# HG changeset patch
# User mingchen0919
# Date 1519360907 18000
# Node ID f1f549e6d0bc2e0e944fb11730a39e44c826fa9c
# Parent  da18ae80603c29f11d9fb9aba4a6cc572ab88e5e
initial tool

diff -r da18ae80603c -r f1f549e6d0bc extract_fields.xml
--- a/extract_fields.xml	Mon Feb 19 12:33:33 2018 -0500
+++ b/extract_fields.xml	Thu Feb 22 23:41:47 2018 -0500
@@ -10,16 +10,17 @@
   <stdio>
     <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
   </stdio>
-  <command><![CDATA[
-                    Rscript '${__tool_directory__}/tool_template_render.R'
-                        -e $echo
-                        -r $report
-                        -d $report.files_path
-                        -s $sink_message
-                        -t '${__tool_directory__}/tool_template.Rmd'
+  <command><![CDATA[                    Rscript '${__tool_directory__}/tool_template_render.R'
+                        -e $echo
+                        -i  $input_txt
+                        -r $report
+                        -d $report.files_path
+                        -s $sink_message
+                        -t '${__tool_directory__}/tool_template.Rmd'
                     ]]></command>
   <inputs>
     <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
+    <param type="data" name="input_txt" optional="False" format="txt"/>
   </inputs>
   <outputs>
     <data name="report" format="html" label="tool name report" hidden="false"/>
diff -r da18ae80603c -r f1f549e6d0bc tool_template.Rmd
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_template.Rmd	Thu Feb 22 23:41:47 2018 -0500
@@ -0,0 +1,16 @@
+---
+title: "r markdown file"
+author: "Ming Chen"
+date: "2/22/2018"
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+
+```{r}
+opt
+```
+
diff -r da18ae80603c -r f1f549e6d0bc tool_template_render.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_template_render.R	Thu Feb 22 23:41:47 2018 -0500
@@ -0,0 +1,9 @@
+zz = file("warnings_and_errors.txt")
+sink(zz)
+sink(zz, type = "message")
+
+## get command line inputs into R
+short_flags = extract_short_flags(xml_file_name = 'extract_fields.xml')
+opt = getopt_specification_matrix(short_flags)
+
+sink()