deseq2: deseq2.R annotate

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

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

rev	line source
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	1 #!/usr/bin/env Rscript
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	2
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	3 # A command-line interface to DESeq2 for use with Galaxy
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	4 # written by Bjoern Gruening and modified by Michael Love 2016.03.30
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	5 #
26 47267a044ef1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 24 diff changeset	6 # This argument is required:
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	7 #
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	8 # 'factors' a JSON list object from Galaxy
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	9 #
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	10 # the output file has columns:
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	11 #
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	12 # baseMean (mean normalized count)
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	13 # log2FoldChange (by default a moderated LFC estimate)
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	14 # lfcSE (the standard error)
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	15 # stat (the Wald statistic)
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	16 # pvalue (p-value from comparison of Wald statistic to a standard Normal)
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	17 # padj (adjusted p-value, Benjamini Hochberg correction on genes which pass the mean count filter)
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	18 #
26 47267a044ef1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 24 diff changeset	19 # the first variable in 'factors' will be the primary factor.
47267a044ef1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 24 diff changeset	20 # the levels of the primary factor are used in the order of appearance in factors.
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	21 #
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	22 # by default, levels in the order A,B,C produces a single comparison of B vs A, to a single file 'outfile'
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	23 #
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	24 # for the 'many_contrasts' flag, levels in the order A,B,C produces comparisons C vs A, B vs A, C vs B,
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	25 # to a number of files using the 'outfile' prefix: 'outfile.condition_C_vs_A' etc.
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	26 # all plots will still be sent to a single PDF, named by the arg 'plots', with extra pages.
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	27 #
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	28 # fit_type is an integer valued argument, with the options from ?estimateDisperions
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	29 # 1 "parametric"
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	30 # 2 "local"
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	31 # 3 "mean"
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	32
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	33 # setup R error handling to go to stderr
42 6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9 iuc parents: 41 diff changeset	34 options(show.error.messages = FALSE, error = function() {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	35 cat(geterrmessage(), file = stderr())
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	36 q("no", 1, FALSE)
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	37 })
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	38
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	39 library("getopt")
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	40 library("tools")
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	41 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	42 args <- commandArgs(trailingOnly = TRUE)
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	43
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	44 # get options, using the spec as defined by the enclosed list.
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	45 # we read the options from the default: commandArgs(TRUE).
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	46 spec <- matrix(c(
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	47 "quiet", "q", 0, "logical",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	48 "help", "h", 0, "logical",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	49 "cores", "s", 0, "integer",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	50 "batch_factors", "w", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	51 "outfile", "o", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	52 "countsfile", "n", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	53 "sizefactorsfile", "F", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	54 "rlogfile", "r", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	55 "vstfile", "v", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	56 "header", "H", 0, "logical",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	57 "factors", "f", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	58 "files_to_labels", "l", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	59 "plots", "p", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	60 "tximport", "i", 0, "logical",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	61 "txtype", "y", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	62 "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF/GFF3 file
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	63 "esf", "e", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	64 "fit_type", "t", 1, "integer",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	65 "many_contrasts", "m", 0, "logical",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	66 "outlier_replace_off", "a", 0, "logical",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	67 "outlier_filter_off", "b", 0, "logical",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	68 "auto_mean_filter_off", "c", 0, "logical",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	69 "use_beta_priors", "d", 0, "logical",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	70 "alpha_ma", "A", 1, "numeric",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	71 "prefilter", "P", 0, "logical",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	72 "prefilter_value", "V", 1, "numeric",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	73 "sample_sheet_mode", "S", 0, "logical",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	74 "sample_sheet", "g", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	75 "factor_columns", "j", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	76 "reference_level", "R", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	77 "target_level", "T", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	78 "collection_files", "C", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	79 "custom_design_formula", "D", 0, "logical",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	80 "design_formula", "G", 1, "character",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	81 "contrast_definition", "K", 1, "character"
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	82 ), byrow = TRUE, ncol = 4)
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	83 opt <- getopt(spec)
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	84
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	85 # if help was asked for print a friendly message
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	86 # and exit with a non-zero error code
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	87 if (!is.null(opt$help)) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	88 cat(getopt(spec, usage = TRUE))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	89 q(status = 1)
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	90 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	91
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	92 # enforce the following required arguments
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	93 if (is.null(opt$outfile)) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	94 cat("'outfile' is required\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	95 q(status = 1)
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	96 }
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	97 if (is.null(opt$factors) && is.null(opt$sample_sheet_mode)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	98 cat("'factors' is required when not using sample_sheet_mode\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	99 q(status = 1)
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	100 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	101
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	102 verbose <- is.null(opt$quiet)
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	103
