# HG changeset patch
# User mingchen0919
# Date 1523977135 14400
# Node ID ebb7afcb2b75357dcbde1bb920c27a9056fa980f

planemo upload

diff -r 000000000000 -r ebb7afcb2b75 aurora_data.Rmd
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aurora_data.Rmd	Tue Apr 17 10:58:55 2018 -0400
@@ -0,0 +1,111 @@
+---
+title: 'HTML report title'
+output:
+    html_document:
+      highlight: pygments
+---
+
+```{r, echo=FALSE}
+# to make the css theme to work, <link></link> tags cannot be added directly 
+# as <script></script> tags as below.
+# it has to be added using a code chunk with the htmltool functions!!!
+css_link = tags$link()
+css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
+css_link
+```
+
+```{r, eval=FALSE, echo=FALSE}
+# this code chunk is purely for adding comments
+# below is to add jQuery and jstree javascripts
+```
+<script src="https://code.jquery.com/jquery-3.3.1.min.js"></script>
+<script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
+
+```{r, eval=FALSE, echo=FALSE}
+# this code chunk is purely for adding comments
+# javascript code below is to build the file tree interface
+# see this for how to implement opening hyperlink: https://stackoverflow.com/questions/18611317/how-to-get-i-get-leaf-nodes-in-jstree-to-open-their-hyperlink-when-clicked-when
+```
+<script>
+  $(function () {
+    // create an instance when the DOM is ready
+    $('#jstree').jstree().bind("select_node.jstree", function (e, data) {
+     window.open( data.node.a_attr.href, data.node.a_attr.target )
+    });
+  });
+</script>
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = TRUE, error = TRUE)
+```
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# Output
+
+```{bash, echo=FALSE}
+# copy jstree directory to output directory
+cp -r ${X_t}/vakata-jstree-3.3.5 ${X_d}
+```
+
+```{r, echo=FALSE}
+# get the OUTPUT_DIR folder data: dataset_NUMBER_files
+output_dir = tail(strsplit(opt$X_d, '/')[[1]], 1)
+# define a recursive function to build html string of the file tree
+file_tree = function(dir = '.'){
+  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)
+  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){
+          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
+        })
+      }
+    }
+  )
+}
+```
+
+```{r, echo=FALSE}
+# create a div container to store the file tree interface
+tags$div(
+  id="jstree",
+  file_tree(opt$X_d)
+)
+```
+
diff -r 000000000000 -r ebb7afcb2b75 aurora_data.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aurora_data.xml	Tue Apr 17 10:58:55 2018 -0400
@@ -0,0 +1,51 @@
+<tool id="aurora_data" name="aurora_data" version="1.0.0">
+    <description>Collect data for other aurora galaxy tools.</description>
+    <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
+    </requirements>
+    <stdio>
+        <regex match="XXX" source="stderr" level="warning"
+               description="Check the warnings_and_errors.txt file for more details."/>
+    </stdio>
+    <command><![CDATA[
+        export TOOL_DIR='${__tool_directory__}' &&
+
+        Rscript '${__tool_directory__}/rmarkdown_report_render.R'
+
+			-o $report
+			-d $report.files_path
+        
+    ]]></command>
+    <inputs>
+        <repeat name="data_repeat" title="data" min="1" default="1">
+            <param type="data" name="data" label="Data from history" optional="False"/>
+            <param type="text" name="data_name" label="data name" optional="False" help="data name has to be unique."/>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="report" format="html" label="${tool.name} on ${on_string}" hidden="false"/>
+    </outputs>
+    <citations>
+        <citation type="bibtex"><![CDATA[
+            @article{allaire2016rmarkdown,
+            title={rmarkdown: Dynamic Documents for R, 2016},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
+            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        ]]></citation>
+        <citation type="bibtex"><![CDATA[
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        ]]></citation>
+    </citations>
+</tool>
diff -r 000000000000 -r ebb7afcb2b75 aurora_data_render.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aurora_data_render.R	Tue Apr 17 10:58:55 2018 -0400
@@ -0,0 +1,51 @@
+##============ Sink warnings and errors to a file ==============
+## use the sink() function to wrap all code within it.
+##==============================================================
+zz = file('warnings_and_errors.txt')
+sink(zz)
+sink(zz, type = 'message')
+
+#------------import libraries--------------------
+options(stringsAsFactors = FALSE)
+
+library(getopt)
+library(rmarkdown)
+#------------------------------------------------
+
+
+#------------get arguments into R--------------------
+# load helper function
+source(paste0(Sys.getenv('TOOL_DIR'), '/helper.R'))
+# import getopt specification matrix from a csv file
+spec_csv = paste0(Sys.getenv('TOOL_DIR'), '/getopt_specification.csv')
+opt = getopt(getopt_specification_matrix(spec_csv))
+opt$X_t = Sys.getenv('TOOL_DIR')
+#----------------------------------------------------
+
+
+#-----------using passed arguments in R 
+#           to define system environment variables---
+do.call(Sys.setenv, opt[-1])
+#----------------------------------------------------
+
+#---------- often used variables ----------------
+# OUTPUT_DIR: path to the output associated directory, which stores all outputs
+# TOOL_DIR: path to the tool installation directory
+OUTPUT_DIR = opt$X_d
+TOOL_DIR =   opt$X_t
+OUTPUT_REPORT = opt$X_o
+RMD_NAME = ''
+
+# create the output associated directory to store all outputs
+dir.create(OUTPUT_DIR, recursive = TRUE)
+
+#-----------------render Rmd--------------
+render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
+#------------------------------------------
+
+#==============the end==============
+
+
+##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================
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diff -r 000000000000 -r ebb7afcb2b75 helper.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/helper.R	Tue Apr 17 10:58:55 2018 -0400
@@ -0,0 +1,55 @@
+#' \code{getopt_specification_matrix} returns a getopt specification matrix.
+#'
+#' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data.
+#' 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)
+  # check if there are duplicated short flags
+  short_flags = df[, 1]
+  if (length(unique(short_flags)) < length(short_flags)) {
+    cat('----Duplicated short flags found ----\n')
+    cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
+    stop('Duplicated short flags are not allowed.')
+  }
+  
+  # use short flags to generate long flags
+  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])
+  
+  as.matrix(df2)
+}
+
+
+
+#' \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.
+file_tree = function(dir = '.'){
+  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)
+  tags$ul(
+    {
+      if (length(files) > 0) {
+        lapply(files, tags$li)
+      }
+    },
+    {
+      if (length(dirs) > 0) {
+        lapply(dirs, function(x){
+          tags$li(x, file_tree(x))
+          
+        })
+      }
+    }
+  )
+}
\ No newline at end of file