--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/unix_tools/find_and_replace.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,154 @@
+<tool id="cshl_find_and_replace" name="Find and Replace">
+  <description>text</description>
+  <command interpreter="perl">
+	find_and_replace.pl
+	#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" />
+
+    <!-- Note: the parameter ane MUST BE 'url_paste' -
+         This is a hack in the galaxy library (see ./lib/galaxy/util/__init__.py line 142)
+	 If the name is 'url_paste' the string won't be sanitized, and all the non-alphanumeric characters 
+	 will be passed to the shell script -->
+	 <param name="url_paste" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > 
+    		<validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator>
+	</param>
+
+	 <param name="file_data" 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." >
+    		<validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator>
+	</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>
+
+		<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;** (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>