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	104 source_local <- function(fname) {
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	105 argv <- commandArgs(trailingOnly = FALSE)
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	106 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	107 source(paste(base_dir, fname, sep = "/"))
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	108 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	109
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	110 source_local("get_deseq_dataset.R")
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	111
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	112 suppressPackageStartupMessages({
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	113 library("DESeq2")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	114 library("RColorBrewer")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	115 library("gplots")
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	116 })
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	117
33 4f497a8a72e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 05bc13637dc9f8e523bc72844ff6eb0794f98ad3 iuc parents: 31 diff changeset	118 if (opt$cores > 1) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	119 library("BiocParallel")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	120 register(MulticoreParam(opt$cores))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	121 parallel <- TRUE
33 4f497a8a72e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 05bc13637dc9f8e523bc72844ff6eb0794f98ad3 iuc parents: 31 diff changeset	122 } else {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	123 parallel <- FALSE
33 4f497a8a72e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 05bc13637dc9f8e523bc72844ff6eb0794f98ad3 iuc parents: 31 diff changeset	124 }
4f497a8a72e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 05bc13637dc9f8e523bc72844ff6eb0794f98ad3 iuc parents: 31 diff changeset	125
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	126 # build or read sample table
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	127
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	128 trim <- function(x) gsub("^\\s+\|\\s+$", "", x)
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	129
45 702bdf59d6c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9 iuc parents: 44 diff changeset	130 # Helper function to decode base64-encoded JSON
702bdf59d6c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9 iuc parents: 44 diff changeset	131 decode_base64_json <- function(encoded_str) {
702bdf59d6c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9 iuc parents: 44 diff changeset	132 decoded_bytes <- base64enc::base64decode(encoded_str)
702bdf59d6c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9 iuc parents: 44 diff changeset	133 decoded_str <- rawToChar(decoded_bytes)
702bdf59d6c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9 iuc parents: 44 diff changeset	134 return(decoded_str)
702bdf59d6c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9 iuc parents: 44 diff changeset	135 }
702bdf59d6c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9 iuc parents: 44 diff changeset	136
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	137 # switch on if 'factors' was provided:
26 47267a044ef1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 24 diff changeset	138 library("rjson")
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	139
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	140 if (!is.null(opt$sample_sheet_mode)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	141 # Sample sheet mode: build factor_list from sample sheet
45 702bdf59d6c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9 iuc parents: 44 diff changeset	142 filenames_to_labels <- fromJSON(decode_base64_json(opt$files_to_labels))
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	143
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	144 # Read sample sheet
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	145 sample_sheet <- read.table(opt$sample_sheet, sep = "\t", header = TRUE, stringsAsFactors = FALSE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	146
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	147 # Parse collection files
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	148 collection_files <- strsplit(opt$collection_files, ",")[[1]]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	149
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	150 # First column of sample sheet should contain sample identifiers
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	151 sample_id_col <- colnames(sample_sheet)[1]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	152
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	153 if (!is.null(opt$custom_design_formula)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	154 # Custom design formula mode
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	155 # Extract variable names from formula (remove ~, +, *, :, whitespace)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	156 formula_str <- gsub("^~\\s*", "", opt$design_formula)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	157 formula_vars <- unique(trimws(unlist(strsplit(formula_str, "[+*:]"))))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	158
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	159 # Validate all variables exist in sample sheet
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	160 missing_vars <- setdiff(formula_vars, colnames(sample_sheet))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	161 if (length(missing_vars) > 0) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	162 cat(paste0("Error: Variables not found in sample sheet: ", paste(missing_vars, collapse = ", "), "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	163 cat(paste0("Available columns: ", paste(colnames(sample_sheet), collapse = ", "), "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	164 q(status = 1)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	165 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	166
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	167 # Use all formula variables as factor columns
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	168 factor_col_names <- formula_vars
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	169 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	170 # Automatic mode: Parse factor columns (comma-separated column numbers, 1-indexed)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	171 factor_col_nums <- as.integer(strsplit(opt$factor_columns, ",")[[1]])
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	172 factor_col_names <- colnames(sample_sheet)[factor_col_nums]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	173 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	174
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	175 # Validate sample sheet matches collection before building factor_list
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	176 # Get element identifiers from collection
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	177 collection_element_ids <- character(length(collection_files))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	178 for (idx in seq_along(collection_files)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	179 file <- collection_files[idx]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	180 file_basename <- basename(file)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	181 if (file_basename %in% names(filenames_to_labels)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	182 collection_element_ids[idx] <- filenames_to_labels[[file_basename]]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	183 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	184 cat("Error: Sample sheet validation failed\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	185 cat(paste0("Collection file '", file_basename, "' does not have a corresponding element identifier.\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	186 cat("This is an internal error - please report this issue.\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	187 q(status = 1)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	188 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	189 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	190
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	191 # Get sample identifiers from sample sheet
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	192 sample_sheet_ids <- sample_sheet[[sample_id_col]]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	193
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	194 # Check for mismatches
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	195 collection_not_in_sheet <- setdiff(collection_element_ids, sample_sheet_ids)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	196 sheet_not_in_collection <- setdiff(sample_sheet_ids, collection_element_ids)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	197
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	198 if (length(collection_not_in_sheet) > 0 \|\| length(sheet_not_in_collection) > 0) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	199 cat("Error: Sample sheet does not match the input collection\n\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	200
