diff list_paired.Rmd @ 1:16e0f4b7a286 draft

planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/list_paired.Rmd	Mon Mar 26 18:40:39 2018 -0400
@@ -0,0 +1,45 @@
+---
+title: 'Dynamic tool'
+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}
+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_paired')
+    write(command_line, append = TRUE, 
+          file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
+  }
+}
+```
+
+