|
1
|
1 ##======= Handle arguments from command line ========
|
|
|
2 # setup R error handline to go to stderr
|
|
|
3 options(show.error.messages=FALSE,
|
|
|
4 error=function(){
|
|
|
5 cat(geterrmessage(), file=stderr())
|
|
|
6 quit("no", 1, F)
|
|
|
7 })
|
|
|
8
|
|
|
9 # we need that to not crash galaxy with an UTF8 error on German LC settings.
|
|
|
10 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
|
|
|
11
|
|
|
12 # suppress warning
|
|
|
13 options(warn = -1)
|
|
|
14
|
|
|
15 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
|
|
|
16 args = commandArgs(trailingOnly=TRUE)
|
|
|
17
|
|
|
18 suppressPackageStartupMessages({
|
|
|
19 library(getopt)
|
|
|
20 library(tools)
|
|
|
21 })
|
|
|
22
|
|
|
23 # column 1: the long flag name
|
|
|
24 # column 2: the short flag alias. A SINGLE character string
|
|
|
25 # column 3: argument mask
|
|
|
26 # 0: no argument
|
|
|
27 # 1: argument required
|
|
|
28 # 2: argument is optional
|
|
|
29 # column 4: date type to which the flag's argument shall be cast.
|
|
|
30 # possible values: logical, integer, double, complex, character.
|
|
|
31 spec_list=list()
|
|
|
32 spec_list$READS = c('reads', 'r', '1', 'character')
|
|
|
33 spec_list$ECHO = c('echo', 'e', '1', 'character')
|
|
|
34 spec_list$FASTQC_TPL = c('fastqc_tpl', 'p', 1, 'character')
|
|
|
35 spec_list$REPORT = c('report', 'o', '1', 'character')
|
|
|
36 spec_list$REPORT_OUTPUT_DIR = c('report_output_dir', 'd', '1', 'character')
|
|
|
37
|
|
|
38
|
|
|
39 spec = t(as.data.frame(spec_list))
|
|
|
40
|
|
|
41 opt = getopt(spec)
|
|
|
42 # arguments are accessed by long flag name (the first column in the spec matrix)
|
|
|
43 # NOT by element name in the spec_list
|
|
|
44 # example: opt$help, opt$expression_file
|
|
|
45 ##====== End of arguments handling ==========
|
|
|
46
|
|
|
47
|
|
|
48 mgsub = function(pattern, replacement, x) {
|
|
|
49 if(length(pattern) != length(replacement) ) {
|
|
|
50 stop("pattern and replacement have to be the same in length")
|
|
|
51 }
|
|
|
52
|
|
|
53 result = x
|
|
|
54
|
|
|
55 for(i in 1:length(pattern)) {
|
|
|
56 result = try( gsub(pattern[i], replacement[i], x = result) )
|
|
|
57 }
|
|
|
58
|
|
|
59 result
|
|
|
60 }
|
|
|
61
|
|
|
62
|
|
|
63 ##====== replace variables in tpl file ======
|
|
|
64 p = c('READS',
|
|
|
65 'ECHO',
|
|
|
66 'FASTQC_TPL',
|
|
|
67 'REPORT_OUTPUT_DIR',
|
|
|
68 'REPORT')
|
|
|
69 r = c(opt$reads,
|
|
|
70 opt$echo,
|
|
|
71 opt$fastqc_tpl,
|
|
|
72 opt$report_output_dir,
|
|
|
73 opt$report)
|
|
|
74
|
|
|
75 fastqc_report_tpl = mgsub(p, r, readLines(opt$fastqc_tpl))
|
|
|
76
|
|
|
77 ##====== write replaced text into Rmd file ===
|
|
|
78 fileConn = file('fastqc_report.Rmd')
|
|
|
79 writeLines(fastqc_report_tpl, con=fileConn)
|
|
|
80 close(fileConn)
|
|
|
81
|
|
|
82 ##====== render Rmd files ====================
|
|
|
83 rmarkdown::render('fastqc_report.Rmd')
|
|
|
84 file.copy('fastqc_report.html', opt$report, recursive=TRUE)
|
|
|
85 paste0('cp -r ./* ', opt$report_output_dir) %>%
|
|
|
86 system()
|
|
|
87
|
