::file_path_sans_ext(basename(filenames))
+  filenames <- paste0(filenames, ".parquet")
+  filenames <- file.path("corrected", filenames)
+  dir.create("corrected")
+  mapply(save_extracted_features, dfs, filenames)
+}
+
+unsupervised_main <- function(sample_files, aligned_file, recovered_file, ...) {
+  sample_files <- sort_samples_by_acquisition_number(sample_files)
+
+  res <- unsupervised(filenames = sample_files, ...)
+
+  save_all_extracted_features(res$extracted_features, sample_files)
+  save_all_corrected_features(res$corrected_features, sample_files)
+
+  save_feature_sample_table(res$aligned_feature_sample_table, aligned_file)
+  save_feature_sample_table(res$recovered_feature_sample_table, recovered_file)
+}
+
+hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, pairing_file, aligned_file, recovered_file, ...) {
+  sample_files <- sort_samples_by_acquisition_number(sample_files)
+
+  known <- read_known_table(known_table_file)
+  res <- hybrid(filenames = sample_files, known_table = known, ...)
+
+  save_known_table(res$updated_known_table, updated_known_table_file)
+  save_pairing(res$features_known_table_pairing, pairing_file)
+
+  save_all_extracted_features(res$extracted_features, sample_files)
+  save_all_corrected_features(res$corrected_features, sample_files)
+
+  save_feature_sample_table(res$aligned_feature_sample_table, aligned_file)
+  save_feature_sample_table(res$recovered_feature_sample_table, recovered_file)
+}

--- a/recetox_aplcms_hybrid.xml	Fri Jun 18 13:54:00 2021 +0000
+++ b/recetox_aplcms_hybrid.xml	Fri Jun 18 20:51:55 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_hybrid" name="apLCMS Hybrid" version="@TOOL_VERSION@+galaxy0">
+<tool id="recetox_aplcms_hybrid" name="apLCMS Hybrid" version="@TOOL_VERSION@+galaxy1">
     <description>generate a feature table from LC/MS spectra</description>
     <macros>
         <import>recetox_aplcms_macros.xml</import>

--- a/recetox_aplcms_macros.xml	Fri Jun 18 13:54:00 2021 +0000
+++ b/recetox_aplcms_macros.xml	Fri Jun 18 20:51:55 2021 +0000
@@ -3,7 +3,6 @@
 
     <xml name="requirements">
         <requirements>
-            <requirement type="set_environment">R_SCRIPT_PATH</requirement>
             <requirement type="package" version="4.1.0">R</requirement>
             <requirement type="package" version="4.0.1">r-arrow</requirement>
             <requirement type="package" version="0.9.3">r-recetox-aplcms</requirement>