Mercurial > repos > lain > xseekerpreparator

comparison galaxy/tools/LC-MSMS/XSeekerPreparator.R @ 9:6748b0663fb4 draft

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" master branch Updating"
author lain
date Thu, 21 Jan 2021 13:31:18 +0000
parents b7ebb4748e59
children bb9ebd6365ea
comparison
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8:b7ebb4748e59 9:6748b0663fb4
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2 2
3 TOOL_NAME <- "XSeekerPreparator" 3 TOOL_NAME <- "XSeekerPreparator"
4 VERSION <- "1.1.4" 4 VERSION <- "1.1.5"
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 sample_peak_list <- peak_list[peak_list[, "sample"] == context$sample_no, , drop=FALSE] 647 sample_peak_list <- peak_list[as.integer(peak_list[, "sample"]) == context$sample_no, , drop=FALSE]
648 if (!identical(sample_peak_list, numeric(0)) && !is.null(nrow(sample_peak_list)) && nrow(sample_peak_list) != 0) { 648 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"))) { 649 if (!is.na(int_o <- extract_peak_var(sample_peak_list, "into"))) {
650 dummy_feature$set_int_o(int_o) 650 dummy_feature$set_int_o(int_o)
651 } 651 }
652 if (!is.na(int_b <- extract_peak_var(sample_peak_list, "intb"))) { 652 if (!is.na(int_b <- extract_peak_var(sample_peak_list, "intb"))) {