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	201 if (length(collection_not_in_sheet) > 0) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	202 cat("The following samples are in the collection but NOT in the sample sheet:\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	203 for (id in collection_not_in_sheet) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	204 cat(paste0(" - ", id, "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	205 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	206 cat("\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	207 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	208
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	209 if (length(sheet_not_in_collection) > 0) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	210 cat("The following samples are in the sample sheet but NOT in the collection:\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	211 for (id in sheet_not_in_collection) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	212 cat(paste0(" - ", id, "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	213 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	214 cat("\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	215 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	216
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	217 cat("Please ensure that:\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	218 cat(paste0("1. The first column ('", sample_id_col, "') of the sample sheet contains sample identifiers\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	219 cat("2. These identifiers exactly match the element identifiers in your collection\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	220 cat("3. All samples in the collection are listed in the sample sheet\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	221 cat("4. All samples in the sample sheet exist in the collection\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	222 q(status = 1)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	223 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	224
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	225 # Determine which factor will be the primary factor for contrasts
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	226 # In custom mode, the primary factor is the last one in the formula (rightmost term)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	227 # In automatic mode, the first selected factor is primary (formula gets reversed)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	228 if (!is.null(opt$custom_design_formula)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	229 primary_factor_index <- length(factor_col_names)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	230 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	231 primary_factor_index <- 1
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	232 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	233
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	234 # Build factor_list structure
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	235 factor_list <- list()
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	236 for (i in seq_along(factor_col_names)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	237 factor_name <- factor_col_names[i]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	238
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	239 # Group files by factor level, preserving the order of first appearance
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	240 level_to_files <- list()
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	241 level_order <- character(0) # Track order of first appearance
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	242 for (file in collection_files) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	243 element_id <- filenames_to_labels[[basename(file)]]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	244 # Find matching row in sample sheet
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	245 matching_row <- which(sample_sheet[[sample_id_col]] == element_id)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	246 if (length(matching_row) > 0) {
46 151ed7b41985 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 8f0f0f51f30cc630daebfeae8acae93e84dbd35c iuc parents: 45 diff changeset	247 # Convert level to character to ensure consistent list indexing
151ed7b41985 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 8f0f0f51f30cc630daebfeae8acae93e84dbd35c iuc parents: 45 diff changeset	248 level <- as.character(sample_sheet[[factor_name]][matching_row[1]])
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	249 if (!(level %in% names(level_to_files))) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	250 level_to_files[[level]] <- character(0)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	251 level_order <- c(level_order, level) # Record order of first appearance
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	252 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	253 level_to_files[[level]] <- c(level_to_files[[level]], file)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	254 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	255 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	256
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	257 # Get all levels in order of first appearance (not alphabetically sorted)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	258 all_levels <- level_order
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	259
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	260 # Handle reference and target levels for the primary contrast factor
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	261 # In custom mode: this is the LAST factor in the formula
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	262 # In automatic mode: this is the FIRST factor selected (formula will be reversed)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	263 if (i == primary_factor_index) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	264 # This is the primary factor for contrasts: handle reference/target
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	265 # Determine reference level
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	266 if (!is.null(opt$reference_level) && nchar(opt$reference_level) > 0) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	267 ref_level <- trim(opt$reference_level)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	268 # Validate that reference level exists
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	269 if (!(ref_level %in% all_levels)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	270 cat(paste0("Error: Reference level '", ref_level, "' not found in factor '", factor_name, "'. Available levels: ", paste(all_levels, collapse = ", "), "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	271 q(status = 1)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	272 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	273 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	274 # Default: use first level encountered in sample sheet as reference
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	275 ref_level <- all_levels[1]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	276 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	277
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	278 # Build factor levels with reference first, then others
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	279 # This applies to both automatic and custom modes
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	280 if (!is.null(opt$target_level) && nchar(opt$target_level) > 0) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	281 target_level <- trim(opt$target_level)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	282 # Validate that target level exists
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	283 if (!(target_level %in% all_levels)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	284 cat(paste0("Error: Target level '", target_level, "' not found in factor '", factor_name, "'. Available levels: ", paste(all_levels, collapse = ", "), "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	285 q(status = 1)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	286 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	287 # Explicit target: reference first, target second
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	288 levels_to_use <- c(ref_level, target_level)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	289 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	290 # Reference first, then others in order of appearance
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	291 other_levels <- all_levels[all_levels != ref_level]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	292 levels_to_use <- c(ref_level, other_levels)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	293 # Target is the first non-reference level
