--- a/find_and_replace.xml	Sun Oct 06 08:22:36 2013 -0400
+++ b/find_and_replace.xml	Wed Jan 07 11:10:52 2015 -0500
@@ -1,30 +1,34 @@
-<tool id="tp_find_and_replace" name="Replace" version="0.1.1">
+<tool id="tp_find_and_replace" name="Replace" version="@BASE_VERSION@.0">
     <description>parts of text</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <command interpreter="perl">
+<![CDATA[
         find_and_replace
-            #if $searchwhere.choice == "column":
+            #if $searchwhere.searchwhere_select == "column":
                 -c $searchwhere.column
             #end if
-            -o $output
+            -o $outfile
             $caseinsensitive
             $wholewords
             $skip_first_line
             $is_regex
-            '$url_paste'
-            '$file_data'
-            '$input'
+            '$find_pattern'
+            '$replace_pattern'
+            '$infile'
+]]>
     </command>
     <inputs>
-        <param format="txt" name="input" type="data" label="File to process" />
-        <param name="url_paste" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > 
+        <param name="infile" format="txt" 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">
                     <remove value="&apos;"/>
                 </valid>
             </sanitizer>
         </param>
-
-        <param name="file_data" type="text" size="20" label="Replace with" help="Use simple text, or $&amp; (dollar-ampersand) and $1 $2 $3 to refer to matched text. See examples below." >
+        <param name="replace_pattern" type="text" size="20" label="Replace with" help="Use simple text, or $&amp; (dollar-ampersand) and $1 $2 $3 to refer to matched text. See examples below." >
             <sanitizer>
                 <valid initial="string.printable">
                     <remove value="&apos;"/>
@@ -32,40 +36,59 @@
             </sanitizer>
         </param>
 
-        <param name="is_regex" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Find-Pattern is a regular expression" 
-            help="see help section for details." />
+        <param name="is_regex" type="boolean" checked="false" truevalue="-r" falsevalue=""
+            label="Find-Pattern is a regular expression" help="see help section for details." />
 
-        <param name="caseinsensitive" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Case-Insensitive search" 
-            help="" />
+        <param name="caseinsensitive" type="boolean" checked="false" truevalue="-i" falsevalue=""
+            label="Case-Insensitive search" help="" />
 
-        <param name="wholewords" type="boolean" checked="false" truevalue="-w" falsevalue="" label="find whole-words" 
-            help="ignore partial matches (e.g. 'apple' will not match 'snapple') " />
+        <param name="wholewords" type="boolean" checked="false" truevalue="-w" falsevalue=""
+            label="Find whole-words" help="ignore partial matches (e.g. 'apple' will not match 'snapple')" />
 
-        <param name="skip_first_line" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Ignore first line" 
-            help="Select this option if the first line contains column headers. Text in the line will not be replaced. " />
+        <param name="skip_first_line" type="boolean" checked="false" truevalue="-s" falsevalue=""
+            label="Ignore first line" help="Select this option if the first line contains column headers. Text in the line will not be replaced. " />
 
         <conditional name="searchwhere">
-            <param name="choice" type="select" label="Find and Replace text in">
+            <param name="searchwhere_select" type="select" label="Find and Replace text in">
                 <option value="line" selected="true">entire line</option>
                 <option value="column">specific column</option>
             </param>
             <when value="line" />
-
             <when value="column">
-                <param name="column" label="in column" type="data_column" data_ref="input" accept_default="true" />
+                <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" />
             </when>
         </conditional>
     </inputs>
-
     <outputs>
-        <data format="input" name="output" metadata_source="input" />
+        <data format="input" name="outfile" metadata_source="infile" />
     </outputs>
-
-<help>
-
+    <tests>
+        <test>
+            <param name="infile" value="find_and_replace1.txt" />
+            <param name="find_pattern" value="day" />
+            <param name="replace_pattern" value="great day" />
+            <param name="is_regex" value="False" />
+            <param name="caseinsensitive" value="False" />
+            <param name="wholewords" value="True" />
+            <output name="outfile" file="find_and_replace_results1.txt" />
+        </test>
+        <test>
+            <param name="infile" value="find_and_replace2.txt" />
+            <param name="find_pattern" value="^chr" />
+            <param name="replace_pattern" value="" />
+            <param name="is_regex" value="True" />
+            <param name="caseinsensitive" value="False" />
+            <param name="wholewords" value="False" />
+            <param name="searchwhere_select" value="column" />
+            <param name="column" value="3" />
+            <output name="outfile" file="find_and_replace_results2.txt" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
 **What it does**
 
-This tool finds &amp; replaces text in an input dataset.
+This tool finds $ replaces text in an input dataset.
 
 .. class:: infomark
 
@@ -93,7 +116,7 @@
 **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. **$&amp;** (dollar-ampersand) represents the matched find pattern.
+- **FOO-$&-BAR**  Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **$&amp;** (dollar-ampersand) represents the matched find pattern.
 - **$1**   The text which matched the first parenthesis in the Find Pattern.
 
 
@@ -106,7 +129,7 @@
 **Regular Expression:** no
 **Replace what:** entire line
 
-Every time the word HELLO is found, it will be replaced with the word WORLD. 
+Every time the word HELLO is found, it will be replaced with the word WORLD.
 
 -----
 
@@ -124,7 +147,7 @@
 
 **Perl's Regular Expression Syntax**
 
-The Find &amp; Replace tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text. 
+The Find & Replace tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text. 
 
 - **( ) { } [ ] . * ? + \\ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
 - **^** matches the beginning of a string(but not an internal line).
@@ -149,7 +172,7 @@
 - **\\w** matches a single letter or digit or an underscore.
 - **\\s** matches a single white-space (space or tabs).
 
-
-</help>
-
+@REFERENCES@
+]]>
+    </help>
 </tool>