# HG changeset patch
# User mingchen0919
# Date 1519393191 18000
# Node ID e1d225154d4a057a586c11aae16bc8bf10118247
# Parent  6da0541944de49f17326ece6865e0e12012014ae
initial tool

diff -r 6da0541944de -r e1d225154d4a extract_fields.xml
--- 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 $sink_message
@@ -20,11 +22,13 @@
                     ]]></command>
   <inputs>
     <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
-    <param type="data" name="input_txt" optional="False" format="txt"/>
+    <param type="text" name="field_numbers" label="Field numbers" optional="False"/>
+    <param type="data" name="input_txt" label="Input text file" optional="False" format="txt"/>
   </inputs>
   <outputs>
     <data name="report" format="html" label="tool name report" hidden="false"/>
     <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
+    <param type="data" name="output_txt" label="Output text file" optional="False" format="txt"/>
   </outputs>
   <help><![CDATA[some help text]]></help>
   <citations>
diff -r 6da0541944de -r e1d225154d4a tool_template.Rmd
--- a/tool_template.Rmd	Thu Feb 22 23:49:26 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
----
-title: "r markdown file"
-author: "Ming Chen"
-date: "2/22/2018"
-output: html_document
----
-
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-```
-
-
-```{r}
-opt
-```
-
diff -r 6da0541944de -r e1d225154d4a tool_template_render.R
--- a/tool_template_render.R	Thu Feb 22 23:49:26 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-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)
-opt
-rmarkdown::render('tool_template.Rmd', output_file = opt$report_html)
-
-sink()