diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index c96d4ecf964..15b9c4ddc01 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -95,7 +95,7 @@
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 6dfb7130ce7..7efff0d3a3c 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -104,7 +104,7 @@
diff --git a/tools/stats/wiggle_to_simple.py b/tools/stats/wiggle_to_simple.py
deleted file mode 100755
index ecae7ec1804..00000000000
--- a/tools/stats/wiggle_to_simple.py
+++ /dev/null
@@ -1,43 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Read a wiggle track and print out a series of lines containing
-"chrom position score". Ignores track lines, handles bed, variableStep
-and fixedStep wiggle lines.
-"""
-import sys
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-import bx.wiggle
-from galaxy.tools.exception_handling import *
-
-def stop_err( msg ):
- sys.stderr.write( msg )
- sys.exit()
-
-def main():
- if len( sys.argv ) > 1:
- in_file = open( sys.argv[1] )
- else:
- in_file = open( sys.stdin )
-
- if len( sys.argv ) > 2:
- out_file = open( sys.argv[2], "w" )
- else:
- out_file = sys.stdout
-
- try:
- for fields in bx.wiggle.IntervalReader( UCSCOutWrapper( in_file ) ):
- out_file.write( "%s\n" % "\t".join( map( str, fields ) ) )
- except UCSCLimitException:
- # Wiggle data was truncated, at the very least need to warn the user.
- print 'Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.'
- except ValueError, e:
- in_file.close()
- out_file.close()
- stop_err( str( e ) )
-
- in_file.close()
- out_file.close()
-
-if __name__ == "__main__": main()
diff --git a/tools/stats/wiggle_to_simple.xml b/tools/stats/wiggle_to_simple.xml
deleted file mode 100644
index f43f2db3ec8..00000000000
--- a/tools/stats/wiggle_to_simple.xml
+++ /dev/null
@@ -1,88 +0,0 @@
-
- converter
- wiggle_to_simple.py $input $out_file1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-**Syntax**
-
-This tool converts wiggle data into interval type.
-
-- **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line. Following the track definition line is the track data, which can be entered in three different formats described below.
-
- - **BED format** with no declaration line and four columns of data::
-
- chromA chromStartA chromEndA dataValueA
- chromB chromStartB chromEndB dataValueB
-
- - **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values::
-
- variableStep chrom=chrN [span=windowSize]
- chromStartA dataValueA
- chromStartB dataValueB
-
- - **fixedStep** single column data; started by a declaration line and followed with data values::
-
- fixedStep chrom=chrN start=position step=stepInterval [span=windowSize]
- dataValue1
- dataValue2
-
------
-
-**Example**
-
-- input wiggle format file::
-
- #track type=wiggle_0 name="Bed Format" description="BED format"
- chr19 59302000 59302300 -1.0
- chr19 59302300 59302600 -0.75
- chr19 59302600 59302900 -0.50
- chr19 59302900 59303200 -0.25
- chr19 59303200 59303500 0.0
- #track type=wiggle_0 name="variableStep" description="variableStep format"
- variableStep chrom=chr19 span=150
- 59304701 10.0
- 59304901 12.5
- 59305401 15.0
- 59305601 17.5
- #track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full
- fixedStep chrom=chr19 start=59307401 step=300 span=200
- 1000
- 900
- 800
- 700
- 600
-
-- convert the above file to interval file::
-
- chr19 59302000 59302300 + -1.0
- chr19 59302300 59302600 + -0.75
- chr19 59302600 59302900 + -0.5
- chr19 59302900 59303200 + -0.25
- chr19 59303200 59303500 + 0.0
- chr19 59304701 59304851 + 10.0
- chr19 59304901 59305051 + 12.5
- chr19 59305401 59305551 + 15.0
- chr19 59305601 59305751 + 17.5
- chr19 59307701 59307901 + 1000.0
- chr19 59308001 59308201 + 900.0
- chr19 59308301 59308501 + 800.0
- chr19 59308601 59308801 + 700.0
- chr19 59308901 59309101 + 600.0
-
-
-