diff extract_fields.xml @ 2:f1f549e6d0bc draft

initial tool

--- 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"/>