# HG changeset patch
# User kellrott
# Date 1386272950 18000
# Node ID 71f6f91d5ca3210c983b22e6742eb0fe33fc5962

Uploaded

diff -r 000000000000 -r 71f6f91d5ca3 regex_search/regex_search.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/regex_search/regex_search.xml	Thu Dec 05 14:49:10 2013 -0500
@@ -0,0 +1,80 @@
+<tool id="regex_search" name="Regex Search" version="1.0.0">
+	<description>Regular Expression search using the Python re module</description>
+	<command interpreter="python">$script_file</command>
+	<inputs>
+		<param name="infile" type="data" label="Input File"/>
+	  	<param name="search_str" type="text" size="70" label="Search String">
+			<sanitizer>
+				<valid initial="string.printable">
+					<remove value="&quot;"/>
+					<remove value="\"/>
+				</valid>
+				<mapping initial="none">
+					<add source="&quot;" target="\&quot;"/>
+					<add source="\" target="\\"/>
+				</mapping>
+			</sanitizer>
+		</param>
+	  	<param name="ignore_case" type="boolean" label="Ignore Case" checked="False"/>
+	  	<param name="return_miss" type="boolean" label="Return Misses" checked="False"/>
+	</inputs>
+	<outputs>
+		<data name="outfile" format="txt"/>
+	</outputs>
+	<configfiles>
+		<configfile name="script_file"><![CDATA[#!/usr/bin/env python
+
+import re
+
+search_str = """${search_str}"""
+
+opts = 0
+#if $ignore_case:
+opts |= re.IGNORECASE
+#end if
+
+cmd = re.compile(search_str, opts)
+
+ihandle = open("""${infile}""")
+ohandle = open("""${outfile}""", "w")
+
+for line in ihandle:
+#if $return_miss:
+	if not cmd.match(line):
+		ohandle.write(line)
+#else
+	if cmd.match(line):
+		ohandle.write(line)
+#end if
+
+ihandle.close()
+ohandle.close()
+
+]]></configfile>
+	</configfiles>
+
+  <help>
+Perform regular expression search using the Python re engine. You can find documentation on the Python regular 
+expression syntax `here &lt;http://docs.python.org/2/library/re.html#regular-expression-syntax&gt;`_
+This is very similar to the 'Select' tool that is included with Galaxy, however this version is powered by 
+Python's RE package, rather then grep, which should eliminate some of the minor differences between the versions of Grep
+one would find in Mac or Linux. 
+
+Example:
+========
+    Search String::
+
+        [^\s]+_\w+.*
+
+
+Additional Options
+==================
+
+Ignore Case:
+    Make searches case insensitive
+
+Return Misses:
+    Return lines that don't match the search string. 
+
+  </help>
+</tool>