Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
changeset 25:8800e1a70b20 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 23:36:00 -0400 |
| parents | 882d249a6418 |
| children | 5391cd0565c9 |
| files | collection_list_paired.Rmd collection_list_paired.xml collection_list_paired_render.R |
| diffstat | 3 files changed, 5 insertions(+), 2 deletions(-) [+] |
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--- a/collection_list_paired.Rmd Mon Sep 25 23:30:06 2017 -0400 +++ b/collection_list_paired.Rmd Mon Sep 25 23:36:00 2017 -0400 @@ -61,6 +61,6 @@ new_files = gsub('\\.dat', '_2\\.FORMAT', original_files) # rename files file.copy(paste0('./reverse_files_directory/', original_files), - paste0('./files_directory/', new_files)) + paste0('./', new_files)) ```
--- a/collection_list_paired.xml Mon Sep 25 23:30:06 2017 -0400 +++ b/collection_list_paired.xml Mon Sep 25 23:36:00 2017 -0400 @@ -47,7 +47,7 @@ <outputs> <data format="html" name="report" label="Collection builder (list:paired collection)" /> <collection type="list:paired" name="list_collection"> - <discover_datasets pattern="__name_and_ext__" directory="files_directory" /> + <discover_datasets pattern="__name_and_ext__" visible="true" /> </collection> </outputs> </tool> \ No newline at end of file
--- a/collection_list_paired_render.R Mon Sep 25 23:30:06 2017 -0400 +++ b/collection_list_paired_render.R Mon Sep 25 23:36:00 2017 -0400 @@ -73,6 +73,9 @@ 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)