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14
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1 library(getopt)
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2 library(rmarkdown)
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3 library(htmltools)
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4 library(plyr)
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5 library(dplyr)
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6 library(stringr)
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7 library(highcharter)
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8 library(DT)
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9 library(reshape2)
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10 library(plotly)
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11 library(formattable)
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16
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12 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
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1
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13
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14
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14 ##============ Sink warnings and errors to a file ==============
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15 ## use the sink() function to wrap all code within it.
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16 ##==============================================================
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17 zz = file('warnings_and_errors.txt')
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18 sink(zz)
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19 sink(zz, type = 'message')
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20 ##---------below is the code for rendering .Rmd templates-----
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21
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22 ##=============STEP 1: handle command line arguments==========
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23 ##
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24 ##============================================================
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25 # column 1: the long flag name
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26 # column 2: the short flag alias. A SINGLE character string
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27 # column 3: argument mask
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28 # 0: no argument
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29 # 1: argument required
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30 # 2: argument is optional
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31 # column 4: date type to which the flag's argument shall be cast.
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32 # possible values: logical, integer, double, complex, character.
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33 #-------------------------------------------------------------
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34 #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
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35 # 1. short flag alias should match the flag in the command section in the XML file.
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36 # 2. long flag name can be any legal R variable names
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37 # 3. two names in args_list can have common string but one name should not be a part of another name.
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38 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
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39 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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40 args_list=list()
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41 ##------- 1. input data ---------------------
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42 args_list$ECHO = c('echo', 'e', '1', 'character')
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16
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43 args_list$READS_1 = c('reads_1', 'r', '1', 'character')
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44 args_list$NAME_1 = c('name_1', 'n', '1', 'character')
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45 args_list$READS_2 = c('reads_2', 'R', '1', 'character')
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46 args_list$NAME_2 = c('name_2', 'N', '1', 'character')
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47 args_list$CONTAMINANTS = c('contaminants', 'c', '1', 'character')
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48 args_list$LIMITS = c('limits', 'l', '1', 'character')
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14
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49 ##--------2. output report and outputs --------------
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15
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50 args_list$REPORT_HTML = c('report_html', 'o', '1', 'character')
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14
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51 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
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52 args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
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53 ##--------3. .Rmd templates in the tool directory ----------
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15
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54 args_list$FASTQC_REPORT_RMD = c('fastqc_report_rmd', 'p', '1', 'character')
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14
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55 ##-----------------------------------------------------------
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56 opt = getopt(t(as.data.frame(args_list)))
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1
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57
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58
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14
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59
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60 ##=======STEP 2: create report directory (optional)==========
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61 ##
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62 ##===========================================================
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63 dir.create(opt$report_dir)
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64
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65 ##=STEP 3: replace placeholders in .Rmd with argument values=
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66 ##
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67 ##===========================================================
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68 #++ need to replace placeholders with args values one by one+
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69 readLines(opt$fastqc_report_rmd) %>%
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70 (function(x) {
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71 gsub('ECHO', opt$echo, x)
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72 }) %>%
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73 (function(x) {
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16
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74 gsub('READS_1', opt$reads_1, x)
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75 }) %>%
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76 (function(x) {
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77 gsub('NAME_1', opt$name_1, x)
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78 }) %>%
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79 (function(x) {
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80 gsub('READS_2', opt$reads_2, x)
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81 }) %>%
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82 (function(x) {
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83 gsub('NAME_2', opt$name_1, x)
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84 }) %>%
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85 (function(x) {
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86 gsub('CONTAMINANTS', opt$contaminants, x)
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87 }) %>%
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88 (function(x) {
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89 gsub('LIMITS', opt$limits, x)
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14
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90 }) %>%
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91 (function(x) {
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15
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92 gsub('REPORT_DIR', opt$report_dir, x)
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14
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93 }) %>%
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94 (function(x) {
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95 fileConn = file('fastqc_report.Rmd')
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96 writeLines(x, con=fileConn)
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97 close(fileConn)
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98 })
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99
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1
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100
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14
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101 ##=============STEP 4: render .Rmd templates=================
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102 ##
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103 ##===========================================================
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104 render('fastqc_report.Rmd', output_file = opt$report_html)
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1
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105
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106
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14
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107 ##--------end of code rendering .Rmd templates----------------
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108 sink()
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109 ##=========== End of sinking output============================= |
