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1 ##======= Handle arguments from command line ========
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2 # setup R error handline to go to stderr
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3 options(show.error.messages=FALSE,
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4 error=function(){
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5 cat(geterrmessage(), file=stderr())
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6 quit("no", 1, F)
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7 })
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8
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9 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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10 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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11
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12 # suppress warning
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13 options(warn = -1)
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14
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15 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
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16 args = commandArgs(trailingOnly=TRUE)
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17
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18 suppressPackageStartupMessages({
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19 library(getopt)
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20 library(tools)
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21 })
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22
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23 # column 1: the long flag name
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24 # column 2: the short flag alias. A SINGLE character string
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25 # column 3: argument mask
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26 # 0: no argument
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27 # 1: argument required
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28 # 2: argument is optional
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29 # column 4: date type to which the flag's argument shall be cast.
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30 # possible values: logical, integer, double, complex, character.
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31 spec_list=list()
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32
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33 ##------- 1. input data ---------------------
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34 spec_list$COUNT_FILES = c('count_files', 'c', '1', 'character')
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35 spec_list$ECHO = c('echo', 'e', '1', 'character')
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36 spec_list$SAMPLE_TABLE = c('sample_table', 's', '1', 'character')
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37 spec_list$DESIGN_FORMULA = c('design_formula', 'p', '1', 'character')
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38
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39 ##--------2. output report and report site directory --------------
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40 spec_list$OUTPUT_HTML = c('deseq_html', 'o', '1', 'character')
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41 spec_list$OUTPUT_DIR = c('deseq_dir', 'd', '1', 'character')
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42 spec_list$WORKSPACE = c('deseq_workspace', 'w', '1', 'character')
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43
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44 ##--------3. Rmd templates sitting in the tool directory ----------
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45
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46 spec_list$DESEQ_RMD = c('deseq_rmd', 'D', '1', 'character')
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47
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48
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49
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50 ##------------------------------------------------------------------
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51
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52 spec = t(as.data.frame(spec_list))
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53 opt = getopt(spec)
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54 # arguments are accessed by long flag name (the first column in the spec matrix)
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55 # NOT by element name in the spec_list
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56 # example: opt$help, opt$expression_file
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57 ##====== End of arguments handling ==========
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58
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59 #------ Load libraries ---------
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60 library(rmarkdown)
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61 library(plyr)
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62 library(stringr)
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63 library(dplyr)
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64 library(highcharter)
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65 library(DT)
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66 library(reshape2)
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67 # library(Kmisc)
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68 library(plotly)
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69 library(formattable)
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70 library(htmltools)
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71
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72
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73 #----- 1. create the report directory ------------------------
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74 system(paste0('mkdir -p ', opt$deseq_dir))
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75
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76
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77 #----- 2. generate Rmd files with Rmd templates --------------
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78 # a. templates without placeholder variables:
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79 # copy templates from tool directory to the working directory.
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80 # b. templates with placeholder variables:
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81 # substitute variables with user input values and place them in the working directory.
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82
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83
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84 #----- 01 DESeq.Rmd -----------------------
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85 readLines(opt$deseq_rmd) %>%
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86 (function(x) {
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87 gsub('ECHO', opt$echo, x)
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88 }) %>%
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89 (function(x) {
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90 gsub('DESEQ_WORKSPACE', opt$deseq_workspace, x)
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91 }) %>%
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92 (function(x) {
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93 gsub('DESIGN_FORMULA', opt$design_formula, x)
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94 }) %>%
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95 (function(x) {
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96 gsub('OUTPUT_DIR', opt$deseq_dir, x)
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97 }) %>%
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98 (function(x) {
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99 fileConn = file('DESeq.Rmd')
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100 writeLines(x, con=fileConn)
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101 close(fileConn)
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102 })
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103
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104
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105 #------ 3. render all Rmd files --------
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106 render('DESeq.Rmd', output_file = opt$deseq_html)
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107
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108
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109 #-------4. manipulate outputs -----------------------------
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110 # document file
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111 # file.copy('DESeq.html', opt$deseq_html, recursive = TRUE)
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112
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113
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