--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/find_and_replace.xml	Thu Sep 05 04:58:21 2013 -0400
@@ -0,0 +1,155 @@
+<tool id="cshl_find_and_replace" name="Find and Replace" version="0.1.1">
+    <description>text</description>
+    <command interpreter="perl">
+        find_and_replace
+            #if $searchwhere.choice == "column":
+                -c $searchwhere.column
+            #end if
+            -o $output
+            $caseinsensitive
+            $wholewords
+            $skip_first_line
+            $is_regex
+            '$url_paste'
+            '$file_data'
+            '$input'
+    </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 // ) " > 
+            <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." >
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </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="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="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="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" />
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data format="input" name="output" metadata_source="input" />
+    </outputs>
+
+<help>
+
+**What it does**
+
+This tool finds &amp; replaces text in an input dataset.
+
+.. class:: infomark
+
+The **pattern to find** can be a simple text string, or a perl **regular expression** string (depending on *pattern is a regex* check-box).
+
+.. class:: infomark
+
+When using regular expressions, the **replace pattern** can contain back-references ( e.g. \\1 )
+
+.. class:: infomark
+
+This tool uses Perl regular expression syntax.
+
+-----
+
+**Examples of *regular-expression* Find Patterns**
+
+- **HELLO**     The word 'HELLO' (case sensitive).
+- **AG.T**      The letters A,G followed by any single character, followed by the letter T.
+- **A{4,}**     Four or more consecutive A's.
+- **chr2[012]\\t**       The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
+- **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;** (dollar-ampersand) represents the matched find pattern.
+- **$1**   The text which matched the first parenthesis in the Find Pattern.
+
+
+-----
+
+**Example 1**
+
+**Find Pattern:** HELLO
+**Replace Pattern:** WORLD
+**Regular Expression:** no
+**Replace what:** entire line
+
+Every time the word HELLO is found, it will be replaced with the word WORLD. 
+
+-----
+
+**Example 2**
+
+**Find Pattern:** ^chr 
+**Replace Pattern:** (empty)
+**Regular Expression:** yes
+**Replace what:** column 11
+
+If column 11 (of every line) begins with ther letters 'chr', they will be removed. Effectively, it'll turn "chr4" into "4" and "chrXHet" into "XHet"
+
+
+-----
+
+**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. 
+
+- **( ) { } [ ] . * ? + \\ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
+- **^** matches the beginning of a string(but not an internal line).
+- **(** .. **)** groups a particular pattern.
+- **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
+
+  - **{n}** The preceding item is matched exactly n times.
+  - **{n,}** The preceding item ismatched n or more times. 
+  - **{n,m}** The preceding item is matched at least n times but not more than m times. 
+
+- **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
+- **.** Matches any single character except a newline.
+- ***** The preceding item will be matched zero or more times.
+- **?** The preceding item is optional and matched at most once.
+- **+** The preceding item will be matched one or more times.
+- **^** has two meaning:
+  - matches the beginning of a line or string. 
+  - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
+- **$** matches the end of a line or string.
+- **\\|** Separates alternate possibilities. 
+- **\\d** matches a single digit
+- **\\w** matches a single letter or digit or an underscore.
+- **\\s** matches a single white-space (space or tabs).
+
+
+</help>
+
+</tool>