@@ -170,7 +188,6 @@ diff -r c67f0eb6a909 -r 87b669bdb51a main.R --- a/main.R Thu May 26 16:47:09 2022 +0000 +++ b/main.R Fri Jun 10 10:15:47 2022 +0000 @@ -79,11 +79,8 @@ res <- unsupervised(filenames = sample_files, ...) - save_all_extracted_features(res$extracted_features, sample_files) - save_all_corrected_features(res$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) + save_all_features(res, sample_files) + save_all_feature_tables(res$aligned_feature_sample_table, res$recovered_feature_sample_table, aligned_file, recovered_file, out_format) } hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, pairing_file, aligned_file, recovered_file, out_format, ...) { @@ -95,11 +92,22 @@ 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_all_features(res, sample_files) + save_all_feature_tables(res$aligned_feature_sample_table, res$recovered_feature_sample_table, aligned_file, recovered_file, out_format) +} - save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file) - save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format) +save_all_features <- function(result, sample_files) { + save_all_extracted_features(result$extracted_features, sample_files) + save_all_corrected_features(result$corrected_features, sample_files) +} + +save_all_feature_tables <- function(aligned_feature_sample_table, + recovered_feature_sample_table, + aligned_file, + recovered_file, + out_format) { + save_aligned_feature_table(aligned_feature_sample_table, aligned_file) + save_recovered_feature_table(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, ...) { diff -r c67f0eb6a909 -r 87b669bdb51a recetox_aplcms_two_step_hybrid.xml --- a/recetox_aplcms_two_step_hybrid.xml Thu May 26 16:47:09 2022 +0000 +++ b/recetox_aplcms_two_step_hybrid.xml Fri Jun 10 10:15:47 2022 +0000 @@ -3,13 +3,7 @@ macros.xml - 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