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	294 target_level <- other_levels[1]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	295 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	296
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	297 # Store reference and target levels for later contrast specification
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	298 # This ensures we use the intended levels, not whatever order files happened to be in
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	299 primary_ref_level <- ref_level
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	300 primary_target_level <- target_level
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	301 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	302 # For secondary factors, use all levels in order of appearance
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	303 levels_to_use <- all_levels
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	304 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	305
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	306 # Build factor structure in the order specified by levels_to_use
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	307 # Following standard DESeq2 convention: reference level is first
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	308 factor_levels <- list()
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	309 for (level in levels_to_use) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	310 if (level %in% names(level_to_files)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	311 level_entry <- list()
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	312 level_entry[[level]] <- level_to_files[[level]]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	313 factor_levels[[length(factor_levels) + 1]] <- level_entry
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	314 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	315 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	316
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	317 factor_list[[length(factor_list) + 1]] <- list(factor_name, factor_levels)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	318 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	319
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	320 # Set primary_factor for sample sheet mode
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	321 # This is the factor that will be used for contrasts
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	322 if (!is.null(opt$custom_design_formula)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	323 # Custom mode: primary factor is the last one in the formula (rightmost term)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	324 primary_factor <- factor_col_names[length(factor_col_names)]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	325 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	326 # Automatic mode: primary factor is the first selected factor (formula will be reversed)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	327 primary_factor <- factor_col_names[1]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	328 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	329
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	330 # Parse contrast_definition if in custom mode
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	331 if (!is.null(opt$custom_design_formula) && !is.null(opt$contrast_definition) && nchar(opt$contrast_definition) > 0) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	332 contrast_parts <- strsplit(opt$contrast_definition, ",")[[1]]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	333 if (length(contrast_parts) != 3) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	334 cat("Error: contrast_definition must be in format 'factor,target,reference'\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	335 q(status = 1)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	336 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	337 custom_contrast <- list(
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	338 factor = trim(contrast_parts[1]),
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	339 target = trim(contrast_parts[2]),
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	340 reference = trim(contrast_parts[3])
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	341 )
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	342 # Validate the contrast
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	343 if (!(custom_contrast$factor %in% factor_col_names)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	344 cat(paste0("Error: Contrast factor '", custom_contrast$factor, "' not found in design formula.\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	345 cat(paste0("Available factors: ", paste(factor_col_names, collapse = ", "), "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	346 q(status = 1)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	347 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	348 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	349 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	350 # Original mode: factors provided directly
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	351 parser <- newJSONParser()
45 702bdf59d6c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9 iuc parents: 44 diff changeset	352 parser$addData(decode_base64_json(opt$factors))
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	353 factor_list <- parser$getObject()
45 702bdf59d6c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9 iuc parents: 44 diff changeset	354 filenames_to_labels <- fromJSON(decode_base64_json(opt$files_to_labels))
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	355
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	356 # For original mode, extract reference and target levels from the first factor
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	357 # In original mode: ref=level1 (denominator), target=level2 (numerator) -> log2(level2/level1)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	358 # So we swap the naming to match the contrast direction used below
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	359 primary_factor_data <- factor_list[[1]]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	360 primary_levels <- sapply(primary_factor_data[[2]], function(x) names(x))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	361 primary_target_level <- primary_levels[1] # First level becomes "target" for the swap below
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	362 primary_ref_level <- if (length(primary_levels) >= 2) primary_levels[2] else primary_levels[1] # Second level becomes "ref"
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	363 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	364
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	365 factors <- sapply(factor_list, function(x) x[[1]])
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	366 # For original mode (not sample_sheet_mode), set primary_factor to first factor
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	367 # In sample_sheet_mode, it's already set correctly above
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	368 if (is.null(opt$sample_sheet_mode)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	369 primary_factor <- factors[1]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	370 }
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	371 filenames_in <- unname(unlist(factor_list[[1]][[2]]))
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	372 labs <- unname(unlist(filenames_to_labels[basename(filenames_in)]))
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	373 sample_table <- data.frame(
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	374 sample = basename(filenames_in),
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	375 filename = filenames_in,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	376 row.names = filenames_in,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	377 stringsAsFactors = FALSE
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	378 )
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	379 for (factor in factor_list) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	380 factor_name <- trim(factor[[1]])
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	381 sample_table[[factor_name]] <- character(nrow(sample_table))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	382 lvls <- sapply(factor[[2]], function(x) names(x))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	383 for (i in seq_along(factor[[2]])) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	384 files <- factor[[2]][[i]][[1]]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	385 sample_table[files, factor_name] <- trim(lvls[i])
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	386 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	387 sample_table[[factor_name]] <- factor(sample_table[[factor_name]], levels = lvls)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	388 # Explicitly set the reference level using relevel() for the primary factor in sample_sheet_mode
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	389 # This ensures DESeq2 knows the reference regardless of factor level order
