Mercurial > repos > recetox > recetox_aplcms_unsupervised

comparison main.R @ 2:10093dea9b3f draft default tip

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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
comparison
equal deleted inserted replaced
1:4e6281945270 2:10093dea9b3f
77 unsupervised_main <- function(sample_files, aligned_file, recovered_file, out_format, ...) { 77 unsupervised_main <- function(sample_files, aligned_file, recovered_file, out_format, ...) {
78 sample_files <- sort_samples_by_acquisition_number(sample_files) 78 sample_files <- sort_samples_by_acquisition_number(sample_files)
79 79
80 res <- unsupervised(filenames = sample_files, ...) 80 res <- unsupervised(filenames = sample_files, ...)
81 81
82 save_all_extracted_features(res$extracted_features, sample_files) 82 save_all_features(res, sample_files)
83 save_all_corrected_features(res$corrected_features, sample_files) 83 save_all_feature_tables(res$aligned_feature_sample_table, res$recovered_feature_sample_table, aligned_file, recovered_file, out_format)
84
85 save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file)
86 save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format)
87 } 84 }
88 85
89 hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, pairing_file, aligned_file, recovered_file, out_format, ...) { 86 hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, pairing_file, aligned_file, recovered_file, out_format, ...) {
90 sample_files <- sort_samples_by_acquisition_number(sample_files) 87 sample_files <- sort_samples_by_acquisition_number(sample_files)
91 88
93 res <- hybrid(filenames = sample_files, known_table = known, ...) 90 res <- hybrid(filenames = sample_files, known_table = known, ...)
94 91
95 save_known_table(res$updated_known_table, updated_known_table_file) 92 save_known_table(res$updated_known_table, updated_known_table_file)
96 save_pairing(res$features_known_table_pairing, pairing_file) 93 save_pairing(res$features_known_table_pairing, pairing_file)
97 94
98 save_all_extracted_features(res$extracted_features, sample_files) 95 save_all_features(res, sample_files)
99 save_all_corrected_features(res$corrected_features, sample_files) 96 save_all_feature_tables(res$aligned_feature_sample_table, res$recovered_feature_sample_table, aligned_file, recovered_file, out_format)
97 }
100 98
101 save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file) 99 save_all_features <- function(result, sample_files) {
102 save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format) 100 save_all_extracted_features(result$extracted_features, sample_files)
101 save_all_corrected_features(result$corrected_features, sample_files)
102 }
103
104 save_all_feature_tables <- function(aligned_feature_sample_table,
105 recovered_feature_sample_table,
106 aligned_file,
107 recovered_file,
108 out_format) {
109 save_aligned_feature_table(aligned_feature_sample_table, aligned_file)
110 save_recovered_feature_table(recovered_feature_sample_table, recovered_file, out_format)
103 } 111 }
104 112
105 two_step_hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, recovered_file, aligned_file, out_format, metadata, ...) { 113 two_step_hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, recovered_file, aligned_file, out_format, metadata, ...) {
106 sample_files <- sort_samples_by_acquisition_number(sample_files) 114 sample_files <- sort_samples_by_acquisition_number(sample_files)
107 metadata <- read.table(metadata, sep = ",", header = TRUE) 115 metadata <- read.table(metadata, sep = ",", header = TRUE)