# HG changeset patch
# User mingchen0919
# Date 1522643524 14400
# Node ID 5838300fc1aab0cd75b635a8d275216b2bc4ec40
# Parent  391394c022b8d5f147fa80e75fdb65022f5fd3d3
add expose individuals

diff -r 391394c022b8 -r 5838300fc1aa elastic_expose_individuals.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/elastic_expose_individuals.xml	Mon Apr 02 00:32:04 2018 -0400
@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="elastic_expose_individuals" name="expose data (individuals)" version="1.0.1">
+  <macros>
+    <import>elastic_tool_wrappers_macros.xml</import>
+  </macros>
+  <description/>
+  <requirements>
+    <expand macro="rmarkdown_requirements"/>
+  </requirements>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+
+        ############ first, create a directory to store all files
+        mkdir -p $report.files_path &&
+
+
+        ############ save the tool installation directory to an environment variable
+        export TOOL_INSTALL_DIR='${__tool_directory__}' &&
+
+
+        #########################
+        ##
+        ## save user input option/argument pairs into a file
+        ##
+        #########################
+
+        ## first line will be the header
+        echo 'tool_output_dir|relative_path' > '$report.files_path/options_and_arguments.txt' &&
+
+
+
+        ####################################################
+        ## loop through repeats to get option/argument pairs
+        ####################################################
+
+
+        ############ option_argument_path_relative_to_a_tool
+        #for i in $option_argument_path_relative_to_a_tool_repeat:
+             #set $item = str($i.a_tool_output_dir) + "|" + str($i.value)
+             echo '$item' >> '$report.files_path/options_and_arguments.txt' &&
+        #end for
+
+
+        ############ output_set
+        ## '$report'
+        ## '$report.files_path'
+        #######################
+        export REPORT='$report' &&
+        export TOOL_LOG='$tool_log' &&
+        export REPORT_FILES_PATH='$report.files_path' &&
+
+
+        ############ run render R script to render R markdowns
+        Rscript '${__tool_directory__}/paired_render.R'
+
+        ]]></command>
+  <inputs>
+    <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="1" default="1">
+      <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/>
+      <param type="text" name="value" optional="true" label="relative path"/>
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="html" name="report" label="${tool.name} report"/>
+    <data format="txt" name="tool_log" label="${tool.name} log"/>
+    <data name="individual_outputs">
+      <discover_datasets pattern="__designation_and_ext__" directory="individual_outputs" visible="true"/>
+    </data>
+  </outputs>
+  <citations>
+    <expand macro="citations"/>
+  </citations>
+</tool>
diff -r 391394c022b8 -r 5838300fc1aa elastic_expose_to_list_collection.xml
--- a/elastic_expose_to_list_collection.xml	Sat Mar 31 21:32:17 2018 -0400
+++ b/elastic_expose_to_list_collection.xml	Mon Apr 02 00:32:04 2018 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="elastic_expose_to_list_collection" name="expose data (list)" version="1.0.0">
+<tool id="elastic_expose_to_list_collection" name="expose data (list)" version="1.0.1">
   <macros>
     <import>elastic_tool_wrappers_macros.xml</import>
   </macros>
diff -r 391394c022b8 -r 5838300fc1aa elastic_expose_to_list_paired_collection.xml
--- a/elastic_expose_to_list_paired_collection.xml	Sat Mar 31 21:32:17 2018 -0400
+++ b/elastic_expose_to_list_paired_collection.xml	Mon Apr 02 00:32:04 2018 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="elastic_expose_to_paired_collection" name="expose data (list:paired)" version="1.0.0">
+<tool id="elastic_expose_to_list_paired_collection" name="expose data (list:paired)" version="1.0.1">
   <macros>
     <import>elastic_tool_wrappers_macros.xml</import>
   </macros>
diff -r 391394c022b8 -r 5838300fc1aa elastic_expose_to_paired_collection.xml
--- a/elastic_expose_to_paired_collection.xml	Sat Mar 31 21:32:17 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,73 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="elastic_expose_list_paired_collection" name="expose data (paired)" version="1.0.0">
-  <macros>
-    <import>elastic_tool_wrappers_macros.xml</import>
-  </macros>
-  <description/>
-  <requirements>
-    <expand macro="rmarkdown_requirements"/>
-  </requirements>
-  <expand macro="stdio"/>
-  <command><![CDATA[
-
-        ############ first, create a directory to store all files
-        mkdir -p $report.files_path &&
-
-
-        ############ save the tool installation directory to an environment variable
-        export TOOL_INSTALL_DIR='${__tool_directory__}' &&
-
-
-        #########################
-        ##
-        ## save user input option/argument pairs into a file
-        ##
-        #########################
-
-        ## first line will be the header
-        echo 'tool_output_dir|relative_path' > '$report.files_path/options_and_arguments.txt' &&
-
-
-
-        ####################################################
-        ## loop through repeats to get option/argument pairs
-        ####################################################
-
-
-        ############ option_argument_path_relative_to_a_tool
-        #for i in $option_argument_path_relative_to_a_tool_repeat:
-             #set $item = str($i.a_tool_output_dir) + "|" + str($i.value)
-             echo '$item' >> '$report.files_path/options_and_arguments.txt' &&
-        #end for
-
-
-        ############ output_set
-        ## '$report'
-        ## '$report.files_path'
-        #######################
-        export REPORT='$report' &&
-        export TOOL_LOG='$tool_log' &&
-        export REPORT_FILES_PATH='$report.files_path' &&
-
-
-        ############ run render R script to render R markdowns
-        Rscript '${__tool_directory__}/paired_render.R'
-
-        ]]></command>
