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1 ##============ Sink warnings and errors to a file ==============
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2 ## use the sink() function to wrap all code within it.
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3 ##==============================================================
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4 zz = file('warnings_and_errors.txt')
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5 sink(zz)
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6 sink(zz, type = 'message')
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7
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8 ##============== load packages ===============================
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9 library(getopt)
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10 library(rmarkdown)
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11 library(htmltools)
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12 library(dplyr)
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13 library(Rsubread)
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14 library(DT)
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15 ##============================================================
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16
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17 ##---------below is the code for rendering .Rmd templates-----
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18
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19 ##=============STEP 1: handle command line arguments==========
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20 ##
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21 ##============================================================
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22 # column 1: the long flag name
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23 # column 2: the short flag alias. A SINGLE character string
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24 # column 3: argument mask
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25 # 0: no argument
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26 # 1: argument required
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27 # 2: argument is optional
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28 # column 4: date type to which the flag's argument shall be cast.
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29 # possible values: logical, integer, double, complex, character.
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30 #-------------------------------------------------------------
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31 #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
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32 # 1. short flag alias should match the flag in the command section in the XML file.
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33 # 2. long flag name can be any legal R variable names
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34 # 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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35 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
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36 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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37 args_list=list()
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38 ##------- 1. input data ---------------------
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39 args_list$e = c('echo', 'e', '1', 'logical')
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40 args_list$a = c('input_bam_paths', 'a', '1', 'character')
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41 args_list$N = c('input_bam_names', 'N', '1', 'character')
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42 args_list$b = c('annot_inbuilt', 'b', '1', 'character')
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43 args_list$c = c('annot_ext', 'c', '1', 'character')
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44 args_list$f = c('isGTFAnnotationFile', 'f', '1', 'logical')
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45 args_list$g = c('gtf_feature_type', 'g', '1', 'character')
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46 args_list$h = c('gtf_attr_type', 'h', '1', 'character')
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47 args_list$i = c('chr_aliases', 'i', '2', 'character')
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48 args_list$j = c('use_meta_features', 'j', '1', 'logical')
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49 args_list$k = c('allow_multi_overlap', 'k', '1', 'logical')
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50 args_list$l = c('min_overlap', 'l', '1', 'integer')
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51 args_list$m = c('largest_overlap', 'm', '1', 'logical')
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52 args_list$n = c('read_extension_5', 'n', '1', 'integer')
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53 args_list$o = c('read_extension_3', 'o', '1', 'integer')
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54 args_list$p = c('read_2_pos', 'p', '1', 'character')
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55 args_list$q = c('count_multi_mapping_reads', 'q', '1', 'logical')
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56 args_list$u = c('fraction', 'u', '1', 'logical')
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57 args_list$v= c('min_mqs', 'v', '1', 'integer')
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58 args_list$w= c('split_only', 'w', '1', 'logical')
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59 args_list$x= c('non_split_only', 'x', '1', 'logical')
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60 args_list$y= c('primary_only', 'y', '1', 'logical')
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61 args_list$z= c('ignore_dup', 'z', '1', 'logical')
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62 args_list$A= c('strand_specific', 'A', '1', 'integer')
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63 args_list$B= c('junc_counts', 'B', '1', 'logical')
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64 args_list$C= c('genome', 'C', '1', 'character')
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65 args_list$D= c('is_paired_end', 'D', '1', 'logical')
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66 args_list$E= c('require_both_ends_mapped', 'E', '1', 'logical')
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67 args_list$F= c('check_frag_length', 'F', '1', 'logical')
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68 args_list$G= c('min_frag_length', 'G', '1', 'integer')
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69 args_list$H= c('max_frag_length', 'H', '1', 'integer')
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70 args_list$I= c('count_chimeric_fragments', 'I', '1', 'logical')
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71 args_list$J= c('auto_sort', 'J', '1', 'logical')
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72 args_list$K= c('n_threads', 'K', '1', 'integer')
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73 args_list$L= c('max_mop', 'L', '1', 'integer')
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74 args_list$M= c('report_reads', 'M', '1', 'logical')
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75
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76 ##--------2. output report and outputs --------------
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77 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
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78 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
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79 args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
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80 ##--------3. .Rmd templates in the tool directory ----------
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81 args_list$TOOL_TEMPLATE_RMD = c('tool_template_rmd', 't', '1', 'character')
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82 ##-----------------------------------------------------------
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83 opt = getopt(t(as.data.frame(args_list)))
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84
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85
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86
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87 ##=======STEP 2: create report directory (optional)==========
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88 ##
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89 ##===========================================================
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90 dir.create(opt$report_dir)
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91
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92 ##=STEP 3: replace placeholders in .Rmd with argument values=
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93 ##
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94 ##===========================================================
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95 #++ need to replace placeholders with args values one by one+
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96 readLines(opt$tool_template_rmd) %>%
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97 (function(x) {
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98 gsub('ECHO', opt$echo, x)
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99 }) %>%
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100 (function(x) {
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101 gsub('REPORT_DIR', opt$report_dir, x)
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102 }) %>%
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103 (function(x) {
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104 fileConn = file('tool_template.Rmd')
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105 writeLines(x, con=fileConn)
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106 close(fileConn)
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107 })
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108
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109
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110 ##=============STEP 4: render .Rmd templates=================
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111 ##
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112 ##===========================================================
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113 render('tool_template.Rmd', output_file = opt$report_html)
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114
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115
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116 ##--------end of code rendering .Rmd templates----------------
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117 sink()
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118 ##=========== End of sinking output=============================
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