Mercurial > repos > mingchen0919 > elastic_expose_data
view list.Rmd @ 2:391394c022b8 draft
planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
author | mingchen0919 |
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date | Sat, 31 Mar 2018 21:32:17 -0400 |
parents | 16e0f4b7a286 |
children | 4f9f1e76f7e6 |
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--- title: 'Expose data (list)' 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']) command_line = paste0('cp -r ', full_path, ' list') write(command_line, append = TRUE, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) } } ```