Mercurial > repos > recetox > recetox_aplcms_unsupervised
diff main.R @ 2:10093dea9b3f draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
| author | recetox |
|---|---|
| date | Fri, 10 Jun 2022 10:14:43 +0000 |
| parents | 4e6281945270 |
| children |
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--- a/main.R Thu May 26 16:46:13 2022 +0000 +++ b/main.R Fri Jun 10 10:14:43 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, ...) {