diff extract_fields.xml @ 4:e1d225154d4a draft

initial tool

--- a/extract_fields.xml	Thu Feb 22 23:49:26 2018 -0500
+++ b/extract_fields.xml	Fri Feb 23 08:39:51 2018 -0500
@@ -12,7 +12,9 @@
   </stdio>
   <command><![CDATA[                    Rscript '${__tool_directory__}/tool_template_render.R'
                         -e $echo
-                        -i  $input_txt
+                        -A $field_numbers
+                        -B $input_txt
+                        -O $output_txt
                         -r $report
                         -d $report.files_path
                         -s $sink_message
@@ -20,11 +22,13 @@
                     ]]></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"/>
+    <param type="text" name="field_numbers" label="Field numbers" optional="False"/>
+    <param type="data" name="input_txt" label="Input text file" optional="False" format="txt"/>
   </inputs>
   <outputs>
     <data name="report" format="html" label="tool name report" hidden="false"/>
     <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
+    <param type="data" name="output_txt" label="Output text file" optional="False" format="txt"/>
   </outputs>
   <help><![CDATA[some help text]]></help>
   <citations>