--- a/replace_text_in_column.xml	Wed Jan 07 11:15:41 2015 -0500
+++ b/replace_text_in_column.xml	Thu Jan 08 09:07:31 2015 -0500
@@ -7,16 +7,14 @@
         <requirement type="package" version="4.1.0">gnu_awk</requirement>
     </expand>
     <version_command>awk --version | head -n 1</version_command>
-    <command interpreter="sh">
+    <command>
 <![CDATA[
-        ##adapt to awk's quirks - to pass an acutal backslash - two backslashes are required (just like in a C string)
-        REPLACE_PATTERN=\${$replace_pattern//\\/\\\\};
         awk
-            -v OFS="\t"
+            -v OFS="	"
             --re-interval
-            --sandbox "{ \$$column = gensub( /$find_pattern/, \"$replace_pattern\", \"g\", \$$column ) ; print \$0 ; }"
+            --sandbox '{ \$$column = gensub( /$find_pattern/, "$replace_pattern", "g", \$$column ) ; print \$0 ; }'
             "$infile"
-        > "$output"
+        > "$outfile"
 ]]>
     </command>
     <inputs>
@@ -39,22 +37,22 @@
         </param>
     </inputs>
     <outputs>
-        <data format="input" name="output" metadata_source="infile" />
+        <data name="outfile" format_source="infile" metadata_source="infile" />
     </outputs>
     <tests>
           <test>
-              <param name="infile" value="replace_text_in_column_in1.txt" ftype="tabular" />
+              <param name="infile" value="replace_text_in_column1.txt" ftype="tabular" />
               <param name="column" value="4" />
               <param name="find_pattern" value=".+_(R.)" />
-              <param name="replace_pattern" value="\1" />
-              <output name="output" file="replace_text_in_column_output1.txt" />
+              <param name="replace_pattern" value="\\1" />
+              <output name="outfile" file="replace_text_in_column_results1.txt" />
         </test>
     </tests>
     <help>
 <![CDATA[
 **What it does**
 
-This tool performs find &amp; replace operation on a specified column in a given file.
+This tool performs find & replace operation on a specified column in a given file.
 
 .. class:: infomark
 
@@ -79,7 +77,7 @@
 **Examples of Replace Patterns**
 
 - **WORLD**  The word 'WORLD' will be placed whereever the find pattern was found.
-- **FOO-&amp;-BAR**  Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **&amp;** (ampersand) represents the matched find pattern.
+- **FOO-&-BAR**  Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **&** (ampersand) represents the matched find pattern.
 - **\\1**   The text which matched the first parenthesis in the Find Pattern.
 
 
@@ -97,7 +95,7 @@
 **Example 2**
 
 **Find Pattern:** ^(.{4}) 
-**Replace Pattern:** &amp;\\t
+**Replace Pattern:** &\\t
 
 Find the first four characters in each line, and replace them with the same text, followed by a tab character. In practice - this will split the first line into two columns. This operation affects only the selected column.