--- a/replace_text_in_column.xml	Sun Oct 06 08:22:36 2013 -0400
+++ b/replace_text_in_column.xml	Wed Jan 07 11:10:52 2015 -0500
@@ -1,16 +1,27 @@
-<tool id="tp_replace_in_column" name="Replace Text" version="0.1">
+<tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.0">
     <description>in a specific column</description>
-    <requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
         <requirement type="package" version="4.1.0">gnu_awk</requirement>
-    </requirements>
+    </expand>
+    <version_command>awk --version | head -n 1</version_command>
     <command interpreter="sh">
-        #adapt to awk's quirks - to pass an acutal backslash - two backslashes are required (just like in a C string)
+<![CDATA[
+        ##adapt to awk's quirks - to pass an acutal backslash - two backslashes are required (just like in a C string)
         REPLACE_PATTERN=\${$replace_pattern//\\/\\\\};
-        awk -v OFS="\t" --re-interval --sandbox "{ \$$column = gensub( /$find_pattern/, \"$replace_pattern\", \"g\", \$$column ) ; print \$0 ; }" "$input" &gt; "$output"
+        awk
+            -v OFS="\t"
+            --re-interval
+            --sandbox "{ \$$column = gensub( /$find_pattern/, \"$replace_pattern\", \"g\", \$$column ) ; print \$0 ; }"
+            "$infile"
+        > "$output"
+]]>
     </command>
     <inputs>
-        <param format="tabular" name="input" type="data" label="File to process" />
-        <param name="column" label="in column" type="data_column" data_ref="input" accept_default="true" />
+        <param format="tabular" name="infile" type="data" label="File to process" />
+        <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" />
 
         <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > 
             <sanitizer>
@@ -19,7 +30,6 @@
                 </valid>
             </sanitizer>
         </param>
-
         <param name="replace_pattern" type="text" size="20" label="Replace with" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." >
             <sanitizer>
                 <valid initial="string.printable">
@@ -27,22 +37,21 @@
                 </valid>
             </sanitizer>
         </param>
-
     </inputs>
+    <outputs>
+        <data format="input" name="output" metadata_source="infile" />
+    </outputs>
     <tests>
           <test>
-              <param name="input" value="replace_text_in_column_in1.txt" ftype="tabular" />
+              <param name="infile" value="replace_text_in_column_in1.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="column"  value="4" />
-              <param name="url_paste"  value=".+_(R.)" />
-              <param name="file_data"  value="\1" />
         </test>
     </tests>
-    <outputs>
-        <data format="input" name="output" metadata_source="input" />
-    </outputs>
     <help>
-
+<![CDATA[
 **What it does**
 
 This tool performs find &amp; replace operation on a specified column in a given file.
@@ -74,8 +83,6 @@
 - **\\1**   The text which matched the first parenthesis in the Find Pattern.
 
 
-
-
 -----
 
 **Example 1**
@@ -124,5 +131,7 @@
 
 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
 
+@REFERENCES@
+]]>
     </help>
 </tool>