diff dynamic_tool.Rmd @ 2:a9579c344a90 draft default tip

planemo upload commit 8f84e3911c6ff4103c0ad5fb8dd774f80d9b2559

--- a/dynamic_tool.Rmd	Fri Mar 23 02:01:52 2018 -0400
+++ b/dynamic_tool.Rmd	Fri Mar 23 21:50:16 2018 -0400
@@ -3,6 +3,15 @@
 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)
 ```
@@ -16,13 +25,23 @@
 df = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), 
                 sep = '|', header = TRUE)
 
+# prepend A_TOOL_OUTPUT_PATH
+if (nrow(df[df$type == 'path_relative_to_a_tool', ]) > 0) {
+  for (i in 1:nrow(df[df$type == 'path_relative_to_a_tool', ])) {
+    root_path = readLines(df[df$type == 'path_relative_to_a_tool', ][i, 'path_type'])[1]
+    df[df$type == 'path_relative_to_a_tool', ][i, 'value'] = paste(root_path, 
+                                                                   df[df$type == 'path_relative_to_a_tool', ][i, 'value'], 
+                                                                   sep = '/')
+  }
+}
+
 # get tool name
 tool_name = df[df$type == 'tool_name', 'value']
 # build script for displaying help messages (this probably should be tool specific)
 write(paste0(tool_name, ' -h'), 
         file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/help.sh'))
 
-knitr::kable(df[, c('flag', 'value')])
+knitr::kable(df)
 
 # if the number of option/argument pairs is larger than 0, build script file
 df2 = df[df$type != 'tool_name', ]
@@ -56,13 +75,31 @@
 sh ${REPORT_FILES_PATH}/help.sh > ${TOOL_HELP_DOC}
 ```
 
-```{bash, results='asis', echo=FALSE}
-echo '## Show help documentation'
-echo ''
-echo ''
-echo '```bash'
-cat ${REPORT_FILES_PATH}/help.sh
-echo '```'
+
+```{r, echo=FALSE}
+# create paths before running the job script
+df_paths = df[df$type == 'path_relative_to_this_tool', ]
+
+if (nrow(df_paths) > 0) {
+  for (i in 1:nrow(df_paths)) {
+    path = paste0(Sys.getenv('REPORT_FILES_PATH'), '/', df_paths[i, 'value'])
+    path_type = df_paths[i, 'path_type']
+  
+    # create file paths
+    if ((path_type == 'file_path') & !file.exists(path)) {
+      dir_path = paste(head(strsplit(path, '/')[[1]], -1), collapse = '/' )
+      if (!dir.exists(dir_path)) {
+        dir.create(dir_path, recursive = TRUE)
+      }
+      file.create(path)
+    }
+    
+    # create dir paths
+    if ((path_type == 'dir_path') & !dir.exists(path)) {
+      dir.create(path, recursive = TRUE)
+    }
+  }
+}
 ```
 
 
@@ -72,6 +109,8 @@
 cd ${REPORT_FILES_PATH} && sh script.sh
 ```
 
+
+
 ```{bash, results='asis', echo=FALSE}
 echo '## Job script'
 echo ''
@@ -82,6 +121,15 @@
 ```
 
 
+```{r, echo=FALSE}
+## obtain REPORT_FILES_PAHT and save it to a galaxy output.
+database_root = paste(head(strsplit(Sys.getenv('TOOL_LOG'), '/')[[1]], -1), collapse = '/')
+tool_output_dir_id = tail(strsplit(Sys.getenv('REPORT_FILES_PATH'), '/')[[1]], 1)
+tool_output_dir = paste0(database_root, '/', tool_output_dir_id)
+write(tool_output_dir, Sys.getenv('TOOL_OUTPUT_DIR'))
+```
+
+
 ```{r, results='asis', echo=FALSE}
 cat('##All output files')
 cat('\n\n')