--- a/replace_text_in_line.xml	Wed Jan 07 11:15:41 2015 -0500
+++ b/replace_text_in_line.xml	Thu Jan 08 09:07:31 2015 -0500
@@ -7,18 +7,18 @@
         <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement>
     </expand>
     <version_command>sed --version | head -n 1</version_command>
-    <command interpreter="sh">
+    <command>
 <![CDATA[
         sed 
             -r
             --sandbox
             "s/$find_pattern/$replace_pattern/g"
-            "$input"
-        > "$output"
+            "$infile"
+        > "$outfile"
 ]]>
     </command>
     <inputs>
-        <param format="txt" name="input" type="data" label="File to process" />
+        <param format="txt" name="infile" type="data" label="File to process" />
          <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > 
             <sanitizer>
                 <valid initial="string.printable">
@@ -35,21 +35,21 @@
         </param>
     </inputs>
     <outputs>
-        <data format="input" name="output" metadata_source="input"/>
+        <data name="outfile" format_source="infile" metadata_source="infile"/>
     </outputs>
     <tests>
         <test>
-            <param name="input" value="replace_text_in_line_in1.txt" />
+            <param name="infile" value="replace_text_in_line1.txt" />
             <param name="find_pattern" value="CTC." />
             <param name="replace_pattern" value="FOOBAR" />
-            <output name="output" file="replace_text_in_line_output1.txt" />
+            <output name="outfile" file="replace_text_in_line_results1.txt" />
         </test>
     </tests>
     <help>
 <![CDATA[
 **What it does**
 
-This tool performs find &amp; replace operation on a specified file.
+This tool performs find & replace operation on a specified file.
 
 .. class:: infomark
 
@@ -61,7 +61,6 @@
 
 -----
 
-
 **Examples of Find Patterns**
 
 - **HELLO**     The word 'HELLO' (case sensitive).
@@ -71,16 +70,13 @@
 - **hsa-mir-([^ ]+)**        The text 'hsa-mir-' followed by one-or-more non-space characters. When using parenthesis, the matched content of the parenthesis can be accessed with **\1** in the **replace** pattern.
 
 
-
 **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.
 
 
-
-
 -----
 
 **Example 1**
@@ -96,7 +92,7 @@
 **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.