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	390 # In original mode, we don't relevel because the order from factor_list is already correct
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	391 # Note: primary_factor is already set correctly in sample_sheet_mode before we get here
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	392 if (exists("primary_factor") && factor_name == primary_factor && exists("primary_ref_level") && !is.null(opt$sample_sheet_mode)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	393 sample_table[[factor_name]] <- relevel(sample_table[[factor_name]], ref = primary_ref_level)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	394 }
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	395 }
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	396 rownames(sample_table) <- labs
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	397
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	398 # Build design formula
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	399 if (!is.null(opt$custom_design_formula)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	400 # Custom mode: use user-provided formula
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	401 design_formula <- as.formula(opt$design_formula)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	402 # In original mode (not sample_sheet), set primary factor to last variable in formula
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	403 # In sample_sheet_mode, it's already set correctly above
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	404 if (is.null(opt$sample_sheet_mode)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	405 primary_factor <- factors[length(factors)]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	406 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	407 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	408 # Automatic mode: build from selected factors
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	409 design_formula <- as.formula(paste("~", paste(rev(factors), collapse = " + ")))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	410 }
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	411
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	412 # these are plots which are made once for each analysis
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	413 generate_generic_plots <- function(dds, factors) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	414 library("ggplot2")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	415 library("ggrepel")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	416 library("pheatmap")
24 1a34aec44d60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418 iuc parents: 23 diff changeset	417
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	418 rld <- rlog(dds)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	419 p <- plotPCA(rld, intgroup = rev(factors))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	420 print(p + geom_text_repel(aes_string(x = "PC1", y = "PC2", label = factor(colnames(dds))), size = 3) + geom_point())
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	421 dat <- assay(rld)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	422 dists_rl <- dist(t(dat))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	423 mat <- as.matrix(dists_rl)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	424 colors <- colorRampPalette(rev(brewer.pal(9, "Blues")))(255)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	425 pheatmap(
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	426 mat,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	427 clustering_distance_rows = dists_rl,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	428 clustering_distance_cols = dists_rl,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	429 col = colors,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	430 main = "Sample-to-sample distances"
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	431 )
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	432 plotDispEsts(dds, main = "Dispersion estimates")
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	433 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	434
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	435 # these are plots which can be made for each comparison, e.g.
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	436 # once for C vs A and once for B vs A
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	437 generate_specific_plots <- function(res, threshold, title_suffix) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	438 use <- res$baseMean > threshold
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	439 if (sum(!use) == 0) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	440 h <- hist(res$pvalue, breaks = 0:50 / 50, plot = FALSE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	441 barplot(
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	442 height = h$counts,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	443 col = "powderblue",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	444 space = 0,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	445 xlab = "p-values",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	446 ylab = "frequency",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	447 main = paste("Histogram of p-values for", title_suffix)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	448 )
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	449 text(x = c(0, length(h$counts)), y = 0, label = paste(c(0, 1)), adj = c(0.5, 1.7), xpd = NA)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	450 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	451 h1 <- hist(res$pvalue[!use], breaks = 0:50 / 50, plot = FALSE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	452 h2 <- hist(res$pvalue[use], breaks = 0:50 / 50, plot = FALSE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	453 colori <- c("filtered (low count)" = "khaki", "not filtered" = "powderblue")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	454 barplot(
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	455 height = rbind(h1$counts, h2$counts),
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	456 beside = FALSE,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	457 col = colori,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	458 space = 0,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	459 xlab = "p-values",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	460 ylab = "frequency",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	461 main = paste("Histogram of p-values for", title_suffix)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	462 )
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	463 text(x = c(0, length(h1$counts)), y = 0, label = paste(c(0, 1)), adj = c(0.5, 1.7), xpd = NA)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	464 legend("topright", fill = rev(colori), legend = rev(names(colori)), bg = "white")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	465 }
39 b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05" iuc parents: 37 diff changeset	466 plotMA(res, main = paste("MA-plot for", title_suffix), ylim = range(res$log2FoldChange, na.rm = TRUE), alpha = opt$alpha_ma)
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	467 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	468
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	469 if (verbose) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	470 cat(paste("primary factor:", primary_factor, "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	471 if (length(factors) > 1) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	472 cat(paste("other factors in design:", paste(factors[-length(factors)], collapse = ","), "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	473 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	474 cat("\n---------------------\n")
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	475 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	476
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	477 dds <- get_deseq_dataset(sample_table, header = opt$header, design_formula = design_formula, tximport = opt$tximport, txtype = opt$txtype, tx2gene = opt$tx2gene)
43 621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	478
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	479 # use/estimate size factors with the chosen method
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	480 if (!is.null(opt$esf)) {
43 621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	481 if (opt$esf %in% list("ratio", "poscounts", "iterate")) {
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	482 cat("Calculating size factors de novo\n")
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	483 dds <- estimateSizeFactors(dds, type = opt$esf)
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	484 } else {
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	485 sf_table <- read.table(opt$esf)
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	486 # Sort the provided size factors just in case the order differs from the input file order.
