Mercurial > repos > mingchen0919 > elastic_expose_data
view list_paired.Rmd @ 6:52ecc1cfd205 draft
planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty
author | mingchen0919 |
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date | Mon, 02 Apr 2018 10:21:30 -0400 |
parents | 4f9f1e76f7e6 |
children |
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--- title: 'Expose data (list: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 it is a directory path, add '/*' to the end. if (dir.exists(full_path)) { full_path = paste0(full_path, '/*') } command_line = paste0('cp -r ', full_path, ' list_paired') write(command_line, append = TRUE, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) } } ```