Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

comparison collection_list_render.R @ 2:56b68a320c0e draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 80b6b0f11380afd437d61ad308fdd3985d2ca60b-dirty
author mingchen0919
date Mon, 25 Sep 2017 16:25:35 -0400
parents 6be61cb4a1d5
children cb6efa0f0cb6
comparison
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1:6be61cb4a1d5 2:56b68a320c0e
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$FORMAT = c('echo', 'f', '1', 'character') 35 spec_list$FORMAT = c('format', 'f', '1', 'character')
36 ##--------2. output report and outputs -------------- 36 ##--------2. output report and outputs --------------
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')
61 readLines(opt$list_collection_rmd) %>% 61 readLines(opt$list_collection_rmd) %>%
62 (function(x) { 62 (function(x) {
63 gsub('ECHO', opt$echo, x) 63 gsub('ECHO', opt$echo, x)
64 }) %>% 64 }) %>%
65 (function(x) { 65 (function(x) {
66 gsub('FORMAT', opt$echo, x) 66 gsub('FORMAT', opt$format, x)
67 }) %>% 67 }) %>%
68 (function(x) { 68 (function(x) {
69 gsub('FILE_LIST', opt$file_list, x) 69 gsub('FILE_LIST', opt$file_list, x)
70 }) %>% 70 }) %>%
71 (function(x) { 71 (function(x) {