# HG changeset patch
# User mingchen0919
# Date 1524686123 14400
# Node ID 5f00aef42904b9c21f09f09bf0a60de42b503d26
# Parent  2fbb7d627af101f7d15a123cd3ed0d6b3ec7bea0
planemo upload commit 58ac10c63c4cc51b4122de0fa07b887ace6df657-dirty

diff -r 2fbb7d627af1 -r 5f00aef42904 expose-outputs.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/expose-outputs.sh	Wed Apr 25 15:55:23 2018 -0400
@@ -0,0 +1,5 @@
+# change directory to tool outputs directory
+cd ${REPORT_FILES_PATH}
+
+# copy outputs from tool outputs directory to corresponding galaxy output path
+cp fastqc.html ${REPORT}
\ No newline at end of file
diff -r 2fbb7d627af1 -r 5f00aef42904 fastqc.Rmd
--- a/fastqc.Rmd	Wed Apr 18 09:04:09 2018 -0400
+++ b/fastqc.Rmd	Wed Apr 25 15:55:23 2018 -0400
@@ -40,6 +40,14 @@
   });
 </script>
 
+```{css}
+pre code, pre, code {
+  white-space: pre !important;
+  overflow-x: scroll !important;
+  word-break: keep-all !important;
+  word-wrap: initial !important;
+}
+```
 ----------------------
 
 
@@ -49,14 +57,14 @@
 # Run FastQC
 
 ```{bash}
-sh ${TOOL_INSTALL_DIR}/run-fastqc.sh
+sh ${TOOL_INSTALL_DIR}/shell-script-template.sh
 ```
 
-
-```{r}
+```{r echo=FALSE,results='asis'}
 # display fastqc job script
-fastqc_sh = paste0(opt$X_d, '/fastqc.sh')
-tags$code(tags$pre(readChar(fastqc_sh, file.info(fastqc_sh)$size )))
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/fastqc.sh')), sep = '\n')
+cat('\n```')
 ```
 
 # Fastqc Output Visualization
@@ -396,11 +404,6 @@
 
 
 
-
-
-
-
-
 -----------------------------------------
 ## Output
 
diff -r 2fbb7d627af1 -r 5f00aef42904 fastqc.xml
--- a/fastqc.xml	Wed Apr 18 09:04:09 2018 -0400
+++ b/fastqc.xml	Wed Apr 25 15:55:23 2018 -0400
@@ -71,7 +71,7 @@
 
     </inputs>
     <outputs>
-        <data format="html" name="report"/>
+        <data format="html" name="report" label="${tool.name} on ${on_string}"/>
     </outputs>
     <citations>
         <citation type="bibtex"><![CDATA[
diff -r 2fbb7d627af1 -r 5f00aef42904 fastqc_render.R
--- a/fastqc_render.R	Wed Apr 18 09:04:09 2018 -0400
+++ b/fastqc_render.R	Wed Apr 25 15:55:23 2018 -0400
@@ -5,45 +5,52 @@
 sink(zz)
 sink(zz, type = 'message')
 
-#-------------------preparation -----------------
+#============== preparation ====================================
 options(stringsAsFactors = FALSE)
 # import libraries
-library(getopt)
-library(rmarkdown)
-library(htmltools)
+#------------------------------------------------------------------
+# ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES
+#------------------------------------------------------------------
+library('getopt')
+library('rmarkdown')
+library('htmltools')
 library(plyr)
 library(dplyr)
 library(stringr)
 library(DT)
 library(reshape2)
 library(plotly)
+
 # load helper functions
 source(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/helper.R'))
 # import getopt specification matrix from a csv file
 opt = getopt(getopt_specification_matrix('getopt_specification.csv', 
                                          tool_dir=Sys.getenv('TOOL_INSTALL_DIR')))
-# define a unix variable versions for all input values. this is useful when we 
+# define environment variables for all input values. this is useful when we 
 # want to use input values by other programming language in r markdown
 do.call(Sys.setenv, opt[-1])
-#------------------------------------------------
+#===============================================================
 
 
-
-#-----------------render Rmd files --------------
+#======================== render Rmd files =========================
 # NOTICE: 
-#       we should copy all rmarkdown files from tool install directory to current working directory.
