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comparison rmarkdown_flagstat_render.R @ 0:ba913054bbff draft

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planemo upload
author mingchen0919
date Tue, 26 Dec 2017 19:27:41 -0500
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-1:000000000000 0:ba913054bbff
1 library(getopt)
2 library(rmarkdown)
3 library(htmltools)
4 library(dplyr)
5
6 ##============ Sink warnings and errors to a file ==============
7 ## use the sink() function to wrap all code within it.
8 ##==============================================================
9 zz = file('warnings_and_errors.txt')
10 sink(zz)
11 sink(zz, type = 'message')
12 ##---------below is the code for rendering .Rmd templates-----
13
14 ##=============STEP 1: handle command line arguments==========
15 ##
16 ##============================================================
17 # column 1: the long flag name
18 # column 2: the short flag alias. A SINGLE character string
19 # column 3: argument mask
20 # 0: no argument
21 # 1: argument required
22 # 2: argument is optional
23 # column 4: date type to which the flag's argument shall be cast.
24 # possible values: logical, integer, double, complex, character.
25 #-------------------------------------------------------------
26 #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
27 # 1. short flag alias should match the flag in the command section in the XML file.
28 # 2. long flag name can be any legal R variable names
29 # 3. two names in args_list can have common string but one name should not be a part of another name.
30 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
31 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
32 args_list=list()
33 ##------- 1. input data ---------------------
34 args_list$ECHO = c('echo', 'e', '1', 'character')
35 ##--------2. output report and outputs --------------
36 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
37 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
38 args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
39 ##--------3. .Rmd templates in the tool directory ----------
40 args_list$TOOL_TEMPLATE_RMD = c('tool_template_rmd', 't', '1', 'character')
41 ##-----------------------------------------------------------
42 opt = getopt(t(as.data.frame(args_list)))
43
44
45
46 ##=======STEP 2: create report directory (optional)==========
47 ##
48 ##===========================================================
49 dir.create(opt$report_dir)
50
51 ##=STEP 3: replace placeholders in .Rmd with argument values=
52 ##
53 ##===========================================================
54 #++ need to replace placeholders with args values one by one+
55 readLines(opt$tool_template_rmd) %>%
56 (function(x) {
57 gsub('ECHO', opt$echo, x)
58 }) %>%
59 (function(x) {
60 gsub('REPORT_DIR', opt$output_dir, x)
61 }) %>%
62 (function(x) {
63 fileConn = file('tool_template.Rmd')
64 writeLines(x, con=fileConn)
65 close(fileConn)
66 })
67
68
69 ##=============STEP 4: render .Rmd templates=================
70 ##
71 ##===========================================================
72 render('tool_template.Rmd', output_file = opt$report_html)
73
74
75 ##--------end of code rendering .Rmd templates----------------
76 sink()
77 ##=========== End of sinking output=============================