Mercurial > repos > lain > xseekerpreparator

comparison galaxy/tools/LC-MSMS/XSeekerPreparator.R @ 10:bb9ebd6365ea draft

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" master branch Updating"
author lain
date Thu, 21 Jan 2021 15:00:39 +0000
parents 6748b0663fb4
children f4fc4a0f41e2
comparison
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9:6748b0663fb4 10:bb9ebd6365ea
1 1
2 2
3 TOOL_NAME <- "XSeekerPreparator" 3 TOOL_NAME <- "XSeekerPreparator"
4 VERSION <- "1.1.5" 4 VERSION <- "1.1.6"
5 5
6 OUTPUT_SPECIFIC_TOOL <- "XSeeker_Galaxy" 6 OUTPUT_SPECIFIC_TOOL <- "XSeeker_Galaxy"
7 7
8 ENRICHED_RDATA_VERSION <- paste("1.1.2", OUTPUT_SPECIFIC_TOOL, sep="-") 8 ENRICHED_RDATA_VERSION <- paste("1.1.2", OUTPUT_SPECIFIC_TOOL, sep="-")
9 ENRICHED_RDATA_DOC <- sprintf(" 9 ENRICHED_RDATA_DOC <- sprintf("
642 } 642 }
643 643
644 curent_var_meta <- var_meta[row, ] 644 curent_var_meta <- var_meta[row, ]
645 645
646 peak_list <- context$peaks[context$groupidx[[row]], ] 646 peak_list <- context$peaks[context$groupidx[[row]], ]
647 if (! ("matrix" %in% class(peak_list))) {
648 peak_list <- matrix(peak_list, nrow=1, ncol=length(peak_list), dimnames=list(c(), names(peak_list)))
649 }
647 sample_peak_list <- peak_list[as.integer(peak_list[, "sample"]) == context$sample_no, , drop=FALSE] 650 sample_peak_list <- peak_list[as.integer(peak_list[, "sample"]) == context$sample_no, , drop=FALSE]
648 if (!identical(sample_peak_list, numeric(0)) && !is.null(nrow(sample_peak_list)) && nrow(sample_peak_list) != 0) { 651 if (!identical(sample_peak_list, numeric(0)) && !is.null(nrow(sample_peak_list)) && nrow(sample_peak_list) != 0) {
649 if (!is.na(int_o <- extract_peak_var(sample_peak_list, "into"))) { 652 if (!is.na(int_o <- extract_peak_var(sample_peak_list, "into"))) {
650 dummy_feature$set_int_o(int_o) 653 dummy_feature$set_int_o(int_o)
651 } 654 }