Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

comparison collection_list_render.R @ 3:cb6efa0f0cb6 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 93b036c66fd754a7af459fa80d3f7f143a68477b-dirty
author mingchen0919
date Mon, 25 Sep 2017 16:33:54 -0400
parents 56b68a320c0e
children 63e9500cdeec
comparison
equal deleted inserted replaced
2:56b68a320c0e 3:cb6efa0f0cb6
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$FORMAT = c('format', 'f', '1', 'character') 35 spec_list$FORMAT = c('format', 'f', '1', 'character')
36 ##--------2. output report and outputs -------------- 36 ##--------2. output report and outputs --------------
37 spec_list$REPORT = c('report', 'r', '1', 'character') 37 spec_list$OUTPUT_HTML = c('list_collection_html', '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
42 spec = t(as.data.frame(spec_list)) 42 spec = t(as.data.frame(spec_list))
76 writeLines(x, con=fileConn) 76 writeLines(x, con=fileConn)
77 close(fileConn) 77 close(fileConn)
78 }) 78 })
79 79
80 #------ 3. render all Rmd files -------- 80 #------ 3. render all Rmd files --------
81 render('list_collection.Rmd', output_file = opt$report) 81 render('list_collection.Rmd', output_file = opt$list_collection_html)
82 cat('test')
82 83
83 #-------4. manipulate outputs ----------------------------- 84 #-------4. manipulate outputs -----------------------------