Mercurial > repos > mingchen0919 > rmarkdown_samtools_flagstat

comparison rmarkdown_samtools_flagstat_render.R @ 2:77e8e7bc5b44 draft

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author mingchen0919
date Wed, 27 Dec 2017 15:19:43 -0500
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1:c5c626653593 2:77e8e7bc5b44
1 library(getopt)
2 library(rmarkdown)
3 library(htmltools)
4 library(dplyr)
5 library(stringr)
6
7 ##============ Sink warnings and errors to a file ==============
8 ## use the sink() function to wrap all code within it.
9 ##==============================================================
10 zz = file('warnings_and_errors.txt')
11 sink(zz)
12 sink(zz, type = 'message')
13 ##---------below is the code for rendering .Rmd templates-----
14
15 ##=============STEP 1: handle command line arguments==========
16 ##
17 ##============================================================
18 # column 1: the long flag name
19 # column 2: the short flag alias. A SINGLE character string
20 # column 3: argument mask
21 # 0: no argument
22 # 1: argument required
23 # 2: argument is optional
24 # column 4: date type to which the flag's argument shall be cast.
25 # possible values: logical, integer, double, complex, character.
26 #-------------------------------------------------------------
27 #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
28 # 1. short flag alias should match the flag in the command section in the XML file.
29 # 2. long flag name can be any legal R variable names
30 # 3. two names in args_list can have common string but one name should not be a part of another name.
31 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
32 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
33 args_list=list()
34 ##------- 1. input data ---------------------
35 args_list$ECHO = c('echo', 'e', '1', 'character')
36 args_list$INPUT_BAM = c('input_bam', 'b', '1', 'character')
37 args_list$INPUT_BAM_NAME = c('input_bam_name', 'n', '1', 'character')
38 ##--------2. output report and outputs --------------
39 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
40 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
41 args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
42 ##--------3. .Rmd templates in the tool directory ----------
43 args_list$TOOL_TEMPLATE_RMD = c('tool_template_rmd', 't', '1', 'character')
44 ##-----------------------------------------------------------
45 opt = getopt(t(as.data.frame(args_list)))
46
47
48
49 ##=======STEP 2: create report directory (optional)==========
50 ##
51 ##===========================================================
52 dir.create(opt$report_dir)
53
54 ##=STEP 3: replace placeholders in .Rmd with argument values=
55 ##
56 ##===========================================================
57 #++ need to replace placeholders with args values one by one+
58 readLines(opt$tool_template_rmd) %>%
59 (function(x) {
60 gsub('ECHO', opt$echo, x)
61 }) %>%
62 (function(x) {
63 gsub('REPORT_DIR', opt$report_dir, x)
64 }) %>%
65 (function(x) {
66 fileConn = file('rmarkdown_samtools_flagstat.Rmd')
67 writeLines(x, con=fileConn)
68 close(fileConn)
69 })
70
71
72 ##=============STEP 4: render .Rmd templates=================
73 ##
74 ##===========================================================
75 render('rmarkdown_samtools_flagstat.Rmd', output_file = opt$report_html)
76
77
78 ##--------end of code rendering .Rmd templates----------------
79 sink()
80 ##=========== End of sinking output=============================