<tool id="regex_replace" name="Regex Replace" version="1.0.0">
	<description>Regular Expression replacement using the Python re module</description>
	<command interpreter="python">$script_file</command>
	<inputs>
		<param name="infile" type="data" label="Input File"/>
	  	<param name="search_str" type="text" size="70" label="Search String">
			<sanitizer>
				<valid initial="string.printable">
					<remove value="&quot;"/>
					<remove value="\"/>
				</valid>
				<mapping initial="none">
					<add source="&quot;" target="\&quot;"/>
					<add source="\" target="\\"/>
				</mapping>
			</sanitizer>
		</param>
	  	<param name="replace_str" type="text" size="70" label="Replace String">
		  	<sanitizer>
				<valid initial="string.printable">
					<remove value="&quot;"/>
					<remove value="\"/>
				</valid>
				<mapping initial="none">
					<add source="&quot;" target="\&quot;"/>
					<add source="\" target="\\"/>
				</mapping>
			</sanitizer>
	  	</param>
	  	<param name="multiline" type="boolean" label="Multi-line" checked="False"/>
	  	<param name="ignore_case" type="boolean" label="Ignore Case" checked="False"/>
	  	<param name="dot_all" type="boolean" label="Dot All" checked="False"/>
	  	<param name="replace_count" type="integer" label="Replace Count(0=all)" value="0"/>
	</inputs>
	<outputs>
		<data name="outfile" format="txt"/>
	</outputs>
	<configfiles>
		<configfile name="script_file"><![CDATA[#!/usr/bin/env python

import re

search_str = """${search_str}"""
replace_str = """${replace_str}"""

opts = 0
#if $ignore_case:
opts |= re.IGNORECASE
#end if
#if $multiline:
opts |= re.MULTILINE
#end if 
#if $dot_all:
opts |= re.DOTALL
#end if
cmd = re.compile(search_str, opts)

ihandle = open("""${infile}""")
ohandle = open("""${outfile}""", "w")

#if $multiline:
itext = ihandle.read()
otext = cmd.sub(replace_str, itext, count=$replace_count )
ohandle.write(otext)
#else
for line in ihandle:
	oline = cmd.sub(replace_str, line, count=$replace_count )
	ohandle.write(oline)
#end if

ihandle.close()
ohandle.close()

]]></configfile>
	</configfiles>

  <help>
Perform regular expression replacement using the Python re engine.

Example:
========
    Search String::

        [^\s]+_(\w+).*

    Replace String::
        
        \1

    On the input file::

        LJP001_BT20_24H:DMSO
        LJP001_BT20_24H:H20
        LJP001_BT20_6H:DMSO

    Outputs::

        24H
        24H
        6H

Additional Options
==================

Replace Count:
    Will define the number of occurrences that can be replaced by the substitution. A count of 0 is equivalent 
    to 'replace all'


Ignore Case:
    Make searches case insensitive

Multi-line:
    Do the search across the entire contents of the file. If not checked, then replacements occur line by line

Dot-All:
    With this checked, the '.' in a matching pattern will also match new-line characters. Generally used with 'multi-line' search

  </help>
</tool>