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	487 merged_table <- merge(sample_table, sf_table, by.x = 0, by.y = 1, sort = FALSE)
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	488 sf_values <- as.numeric(unlist(merged_table[5]))
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	489 "sizeFactors"(dds) <- sf_values
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	490
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	491 cat("Using user-provided size factors:\n")
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	492 print(sf_values)
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	493 }
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	494 } else {
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	495 cat("No size factor was used\n")
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	496 }
41 0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	497
43 621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	498
41 0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	499 # estimate size factors for each sample
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	500 # - https://support.bioconductor.org/p/97676/
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	501 if (!is.null(opt$sizefactorsfile)) {
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	502 nm <- assays(dds)[["avgTxLength"]]
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	503 if (!is.null(nm)) {
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	504 ## Recommended: takes into account tximport data
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	505 cat("\nsize factors for samples: taking tximport data into account\n")
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	506 size_factors <- estimateSizeFactorsForMatrix(counts(dds) / nm)
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	507 } else {
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	508 norm_factors <- normalizationFactors(dds)
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	509 if (!is.null(norm_factors)) {
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	510 ## In practice, gives same results as above.
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	511 cat("\nsize factors for samples: no tximport data, using derived normalization factors\n")
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	512 size_factors <- estimateSizeFactorsForMatrix(norm_factors)
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	513 } else {
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	514 ## If we have no other information, estimate from raw.
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	515 cat("\nsize factors for samples: no tximport data, no normalization factors, estimating from raw data\n")
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	516 size_factors <- estimateSizeFactorsForMatrix(counts(dds))
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	517 }
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	518 }
42 6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9 iuc parents: 41 diff changeset	519 write.table(size_factors, file = opt$sizefactorsfile, sep = "\t", col.names = FALSE, quote = FALSE)
41 0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	520 }
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07" iuc parents: 39 diff changeset	521
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	522 apply_batch_factors <- function(dds, batch_factors) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	523 rownames(batch_factors) <- batch_factors$identifier
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	524 batch_factors <- subset(batch_factors, select = -c(identifier, condition))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	525 dds_samples <- colnames(dds)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	526 batch_samples <- rownames(batch_factors)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	527 if (!setequal(batch_samples, dds_samples)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	528 stop("Batch factor names don't correspond to input sample names, check input files")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	529 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	530 dds_data <- colData(dds)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	531 # Merge dds_data with batch_factors using indexes, which are sample names
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	532 # Set sort to False, which maintains the order in dds_data
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	533 reordered_batch <- merge(dds_data, batch_factors, by.x = 0, by.y = 0, sort = FALSE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	534 batch_factors <- reordered_batch[, ncol(dds_data):ncol(reordered_batch)]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	535 for (factor in colnames(batch_factors)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	536 dds[[factor]] <- batch_factors[[factor]]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	537 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	538 colnames(dds) <- reordered_batch[, 1]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	539 return(dds)
29 66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	540 }
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	541
29 66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	542 if (!is.null(opt$batch_factors)) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	543 batch_factors <- read.table(opt$batch_factors, sep = "\t", header = TRUE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	544 dds <- apply_batch_factors(dds = dds, batch_factors = batch_factors)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	545 batch_design <- colnames(batch_factors)[-c(1, 2)]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	546
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	547 if (!is.null(opt$custom_design_formula)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	548 # Custom mode: prepend batch factors to user's formula
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	549 user_formula_rhs <- gsub("^~\\s*", "", opt$design_formula)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	550 design_formula <- as.formula(paste("~", paste(c(batch_design, user_formula_rhs), collapse = " + ")))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	551 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	552 # Automatic mode: prepend batch factors to generated formula
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	553 design_formula <- as.formula(paste("~", paste(c(batch_design, rev(factors)), collapse = " + ")))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	554 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	555 design(dds) <- design_formula
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	556 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	557
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	558 if (verbose) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	559 cat("DESeq2 run information\n\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	560 cat("sample table:\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	561 print(sample_table[, -c(1:2), drop = FALSE])
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	562 cat("\ndesign formula:\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	563 print(design_formula)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	564 cat("\n\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	565 cat(paste(ncol(dds), "samples with counts over", nrow(dds), "genes\n"))
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	566 }
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	567
42 6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9 iuc parents: 41 diff changeset	568 # minimal pre-filtering
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9 iuc parents: 41 diff changeset	569 if (!is.null(opt$prefilter)) {
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9 iuc parents: 41 diff changeset	570 keep <- rowSums(counts(dds)) >= opt$prefilter_value
