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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$ECHO = c('echo', 'e', '1', 'character')
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35 spec_list$DESEQ_WORKSPACE = c('deseq_workspace', 'w', '1', 'character')
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36 spec_list$SAMPLE_TABLE = c('sample_table', 's', '1', 'character')
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37 spec_list$CONTRAST_GROUP = c('contrast_group', 'c', '1', 'character')
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38 spec_list$TREATMENT_LEVEL = c('treatment_level', 't', '1', 'character')
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39 spec_list$CONDITION_LEVEL = c('condition_level', 'k', '1', 'character')
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40 spec_list$CLUSTERING_GROUPS = c('clustering_groups', 'm', '1', 'character')
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41
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42 ##--------2. output report and report site directory --------------
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43 spec_list$OUTPUT_HTML = c('deseq_results_html', 'o', '1', 'character')
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44 spec_list$OUTPUT_DIR = c('deseq_results_dir', 'd', '1', 'character')
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45
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46 ##--------3. Rmd templates sitting in the tool directory ----------
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47
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48 spec_list$DESEQ_VISUALIZATION_RMD = c('deseq_results_rmd', 'D', '1', 'character')
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49
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50
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51
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52 ##------------------------------------------------------------------
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53
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54 spec = t(as.data.frame(spec_list))
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55 opt = getopt(spec)
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56 # arguments are accessed by long flag name (the first column in the spec matrix)
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57 # NOT by element name in the spec_list
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58 # example: opt$help, opt$expression_file
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59 ##====== End of arguments handling ==========
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60
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61 #------ Load libraries ---------
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62 library(rmarkdown)
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63 library(plyr)
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64 library(stringr)
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65 library(dplyr)
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66 library(highcharter)
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67 library(DT)
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68 library(reshape2)
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69 # library(Kmisc)
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70 library(plotly)
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71 library(formattable)
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72 library(htmltools)
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73
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74
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75 #----- 1. create the report directory ------------------------
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76 system(paste0('mkdir -p ', opt$deseq_results_dir))
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77
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78
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79 #----- 2. generate Rmd files with Rmd templates --------------
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80 # a. templates without placeholder variables:
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81 # copy templates from tool directory to the working directory.
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82 # b. templates with placeholder variables:
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83 # substitute variables with user input values and place them in the working directory.
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84
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85
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86 #----- 01 DESeq_results.Rmd -----------------------
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87 readLines(opt$deseq_results_rmd) %>%
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88 (function(x) {
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89 gsub('ECHO', opt$echo, x)
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90 }) %>%
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91 (function(x) {
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92 gsub('DESEQ_WORKSPACE', opt$deseq_workspace, x)
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93 }) %>%
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94 (function(x) {
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95 gsub('CONTRAST_GROUP', opt$contrast_group, x)
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96 }) %>%
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97 (function(x) {
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98 gsub('TREATMENT_LEVEL', opt$treatment_level, x)
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99 }) %>%
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100 (function(x) {
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101 gsub('CONDITION_LEVEL', opt$condition_level, x)
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102 }) %>%
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103 (function(x) {
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104 gsub('CLUSTERING_GROUPS', opt$clustering_groups, x)
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105 }) %>%
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106 (function(x) {
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107 gsub('OUTPUT_DIR', opt$deseq_results_dir, x)
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108 }) %>%
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109 (function(x) {
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110 fileConn = file('DESeq_results.Rmd')
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111 writeLines(x, con=fileConn)
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112 close(fileConn)
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113 })
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114
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115
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116 #------ 3. render all Rmd files --------
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117 render('DESeq_results.Rmd', output_file = opt$deseq_results_html)
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118
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119
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120 #-------4. manipulate outputs -----------------------------
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