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comparison rmarkdown_deseq2_count_matrix_render.R @ 0:c1f718dd6c7a draft

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planemo upload
author mingchen0919
date Sat, 30 Dec 2017 00:25:38 -0500
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children 629323b5fc0c
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-1:000000000000 0:c1f718dd6c7a
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$ECHO = c('echo', 'e', '1', 'character')
35 args_list$c = c('count_data', 'c', '1', 'character')
36 args_list$C = c('col_data', 'C', '1', 'character')
37 args_list$D = c('design_formula', 'D', '1', 'character')
38 args_list$k = c('contrast_condition', 'k', '1', 'character')
39 args_list$T = c('treatment', 'T', '1', 'character')
40 args_list$K = c('control', 'K', '1', 'character')
41 ##--------2. output report and outputs --------------
42 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
43 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
44 args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
45 ##--------3. .Rmd templates in the tool directory ----------
46 args_list$TOOL_TEMPLATE_RMD = c('tool_template_rmd', 't', '1', 'character')
47 ##-----------------------------------------------------------
48 opt = getopt(t(as.data.frame(args_list)))
49
50
51
52 ##=======STEP 2: create report directory (optional)==========
53 ##
54 ##===========================================================
55 dir.create(opt$report_dir)
56
57 ##=STEP 3: replace placeholders in .Rmd with argument values=
58 ##
59 ##===========================================================
60 #++ need to replace placeholders with args values one by one+
61 readLines(opt$tool_template_rmd) %>%
62 # (function(x) {
63 # gsub('ECHO', opt$echo, x)
64 # }) %>%
65 # (function(x) {
66 # gsub('REPORT_DIR', opt$report_dir, x)
67 # }) %>%
68 (function(x) {
69 fileConn = file('tool_template.Rmd')
70 writeLines(x, con=fileConn)
71 close(fileConn)
72 })
73
74
75 ##=============STEP 4: render .Rmd templates=================
76 ##
77 ##===========================================================
78 render('tool_template.Rmd', output_file = opt$report_html)
79
80
81 ##--------end of code rendering .Rmd templates----------------
82 sink()
83 ##=========== End of sinking output=============================