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9 iuc parents: 41 diff changeset	571 dds <- dds[keep, ]
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9 iuc parents: 41 diff changeset	572 }
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9 iuc parents: 41 diff changeset	573
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	574 # optional outlier behavior
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	575 if (is.null(opt$outlier_replace_off)) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	576 min_rep <- 7
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	577 } else {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	578 min_rep <- Inf
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	579 if (verbose) cat("outlier replacement off\n")
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	580 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	581 if (is.null(opt$outlier_filter_off)) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	582 cooks_cutoff <- TRUE
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	583 } else {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	584 cooks_cutoff <- FALSE
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	585 if (verbose) cat("outlier filtering off\n")
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	586 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	587
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	588 # optional automatic mean filtering
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	589 if (is.null(opt$auto_mean_filter_off)) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	590 independent_filtering <- TRUE
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	591 } else {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	592 independent_filtering <- FALSE
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	593 if (verbose) cat("automatic filtering on the mean off\n")
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	594 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	595
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	596 # shrinkage of LFCs
43 621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	597 if (is.null(opt$use_beta_priors)) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	598 beta_prior <- FALSE
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	599 if (verbose) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	600 cat("Applied default - beta prior off\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	601 }
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	602 } else {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	603 beta_prior <- opt$use_beta_priors
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	604 }
43 621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	605 sprintf("use_beta_prior is set to %s", beta_prior)
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf iuc parents: 42 diff changeset	606
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	607
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	608 # dispersion fit type
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	609 if (is.null(opt$fit_type)) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	610 fit_type <- "parametric"
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	611 } else {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	612 fit_type <- c("parametric", "local", "mean")[opt$fit_type]
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	613 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	614
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	615 if (verbose) cat(paste("using disperion fit type:", fit_type, "\n"))
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	616
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	617 # run the analysis
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	618 dds <- DESeq(dds, fitType = fit_type, betaPrior = beta_prior, minReplicatesForReplace = min_rep, parallel = parallel)
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	619
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	620 # create the generic plots and leave the device open
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	621 if (!is.null(opt$plots)) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	622 if (verbose) cat("creating plots\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	623 pdf(opt$plots)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	624 generate_generic_plots(dds, factors)
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	625 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	626
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	627 n <- nlevels(colData(dds)[[primary_factor]])
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	628 all_levels <- levels(colData(dds)[[primary_factor]])
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	629
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	630 if (!is.null(opt$countsfile)) {
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	631 normalized_counts <- counts(dds, normalized = TRUE)
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	632 write.table(normalized_counts, file = opt$countsfile, sep = "\t", col.names = NA, quote = FALSE)
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	633 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	634
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	635 if (!is.null(opt$rlogfile)) {
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	636 rlog_normalized <- rlogTransformation(dds)
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	637 rlog_normalized_mat <- assay(rlog_normalized)
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	638 write.table(rlog_normalized_mat, file = opt$rlogfile, sep = "\t", col.names = NA, quote = FALSE)
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	639 }
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	640
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	641 if (!is.null(opt$vstfile)) {
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	642 vst_normalized <- varianceStabilizingTransformation(dds)
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	643 vst_normalized_mat <- assay(vst_normalized)
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	644 write.table(vst_normalized_mat, file = opt$vstfile, sep = "\t", col.names = NA, quote = FALSE)
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	645 }
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	646
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	647
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	648 if (is.null(opt$many_contrasts)) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	649 # Single contrast mode
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	650 if (!is.null(opt$custom_design_formula) && exists("custom_contrast")) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	651 # Use explicit custom contrast
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	652 ref <- custom_contrast$reference
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	653 lvl <- custom_contrast$target
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	654 contrast_factor <- custom_contrast$factor
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	655 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	656 # Default: contrast using stored reference and target levels
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	657 # This ensures we use the intended reference, not whatever order files happened to be in
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	658
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	659 # Check if we have more than 2 levels without explicit target
