Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
changeset 8:f555686ca340 draft default tip
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 88ca36a41aa577ba888cee39cf81b176bf7e68db-dirty
| author | mingchen0919 |
|---|---|
| date | Tue, 26 Sep 2017 16:22:18 -0400 |
| parents | abf9cbd7578f |
| children | |
| files | collection_list_paired.Rmd collection_paired.Rmd collection_paired.xml |
| diffstat | 3 files changed, 4 insertions(+), 6 deletions(-) [+] |
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--- a/collection_list_paired.Rmd Tue Sep 26 13:43:32 2017 -0400 +++ b/collection_list_paired.Rmd Tue Sep 26 16:22:18 2017 -0400 @@ -40,9 +40,7 @@ # get original file names original_files = list.files('./forward_files_directory') # create new files names from original file names -new_files = gsub('\\.dat', '_forward\\.FORMAT', original_files) new_files = paste0('input', 1:length(original_files), '_forward.FORMAT') -new_files # rename files file.copy(paste0('./forward_files_directory/', original_files), paste0('./files_directory/', new_files)) @@ -60,9 +58,7 @@ # get original file names original_files = list.files('./reverse_files_directory') # create new files names from original file names -new_files = gsub('\\.dat', '_reverse\\.FORMAT', original_files) new_files = paste0('input', 1:length(original_files), '_reverse.FORMAT') -new_files # rename files file.copy(paste0('./reverse_files_directory/', original_files), paste0('./files_directory/', new_files))
--- a/collection_paired.Rmd Tue Sep 26 13:43:32 2017 -0400 +++ b/collection_paired.Rmd Tue Sep 26 16:22:18 2017 -0400 @@ -23,7 +23,8 @@ # Rename files ```{r} -file.copy("FORWARD_INPUT", './forward.FORMAT') -file.copy("REVERSE_INPUT", './reverse.FORMAT') +dir.create('files_directory') +file.copy("FORWARD_INPUT", './files_directory/forward.FORMAT') +file.copy("REVERSE_INPUT", './files_directory/reverse.FORMAT') ```
--- a/collection_paired.xml Tue Sep 26 13:43:32 2017 -0400 +++ b/collection_paired.xml Tue Sep 26 16:22:18 2017 -0400 @@ -47,6 +47,7 @@ <outputs> <data format="html" name="report" label="Collection builder (paired collection)" /> <collection type="paired" name="list_collection"> + <discover_datasets pattern="__name_and_ext__" directory="files_directory" /> </collection> </outputs> </tool> \ No newline at end of file