Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
changeset 42:fb9d2ec76d30 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fcfbe7caa4638f88ab234d0f62119819d06779f0-dirty
| author | mingchen0919 |
|---|---|
| date | Tue, 26 Sep 2017 09:14:48 -0400 |
| parents | a660c2aa20d6 |
| children | 15a54d5fef55 |
| files | collection_list_paired.Rmd collection_paired.xml |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/collection_list_paired.Rmd Tue Sep 26 08:59:49 2017 -0400 +++ b/collection_list_paired.Rmd Tue Sep 26 09:14:48 2017 -0400 @@ -41,7 +41,7 @@ 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 = paste0('input', 1:length(original_files), '_forward.FORMAT') new_files # rename files file.copy(paste0('./forward_files_directory/', original_files), @@ -61,7 +61,7 @@ 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 = paste0('input', 1:length(original_files), '_reverse.FORMAT') new_files # rename files file.copy(paste0('./reverse_files_directory/', original_files),
--- a/collection_paired.xml Tue Sep 26 08:59:49 2017 -0400 +++ b/collection_paired.xml Tue Sep 26 09:14:48 2017 -0400 @@ -46,8 +46,8 @@ </inputs> <outputs> <data format="html" name="report" label="Collection builder (paired collection)" /> - <collection type="list:paired" name="list_collection"> - <discover_datasets pattern="(?P<identifier_0>)_(?P<identifier_1>)\.fq" ext="fastqsanger" directory="files_directory"/> + <collection type="paired" name="list_collection"> + <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.(?P<ext>[^\._]+)?" directory="files_directory"/> </collection> </outputs> </tool> \ No newline at end of file