Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
comparison collection_list_render.R @ 8:9c2059916485 draft
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 15:30:55 -0400 |
| parents | 2730c4979dcb |
| children | ff1cb127967e |
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| 7:566d487c9518 | 8:9c2059916485 |
|---|---|
| 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 ##--------2. output report and outputs -------------- | 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') | 36 spec_list$REPORT = c('report', 'r', '1', 'character') |
| 38 spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character') | 37 spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character') |
| 39 ##--------3. Rmd templates in the tool directory ---------- | 38 ##--------3. Rmd templates in the tool directory ---------- |
| 40 spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character') | 39 spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character') |
| 41 | 40 |
| 73 writeLines(x, con=fileConn) | 72 writeLines(x, con=fileConn) |
| 74 close(fileConn) | 73 close(fileConn) |
| 75 }) | 74 }) |
| 76 | 75 |
| 77 #------ 3. render all Rmd files -------- | 76 #------ 3. render all Rmd files -------- |
| 78 render('list_collection.Rmd', output_file = opt$list_collection_html) | 77 render('list_collection.Rmd', output_file = opt$report) |
| 79 | 78 |
| 80 #-------4. manipulate outputs ----------------------------- | 79 #-------4. manipulate outputs ----------------------------- |