Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

comparison collection_list_render.R @ 1:6be61cb4a1d5 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
author mingchen0919
date Mon, 25 Sep 2017 16:19:52 -0400
parents 78018b735124
children 56b68a320c0e
comparison
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0:78018b735124 1:6be61cb4a1d5
30 # possible values: logical, integer, double, complex, character. 30 # possible values: logical, integer, double, complex, character.
31 ##------- 1. input data --------------------- 31 ##------- 1. input data ---------------------
32 spec_list=list() 32 spec_list=list()
33 spec_list$FILE_LIST = c('file_list', 'l', '1', 'character') 33 spec_list$FILE_LIST = c('file_list', 'l', '1', 'character')
34 spec_list$ECHO = c('echo', 'e', '1', 'character') 34 spec_list$ECHO = c('echo', 'e', '1', 'character')
35 spec_list$FORMAT = c('echo', 'f', '1', 'character')
35 ##--------2. output report and outputs -------------- 36 ##--------2. output report and outputs --------------
36 spec_list$LIST_COLLECTION = c('list_collection', 'o', '1', 'character')
37 spec_list$REPORT = c('report', 'r', '1', 'character') 37 spec_list$REPORT = c('report', 'r', '1', 'character')
38 spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character') 38 spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character')
39 ##--------3. Rmd templates in the tool directory ---------- 39 ##--------3. Rmd templates in the tool directory ----------
40 spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character') 40 spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character')
41 41
44 ##====== End of arguments handling ========== 44 ##====== End of arguments handling ==========
45 45
46 #------ Load libraries --------- 46 #------ Load libraries ---------
47 library(rmarkdown) 47 library(rmarkdown)
48 library(htmltools) 48 library(htmltools)
49 library(dplyr)
49 50
50 #----- 1. create the report directory ------------------------ 51 #----- 1. create the report directory ------------------------
51 system(paste0('mkdir -p ', opt$list_collection_dir)) 52 system(paste0('mkdir -p ', opt$list_collection_dir))
52 53
53 #----- 2. generate Rmd files with Rmd templates -------------- 54 #----- 2. generate Rmd files with Rmd templates --------------
60 readLines(opt$list_collection_rmd) %>% 61 readLines(opt$list_collection_rmd) %>%
61 (function(x) { 62 (function(x) {
62 gsub('ECHO', opt$echo, x) 63 gsub('ECHO', opt$echo, x)
63 }) %>% 64 }) %>%
64 (function(x) { 65 (function(x) {
66 gsub('FORMAT', opt$echo, x)
67 }) %>%
68 (function(x) {
65 gsub('FILE_LIST', opt$file_list, x) 69 gsub('FILE_LIST', opt$file_list, x)
66 }) %>% 70 }) %>%
67 (function(x) { 71 (function(x) {
68 gsub('OUTPUT_DIR', opt$list_collection_dir, x) 72 gsub('OUTPUT_DIR', opt$list_collection_dir, x)
69 }) %>% 73 }) %>%
72 writeLines(x, con=fileConn) 76 writeLines(x, con=fileConn)
73 close(fileConn) 77 close(fileConn)
74 }) 78 })
75 79
76 #------ 3. render all Rmd files -------- 80 #------ 3. render all Rmd files --------
77 render('list_collection.Rmd', output_file = opt$list_collection_html) 81 render('list_collection.Rmd', output_file = opt$report)
78 82
79 #-------4. manipulate outputs ----------------------------- 83 #-------4. manipulate outputs -----------------------------