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	660 if (length(all_levels) > 2 && is.null(opt$target_level)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	661 cat("Error: Multiple factor levels detected without explicit target_level specification.\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	662 cat(paste0("Factor '", primary_factor, "' has ", length(all_levels), " levels: ", paste(all_levels, collapse = ", "), "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	663 cat("Please either:\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	664 cat(" 1. Specify target_level to indicate which level to compare against the reference, or\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	665 cat(" 2. Use many_contrasts mode to compare all levels pairwise\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	666 q(status = 1)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	667 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	668
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	669 # Use stored reference and target levels
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	670 # contrast = c(factor, level1, level2) computes log2(level1 / level2)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	671 # In original mode: variable names were swapped for backward compatibility
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	672 # In sample_sheet_mode: use them directly (ref=denominator, target=numerator)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	673 if (!is.null(opt$sample_sheet_mode)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	674 # Sample sheet mode: use natural order
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	675 ref <- primary_ref_level # Reference is denominator
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	676 lvl <- primary_target_level # Target is numerator
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	677 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	678 # Original mode: swap for backward compatibility
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	679 ref <- primary_target_level # This becomes the denominator
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	680 lvl <- primary_ref_level # This becomes the numerator
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	681 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	682 contrast_factor <- primary_factor
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	683 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	684
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	685 res <- results(
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	686 dds,
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	687 contrast = c(contrast_factor, lvl, ref),
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	688 cooksCutoff = cooks_cutoff,
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	689 independentFiltering = independent_filtering
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	690 )
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	691 if (verbose) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	692 cat("summary of results\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	693 cat(paste0(contrast_factor, ": ", lvl, " vs ", ref, "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	694 print(summary(res))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	695 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	696 res_sorted <- res[order(res$padj), ]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	697 out_df <- as.data.frame(res_sorted)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	698 out_df$geneID <- rownames(out_df) # nolint
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	699 out_df <- out_df[, c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	700 filename <- opt$outfile
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	701 write.table(out_df, file = filename, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	702 if (independent_filtering) {
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	703 threshold <- unname(attr(res, "filterThreshold"))
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	704 } else {
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	705 threshold <- 0
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	706 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	707 title_suffix <- paste0(primary_factor, ": ", lvl, " vs ", ref)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	708 if (!is.null(opt$plots)) {
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	709 generate_specific_plots(res, threshold, title_suffix)
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	710 }
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	711 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	712 # rotate through the possible contrasts of the primary factor
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	713 # write out a sorted table of results with the contrast as a suffix
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	714 # add contrast specific plots to the device
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	715 for (i in seq_len(n - 1)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	716 ref <- all_levels[i]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	717 contrast_levels <- all_levels[(i + 1):n]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	718 for (lvl in contrast_levels) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	719 res <- results(
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	720 dds,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	721 contrast = c(primary_factor, lvl, ref),
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	722 cooksCutoff = cooks_cutoff,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	723 independentFiltering = independent_filtering
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	724 )
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	725 res_sorted <- res[order(res$padj), ]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	726 out_df <- as.data.frame(res_sorted)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	727 out_df$geneID <- rownames(out_df) # nolint
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	728 out_df <- out_df[, c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	729 filename <- paste0(primary_factor, "_", lvl, "_vs_", ref)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	730 write.table(out_df, file = filename, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	731 if (independent_filtering) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	732 threshold <- unname(attr(res, "filterThreshold"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	733 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	734 threshold <- 0
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	735 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	736 title_suffix <- paste0(primary_factor, ": ", lvl, " vs ", ref)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	737 if (!is.null(opt$plots)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	738 generate_specific_plots(res, threshold, title_suffix)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	739 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	740 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	741 }
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	742 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	743
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	744 # close the plot device
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	745 if (!is.null(opt$plots)) {
44 1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	746 cat("closing plot device\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594 iuc parents: 43 diff changeset	747 dev.off()
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	748 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	749
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	750 cat("Session information:\n\n")
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	751
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: diff changeset	752 sessionInfo()

Mercurial > repos > iuc > deseq2

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