-#       we should render rmarkdown files in the current working directory.
+#       we should copy all rmarkdown files from tool install directory to REPORT_FILES_PATH directory.
+#       and render rmarkdown files in the REPORT_FILES_PATH directory.
 file.copy(from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'),
           to = Sys.getenv('REPORT_FILES_PATH'), recursive = TRUE)
 system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}')
-# render Rmd files in order
+
+#----------------BELOW IS WHERE YOU NEED TO CUSTOMIZE ---------------------
 render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/fastqc.Rmd'))
-#------------------------------------------
+# add more lines below if there are more Rmd files to be rendered
+
+#===============================================================
 
 
-#---------------- copy the output html to REPORT and OUTPUT_FILE_TREE----
-system(command = 'cp ${REPORT_FILES_PATH}/fastqc.html ${REPORT}')
-#==============the end==============
+#============== expose outputs to galaxy history ===============
+system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs.sh')
+#===============================================================
+
 
 ##--------end of code rendering .Rmd templates----------------
 sink()
diff -r 2fbb7d627af1 -r 5f00aef42904 helper.R
--- a/helper.R	Wed Apr 18 09:04:09 2018 -0400
+++ b/helper.R	Wed Apr 25 15:55:23 2018 -0400
@@ -4,9 +4,14 @@
 #' The first column are short flags, the second column are argument masks, the third column
 #' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
 #' @param gtg_name the name of a running GTG.
-getopt_specification_matrix = function(specification_file, gtg_name = 'gtg', tool_dir = Sys.getenv('TOOL_DIR')) {
-  df = read.csv(paste0(tool_dir, '/', specification_file),
-                header = TRUE, stringsAsFactors = FALSE)
+getopt_specification_matrix = function(specification_file,
+                                       gtg_name = 'gtg',
+                                       tool_dir = Sys.getenv('TOOL_DIR')) {
+  df = read.csv(
+    paste0(tool_dir, '/', specification_file),
+    header = TRUE,
+    stringsAsFactors = FALSE
+  )
   # check if there are duplicated short flags
   short_flags = df[, 1]
   if (length(unique(short_flags)) < length(short_flags)) {
@@ -19,10 +24,12 @@
   long_flags = paste0('X_', df[, 1])
   
   # specification matrix
-  df2 = data.frame(long_flags = long_flags,
-                   short_flags = df[, 1],
-                   argument_mask = df[, 2],
-                   data_type = df[, 3])
+  df2 = data.frame(
+    long_flags = long_flags,
+    short_flags = df[, 1],
+    argument_mask = df[, 2],
+    data_type = df[, 3]
+  )
   
   as.matrix(df2)
 }
@@ -30,43 +37,46 @@
 
 
 #' \code{file_tree} generate file tree of a directory in the format of HTML lists.
-#' 
+#'
 #' @param dir the path to the directory for generating the file tree.
 #' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files.