-  <inputs>
-    <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="2" default="2" max="2">
-      <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/>
-      <param type="text" name="value" optional="true" label="relative path"/>
-    </repeat>
-  </inputs>
-  <outputs>
-    <data format="html" name="report" label="${tool.name} report"/>
-    <data format="txt" name="tool_log" label="${tool.name} log"/>
-    <collection type="paired" name="paired_collection">
-      <discover_datasets pattern="__name_and_ext__" directory="paired" />
-    </collection>
-  </outputs>
-  <citations>
-    <expand macro="citations"/>
-  </citations>
-</tool>
diff -r 391394c022b8 -r 5838300fc1aa individuals.Rmd
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/individuals.Rmd	Mon Apr 02 00:32:04 2018 -0400
@@ -0,0 +1,53 @@
+---
+title: 'Expose data (paired)'
+output: html_document
+---
+
+<style>
+pre code, pre, code {
+  white-space: pre !important;
+  overflow-x: scroll !important;
+  word-break: keep-all !important;
+  word-wrap: initial !important;
+}
+</style>
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$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'])
+    if (dir.exists(full_path)) {
+      from_files = list.files(full_path, full.names = TRUE)
+      to_files = paste0(Sys.getenv('individual_outputs/'), list.files(full_path))
+      file.copy(from = from_files, to = to_files)
+    }
+    if (file.exists(full_path)) {
+      file.copy(from = full_path, to = paste0(Sys.getenv('individual_outputs/'), df[i, 'relative_path']))
+    }
+    # command_line = paste0('cp -r ', full_path, ' paired')
+    # write(command_line, append = TRUE, 
+    #       file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
+  }
+}
+```
+
+
diff -r 391394c022b8 -r 5838300fc1aa individuals_render.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/individuals_render.R	Mon Apr 02 00:32:04 2018 -0400
@@ -0,0 +1,38 @@
+##============ Sink warnings and errors to a file ==============
+## use the sink() function to wrap all code within it.
+##==============================================================
+zz = file(Sys.getenv('TOOL_LOG'))
+sink(zz)
+sink(zz, type = 'message')
+
+#------------import libraries--------------------
+options(stringsAsFactors = FALSE)
+
+library(rmarkdown)
+#------------------------------------------------
+
+#------------------------------------------------
+options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), 
+                                   sep = '|', header = TRUE)
+
+#------------------------------------------------
+# create three folders within working directory
+dir.create('individual_outputs')
+
+#-----------------render Rmd--------------
+# copy R markdown file to working directory and render it within the working directory.
+render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/paired.Rmd'),
+       output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html'))
+
+# for some unknow reason, directly using REPORT as the input value for output_file parameter
+# in the render function can cause empty report file when the tool runs in batch mode.
+# the solution is to render the rmarkdown to a explicitly specified file and then copy the
+# file to ${REPORT}
+system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}')
+# system(command = 'sh ${REPORT_FILES_PATH}/script.sh')
+#------------------------------------------
+
+
+##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================
\ No newline at end of file
diff -r 391394c022b8 -r 5838300fc1aa paired.Rmd
--- a/paired.Rmd	Sat Mar 31 21:32:17 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
----
-title: 'Expose data (paired)'
-output: html_document
----
-
-<style>
-pre code, pre, code {
-  white-space: pre !important;
-  overflow-x: scroll !important;
-  word-break: keep-all !important;
-  word-wrap: initial !important;
-}
-</style>
-
-```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$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, ' paired')
-    write(command_line, append = TRUE, 
-          file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
-  }
-}
-```
-
-
diff -r 391394c022b8 -r 5838300fc1aa paired_render.R
--- a/paired_render.R	Sat Mar 31 21:32:17 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-##============ Sink warnings and errors to a file ==============
-## use the sink() function to wrap all code within it.
-##==============================================================
-zz = file(Sys.getenv('TOOL_LOG'))
-sink(zz)
-sink(zz, type = 'message')
-
-#------------import libraries--------------------
-options(stringsAsFactors = FALSE)
-
-library(rmarkdown)
-#------------------------------------------------
-
-#------------------------------------------------
-options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), 
-                                   sep = '|', header = TRUE)
-
-#------------------------------------------------
-# create three folders within working directory
-dir.create('paired')
-
-#-----------------render Rmd--------------
-# copy R markdown file to working directory and render it within the working directory.
-render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/paired.Rmd'),
-       output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html'))
-
-# for some unknow reason, directly using REPORT as the input value for output_file parameter
-# in the render function can cause empty report file when the tool runs in batch mode.
-# the solution is to render the rmarkdown to a explicitly specified file and then copy the
-# file to ${REPORT}
-system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}')
-system(command = 'sh ${REPORT_FILES_PATH}/script.sh')
-#------------------------------------------
-
-
-##--------end of code rendering .Rmd templates----------------
-sink()
-##=========== End of sinking output=============================
\ No newline at end of file