Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
changeset 18:a5dcb110f213 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 22:56:25 -0400 |
| parents | 2f6a7c67440f |
| children | e99c2267ef57 |
| files | collection_list.xml collection_list_paired.Rmd collection_list_paired.xml |
| diffstat | 3 files changed, 7 insertions(+), 5 deletions(-) [+] |
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--- a/collection_list.xml Mon Sep 25 22:47:21 2017 -0400 +++ b/collection_list.xml Mon Sep 25 22:56:25 2017 -0400 @@ -38,8 +38,9 @@ </command> <inputs> <param type="data" name="file_list" multiple="true" /> + <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/> + <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> - <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/> </inputs> <outputs> <data format="html" name="report" label="Collection builder (list collection)" />
--- a/collection_list_paired.Rmd Mon Sep 25 22:47:21 2017 -0400 +++ b/collection_list_paired.Rmd Mon Sep 25 22:56:25 2017 -0400 @@ -37,7 +37,7 @@ # get original file names original_files = list.files('./files_directory') # create new files names from original file names -new_files = gsub('\\.dat', '\\.FORMAT_1', original_files) +new_files = gsub('\\.dat', '_1\\.FORMAT', original_files) # rename files file.copy(paste0('./files_directory/', original_files), paste0('./files_directory/', new_files)) @@ -47,13 +47,13 @@ ```{r 'rename reverse files'} # get full paths of original files -from_files = strsplit("FOWARD_FILE_LIST", ',')[[1]] +from_files = strsplit("REVERSE_FILE_LIST", ',')[[1]] # copy files to the created directory. file.copy(from_files, './files_directory') # get original file names original_files = list.files('./files_directory') # create new files names from original file names -new_files = gsub('\\.dat', '\\.FORMAT_2', original_files) +new_files = gsub('\\.dat', '_2\\.FORMAT', original_files) # rename files file.copy(paste0('./files_directory/', original_files), paste0('./files_directory/', new_files))
--- a/collection_list_paired.xml Mon Sep 25 22:47:21 2017 -0400 +++ b/collection_list_paired.xml Mon Sep 25 22:56:25 2017 -0400 @@ -40,8 +40,9 @@ <inputs> <param type="data" name="forward_file_list" multiple="true" label="forward inputs"/> <param type="data" name="reverse_file_list" multiple="true" label="reverse inputs"/> + <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/> + <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> - <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/> </inputs> <outputs> <data format="html" name="report" label="Collection builder (list:paired collection)" />