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comparison deseq2.R @ 46:151ed7b41985 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 8f0f0f51f30cc630daebfeae8acae93e84dbd35c
author iuc
date Tue, 06 Jan 2026 11:22:10 +0000
parents 702bdf59d6c8
children
comparison
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45:702bdf59d6c8 46:151ed7b41985
242 for (file in collection_files) { 242 for (file in collection_files) {
243 element_id <- filenames_to_labels[[basename(file)]] 243 element_id <- filenames_to_labels[[basename(file)]]
244 # Find matching row in sample sheet 244 # Find matching row in sample sheet
245 matching_row <- which(sample_sheet[[sample_id_col]] == element_id) 245 matching_row <- which(sample_sheet[[sample_id_col]] == element_id)
246 if (length(matching_row) > 0) { 246 if (length(matching_row) > 0) {
247 level <- sample_sheet[[factor_name]][matching_row[1]] 247 # Convert level to character to ensure consistent list indexing
248 level <- as.character(sample_sheet[[factor_name]][matching_row[1]])
248 if (!(level %in% names(level_to_files))) { 249 if (!(level %in% names(level_to_files))) {
249 level_to_files[[level]] <- character(0) 250 level_to_files[[level]] <- character(0)
250 level_order <- c(level_order, level) # Record order of first appearance 251 level_order <- c(level_order, level) # Record order of first appearance
251 } 252 }
252 level_to_files[[level]] <- c(level_to_files[[level]], file) 253 level_to_files[[level]] <- c(level_to_files[[level]], file)