# HG changeset patch
# User mingchen0919
# Date 1519361366 18000
# Node ID 6da0541944de49f17326ece6865e0e12012014ae
# Parent  f1f549e6d0bc2e0e944fb11730a39e44c826fa9c
initial tool

diff -r f1f549e6d0bc -r 6da0541944de tool_template_render.R
--- a/tool_template_render.R	Thu Feb 22 23:41:47 2018 -0500
+++ b/tool_template_render.R	Thu Feb 22 23:49:26 2018 -0500
@@ -5,5 +5,7 @@
 ## get command line inputs into R
 short_flags = extract_short_flags(xml_file_name = 'extract_fields.xml')
 opt = getopt_specification_matrix(short_flags)
+opt
+rmarkdown::render('tool_template.Rmd', output_file = opt$report_html)
 
 sink()