 # define a recursive function to build html string of the file tree
-file_tree = function(dir = '.'){
+file_tree = function(dir = '.') {
   # get the OUTPUT_DIR folder data: dataset_NUMBER_files
   report_files_path = Sys.getenv('REPORT_FILES_PATH')
   output_dir = tail(strsplit(report_files_path, '/')[[1]], 1)
   
-  files = list.files(path = dir, recursive = FALSE, full.names = TRUE)
+  files = list.files(path = dir,
+                     recursive = FALSE,
+                     full.names = TRUE)
   # files also include directorys, need to remove directorys
   files = files[!dir.exists(files)]
-  dirs = list.dirs(path = dir, recursive = FALSE, full.names = TRUE)
-  # hide vakata-jstree-3.3.5 folder
-  #jstree_index = grep(pattern = 'vakata-jstree-3.3.5', x = dirs)
-  #dirs = dirs[-jstree_index]
-  tags$ul(
-    {
-      if (length(files) > 0) {
-        lapply(files, function(x){
-          path_end = tail(strsplit(x, '/')[[1]],1)
-          href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
-          li_item = tags$li(tags$a(path_end, href=href_path))
-          li_item$attribs = list('data-jstree'='{"icon":"jstree-file"}')
+  dirs = list.dirs(path = dir,
+                   recursive = FALSE,
+                   full.names = TRUE)
+  tags$ul({
+    if (length(files) > 0) {
+      lapply(files, function(x) {
+        path_end = tail(strsplit(x, '/')[[1]], 1)
+        href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
+        li_item = tags$li(tags$a(path_end, href = href_path))
+        li_item$attribs = list('data-jstree' = '{"icon":"jstree-file"}')
+        li_item
+      })
+    }
+  },
+  {
+    if (length(dirs) > 0) {
+      lapply(dirs, function(x) {
+        path_end = tail(strsplit(x, '/')[[1]], 1)
+        # hide vakata-jstree-3.3.5 folder
+        if (path_end != 'vakata-jstree-3.3.5') {
+          # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
+          li_item = tags$li(path_end, file_tree(x))
+          li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}')
           li_item
-        })
-      }
-    },
-    {
-      if (length(dirs) > 0) {
-        lapply(dirs, function(x){
-          x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
-          li_item = tags$li(x_path, file_tree(x))
-          li_item$attribs = list('data-jstree'='{"icon":"jstree-folder"}')
-          li_item
-        })
-      }
+        }
+      })
     }
-  )
+  })
 }
diff -r 2fbb7d627af1 -r 5f00aef42904 run-fastqc.sh
--- a/run-fastqc.sh	Wed Apr 18 09:04:09 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-
-#create extra file directory
-mkdir -p ${X_d}
-
-cd ${X_d}
-cp ${X_r} ${X_d}/read_1.fq
-cp ${X_R} ${X_d}/read_2.fq
-
-cat >temp.sh <<EOL
-fastqc \\
-  -q \\
-  -c ${X_c} \\
-  -l ${X_l} \\
-  ${X_d}/read_1.fq > /dev/null 2>&1
-  
-fastqc \\
-  -q \\
-  -c ${X_c} \\
-  -l ${X_l} \\
-  ${X_d}/read_2.fq > /dev/null 2>&1
-EOL
-
-grep -v None temp.sh > fastqc.sh
-rm temp.sh
-
-# run fastqc
-sh fastqc.sh
-
-# unzip outputs
-unzip -q read_1_fastqc.zip
-unzip -q read_2_fastqc.zip
\ No newline at end of file
diff -r 2fbb7d627af1 -r 5f00aef42904 shell-script-template.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shell-script-template.sh	Wed Apr 25 15:55:23 2018 -0400
@@ -0,0 +1,36 @@
+# SHELL_SCRIPT file name
+SHELL_SCRIPT='fastqc.sh'
+
+# run SHELL_SCRIPT within tool outputs directory
+cd ${REPORT_FILES_PATH}
+
+# build job-script.sh
+cat >temp.sh <<EOF
+
+cp ${X_r} read_1.fq
+cp ${X_R} read_2.fq
+
+fastqc \\
+  -q \\
+  -c ${X_c} \\
+  -l ${X_l} \\
+  ${X_d}/read_1.fq > /dev/null 2>&1
+  
+fastqc \\
+  -q \\
+  -c ${X_c} \\
+  -l ${X_l} \\
+  ${X_d}/read_2.fq > /dev/null 2>&1
+
+EOF
+
+grep -v None temp.sh > ${SHELL_SCRIPT}
+rm temp.sh
+
+# run SHELL_SCRIPT
+sh ${SHELL_SCRIPT}
+
+
+# unzip outputs
+unzip -q read_1_fastqc.zip
+unzip -q read_2_fastqc.zip
\ No newline at end of file