Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
comparison collection_list_render.R @ 0:78018b735124 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
author | mingchen0919 |
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date | Mon, 25 Sep 2017 14:28:52 -0400 |
parents | |
children | 6be61cb4a1d5 |
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-1:000000000000 | 0:78018b735124 |
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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 ##------- 1. input data --------------------- | |
32 spec_list=list() | |
33 spec_list$FILE_LIST = c('file_list', 'l', '1', 'character') | |
34 spec_list$ECHO = c('echo', 'e', '1', 'character') | |
35 ##--------2. output report and outputs -------------- | |
36 spec_list$LIST_COLLECTION = c('list_collection', 'o', '1', 'character') | |
37 spec_list$REPORT = c('report', 'r', '1', 'character') | |
38 spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character') | |
39 ##--------3. Rmd templates in the tool directory ---------- | |
40 spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character') | |
41 | |
42 spec = t(as.data.frame(spec_list)) | |
43 opt = getopt(spec) | |
44 ##====== End of arguments handling ========== | |
45 | |
46 #------ Load libraries --------- | |
47 library(rmarkdown) | |
48 library(htmltools) | |
49 | |
50 #----- 1. create the report directory ------------------------ | |
51 system(paste0('mkdir -p ', opt$list_collection_dir)) | |
52 | |
53 #----- 2. generate Rmd files with Rmd templates -------------- | |
54 # a. templates without placeholder variables: | |
55 # copy templates from tool directory to the working directory. | |
56 # b. templates with placeholder variables: | |
57 # substitute variables with user input values and place them in the working directory. | |
58 | |
59 #----- 01 list_collection.Rmd ----------------------- | |
60 readLines(opt$list_collection_rmd) %>% | |
61 (function(x) { | |
62 gsub('ECHO', opt$echo, x) | |
63 }) %>% | |
64 (function(x) { | |
65 gsub('FILE_LIST', opt$file_list, x) | |
66 }) %>% | |
67 (function(x) { | |
68 gsub('OUTPUT_DIR', opt$list_collection_dir, x) | |
69 }) %>% | |
70 (function(x) { | |
71 fileConn = file('list_collection.Rmd') | |
72 writeLines(x, con=fileConn) | |
73 close(fileConn) | |
74 }) | |
75 | |
76 #------ 3. render all Rmd files -------- | |
77 render('list_collection.Rmd', output_file = opt$list_collection_html) | |
78 | |
79 #-------4. manipulate outputs ----------------------------- |