# HG changeset patch
# User mingchen0919
# Date 1519403010 18000
# Node ID 26a2393009895e660b87b630fa01ca4b9faa1847
# Parent  8c3b0ffa0d14e23415edf42371837b38ba081494
initial tool

diff -r 8c3b0ffa0d14 -r 26a239300989 extract_fields.xml
--- a/extract_fields.xml	Fri Feb 23 10:46:48 2018 -0500
+++ b/extract_fields.xml	Fri Feb 23 11:23:30 2018 -0500
@@ -12,18 +12,19 @@
   </stdio>
   <command><![CDATA[                    Rscript '${__tool_directory__}/tool_template_render.R'
                         -e $echo
-                        -A $input_field_numbers
-                        -B $input_txt
-                        -O $output_txt
                         -r $report
                         -d $report.files_path
                         -s $sink_message
                         -t '${__tool_directory__}/tool_template.Rmd'
+
+                        -A $input_field_numbers
+                        -B $input_file
+                        -O $output_txt
                     ]]></command>
   <inputs>
     <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
-    <param type="text" name="input_field_numbers" label="input field numbers" optional="False"/>
-    <param type="data" name="input_txt" label="Input text file" optional="False" format="txt"/>
+    <param type="data" name="input_file" label="Input file" optional="False"/>
+    <param type="text" name="input_field_numbers" label="Field numbers" optional="False"/>
   </inputs>
   <outputs>
     <data name="report" format="html" label="tool name report" hidden="false"/>
diff -r 8c3b0ffa0d14 -r 26a239300989 tool_template_render.R
--- a/tool_template_render.R	Fri Feb 23 10:46:48 2018 -0500
+++ b/tool_template_render.R	Fri Feb 23 11:23:30 2018 -0500
@@ -2,16 +2,17 @@
 sink(zz)
 sink(zz, type = "message")
 
+
 # bring user inputs and command line arguments to R
 spec_matrix = as.matrix(
   data.frame(stringsAsFactors=FALSE,
-              long_flags = c("X_e", "X_A", "X_B", "X_O", "X_r", "X_d", "X_s",
-                             "X_t"),
+             long_flags = c("X_e", "X_A", "X_B", "X_O", "X_r", "X_d", "X_s",
+                            "X_t"),
              short_flags = c("e", "A", "B", "O", "r", "d", "s", "t"),
-     argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
-         data_type_flags = c("character", "character", "character", "character",
-                             "character", "character", "character",
-                             "character")
+             argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
+             data_type_flags = c("character", "character", "character", "character",
+                                 "character", "character", "character",
+                                 "character")
   )
 )
 opt = getopt::getopt(spec_matrix)