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comparison bdss_client_sra_render.R @ 0:512d008295db draft default tip

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
author mingchen0919
date Tue, 17 Oct 2017 14:09:01 -0400
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-1:000000000000 0:512d008295db
1 library(getopt)
2 library(rmarkdown)
3 library(htmltools)
4 library(dplyr)
5 library(RCurl)
6
7
8 ##============ Sink warnings and errors to a file ==============
9 ## use the sink() function to wrap all code within it.
10 ##==============================================================
11 zz = file('warnings_and_errors.txt')
12 sink(zz)
13 sink(zz, type = 'message')
14 ##---------below is the code for rendering .Rmd templates-----
15
16 ##=============STEP 1: handle command line arguments==========
17 ##
18 ##============================================================
19 # column 1: the long flag name
20 # column 2: the short flag alias. A SINGLE character string
21 # column 3: argument mask
22 # 0: no argument
23 # 1: argument required
24 # 2: argument is optional
25 # column 4: date type to which the flag's argument shall be cast.
26 # possible values: logical, integer, double, complex, character.
27 #-------------------------------------------------------------
28 #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
29 # 1. short flag alias should match the flag in the command section in the XML file.
30 # 2. long flag name can be any legal R variable names
31 # 3. two names in args_list can have common string but one name should not be a part of another name.
32 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
33 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
34 ##------- 1. input data ---------------------
35 args_list=list()
36 args_list$SRA_IDS_SE = c('sra_ids_se', 'i', '1', 'character')
37 args_list$SRA_IDS_PE = c('sra_ids_pe', 'p', '1', 'character')
38 args_list$FORMAT = c('format', 'f', '1', 'character')
39 args_list$ECHO = c('echo', 'e', '1', 'character')
40 ##--------2. output report and outputs --------------
41 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
42 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
43 args_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
44 ##--------3. Rmd templates in the tool directory ----------
45 args_list$BDSS_CLIENT_RMD = c('bdss_client_rmd', 't', '1', 'character')
46
47 opt = getopt(t(as.data.frame(args_list)))
48
49
50 ##=======STEP 2: create report directory (optional)==========
51 ##
52 ##===========================================================
53 dir.create(opt$report_dir)
54
55 ##=STEP 3: replace placeholders in .Rmd with argument values=
56 ##
57 ##===========================================================
58 #++ need to replace placeholders with args values one by one+
59 #----- 01 bdss_client.Rmd -----------------------
60 readLines(opt$bdss_client_rmd) %>%
61 (function(x) {
62 gsub('SRA_IDS_SE', opt$sra_ids_se, x)
63 }) %>%
64 (function(x) {
65 gsub('SRA_IDS_PE', opt$sra_ids_pe, x)
66 }) %>%
67 (function(x) {
68 gsub('FORMAT', opt$format, x)
69 }) %>%
70 (function(x) {
71 gsub('ECHO', opt$echo, x)
72 }) %>%
73 (function(x) {
74 gsub('REPORT_DIR', opt$report_dir, x)
75 }) %>%
76 (function(x) {
77 fileConn = file('bdss_client.Rmd')
78 writeLines(x, con=fileConn)
79 close(fileConn)
80 })
81
82 ##=============STEP 4: render .Rmd templates=================
83 ##
84 ##===========================================================
85 render('bdss_client.Rmd', output_file = opt$report_html)
86
87
88 ##--------end of code rendering .Rmd templates----------------
89 sink()
90 ##=========== End of sinking output=============================