Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
changeset 23:025ca0833787 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
| author | mingchen0919 |
|---|---|
| date | Mon, 25 Sep 2017 23:18:44 -0400 |
| parents | a25b427a1f38 |
| children | 882d249a6418 |
| files | collection_list_paired_render.R |
| diffstat | 1 files changed, 2 insertions(+), 5 deletions(-) [+] |
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--- a/collection_list_paired_render.R Mon Sep 25 23:15:32 2017 -0400 +++ b/collection_list_paired_render.R Mon Sep 25 23:18:44 2017 -0400 @@ -36,7 +36,7 @@ spec_list$FORMAT = c('format', 'f', '1', 'character') ##--------2. output report and outputs -------------- spec_list$OUTPUT_HTML = c('list_paired_collection_html', 'r', '1', 'character') -spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character') +spec_list$OUTPUT_DIR = c('list_paired_collection_dir', 'd', '1', 'character') ##--------3. Rmd templates in the tool directory ---------- spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character') @@ -50,7 +50,7 @@ library(dplyr) #----- 1. create the report directory ------------------------ -system(paste0('mkdir -p ', opt$list_collection_dir)) +system(paste0('mkdir -p ', opt$list_paired_collection_dir)) #----- 2. generate Rmd files with Rmd templates -------------- # a. templates without placeholder variables: @@ -73,9 +73,6 @@ gsub('REVERSE_FILE_LIST', opt$reverse_file_list, x) }) %>% (function(x) { - gsub('OUTPUT_DIR', opt$list_paired_collection_dir, x) - }) %>% - (function(x) { fileConn = file('list_paired_collection.Rmd') writeLines(x, con=fileConn) close(fileConn)