Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
changeset 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 | 566d487c9518 |
| children | 9cf2069b31c0 |
| files | collection_list.Rmd collection_list_render.R |
| diffstat | 2 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/collection_list.Rmd Mon Sep 25 15:19:06 2017 -0400 +++ b/collection_list.Rmd Mon Sep 25 15:30:55 2017 -0400 @@ -14,12 +14,14 @@ ) ``` +# Command line arguments + ```{r} str(opt) ``` -```{bash 'copy data to working directory', echo=FALSE} +```{bash 'copy data to working directory'} mkdir files_directory # Copy uploaded data to the working directory for f in $(echo FILE_LIST | sed "s/,/ /g")
--- a/collection_list_render.R Mon Sep 25 15:19:06 2017 -0400 +++ b/collection_list_render.R Mon Sep 25 15:30:55 2017 -0400 @@ -33,7 +33,6 @@ spec_list$FILE_LIST = c('file_list', 'l', '1', 'character') spec_list$ECHO = c('echo', 'e', '1', 'character') ##--------2. output report and outputs -------------- -# spec_list$LIST_COLLECTION = c('list_collection', 'o', '1', 'character') spec_list$REPORT = c('report', 'r', '1', 'character') spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character') ##--------3. Rmd templates in the tool directory ---------- @@ -75,6 +74,6 @@ }) #------ 3. render all Rmd files -------- -render('list_collection.Rmd', output_file = opt$list_collection_html) +render('list_collection.Rmd', output_file = opt$report) #-------4. manipulate outputs -----------------------------