Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
comparison collection_list_render.R @ 3:cb6efa0f0cb6 draft
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 |
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| 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 ----------------------------- |