Mercurial > repos > mingchen0919 > elastic_expose_data
view individuals.Rmd @ 5:4f9f1e76f7e6 draft
planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty
author | mingchen0919 |
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date | Mon, 02 Apr 2018 09:16:17 -0400 |
parents | 9ff33a3631fa |
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--- title: 'Expose data (paired)' output: html_document --- <style> pre code, pre, code { white-space: pre !important; overflow-x: scroll !important; word-break: keep-all !important; word-wrap: initial !important; } </style> ```{r setup, include=FALSE, warning=FALSE, message=FALSE} knitr::opts_chunk$set(error = TRUE) ``` ## User input ```{r, echo=FALSE, eval=TRUE} ##-------- build script files ----------- # build script file: script.sh df = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), sep = '|', header = TRUE) knitr::kable(df) ``` ```{r, echo=FALSE} # write('', file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) if (nrow(df) > 0) { for (i in 1:nrow(df)) { tool_output_dir = readLines(df[i, 'tool_output_dir'])[1] full_path = paste0(tool_output_dir, '/', df[i, 'relative_path']) if (dir.exists(full_path)) { from_files = list.files(full_path, full.names = TRUE) to_files = list.files(full_path) to_files = paste0(individual_outputs_path, to_files) file.copy(from = from_files, to = to_files) } if (file.exists(full_path)) { # to_files = list.files(full_path) to_file = tail(strsplit(full_path, '/')[[1]], 1) file.copy(from = full_path, to = paste0(individual_outputs_path, to_file)) } # command_line = paste0('cp -r ', full_path, ' paired') # write(command_line, append = TRUE, # file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) } } ```