diff --git a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py
deleted file mode 100644
index a2ea97d6fb6..00000000000
--- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py
+++ /dev/null
@@ -1,165 +0,0 @@
-"""
-Contains the UCSC proxy
-"""
-
-from galaxy.web.base.controller import BaseUIController
-
-import json
-from galaxy import web, util
-
-import re
-import urllib
-import logging
-
-log = logging.getLogger( __name__ )
-
-
-class UCSCProxy( BaseUIController ):
-
-    def create_display(self, store):
-        """Creates a more meaningulf display name"""
-        track = store.get('hgta_track', 'no track')
-        table = store.get('hgta_table', 'no table')
-        region = store.get('hgta_regionType', '')
-        if region not in [ 'genome', 'encode']:
-            region = store.get('position', '')
-        if track == table:
-            display = 'UCSC: %s (%s)' % (track, region)
-        else:
-            display = 'UCSC: %s, %s (%s)' % (track, table, region)
-        return display
-
-    @web.expose
-    def index(self, trans, init=False, **kwd):
-        base_url = None
-        params = dict(kwd)
-        try:
-            store = params.get("__GALAXY__", None)
-            if store:
-                store = json.loads(util.string_to_object(store))
-            else:
-                store = {}
-            UCSC_URL = 'UCSC_URL'
-            base_url = store.get(UCSC_URL, "http://genome.ucsc.edu/cgi-bin/hgTables?")
-            params = dict(kwd)
-            params['init'] = init
-
-            if not init:
-                for key, value in kwd.items():
-                    store[key] = value
-                try:
-                    del store["__GALAXY__"]
-                except:
-                    pass
-            else:
-                store = {}
-
-            if init == "1":
-                base_url = "http://genome.ucsc.edu/cgi-bin/hgTables?"
-                params['db'] = 'hg17'
-            if init == "2":
-                base_url = "http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?"
-                params['db'] = 'hg17'
-            if init == "3":
-                base_url = "http://archaea.ucsc.edu/cgi-bin/hgTables?"
-
-            store[UCSC_URL] = base_url
-
-            try:
-                del params["__GALAXY__"]
-            except:
-                pass
-            url = base_url + urllib.urlencode(params)
-
-            page = urllib.urlopen(url)
-            content = page.info().get('Content-type', '')
-        except Exception, exc:
-            trans.log_event( "Proxy Error -> %s" % str(exc) )
-            msg = 'There has been a problem connecting to <i>%s</i> <p> <b>%s<b>' % (base_url, exc)
-            return msg
-
-        if content.startswith('text/plain'):
-            params['display'] = self.create_display(store)
-            params['dbkey'] = store.get('db', '*')
-            params['tool_id'] = 'ucsc_proxy'
-            params['proxy_url'] = base_url
-            params['runtool_btn'] = 'T'
-            url = "/tool_runner/index?" + urllib.urlencode(params)
-            trans.response.send_redirect(url)
-        else:
-            try:
-                text = page.read()
-
-                # Serialize store into a form element
-                store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \
-                             + json.dumps(util.object_to_string(store)) + "\" \>"
-
-                # Remove text regions that should not be exposed
-                for key, value in altered_regions.items():
-                    text = text.replace(key, value)
-                # Capture only the forms
-                newtext = beginning
-                for form in re.finditer("(?s)(<FORM.*?)(</FORM>)", text):
-                    newtext = newtext + form.group(1) + store_text + form.group(2)
-                if 'hgta_doLookupPosition' in params:
-                    lookup = re.search("(?s).*?(<H2>.*</PRE>)", text)
-                    if lookup:
-                        newtext = newtext + lookup.group(1)
-                # if these keys are in the params, then pass the content through
-                passthruContent = ['hgta_doSummaryStats', 'hgta_doSchema', 'hgta_doSchemaDb']
-                for k in passthruContent:
-                    if k in params:
-                        content = re.search("(?s)CONTENT TABLES.*?-->(.*/TABLE>)", text)
-                        if content:
-                            newtext = newtext + "<TABLE>" + content.group(1)
-
-                newtext = newtext + ending
-                return newtext
-            except KeyError, exc:
-                log.error(str(exc))
-                trans.log_event( "Proxy Error -> %s" % str(exc) )
-                msg = 'There has been a problem connecting to <i>%s</i> <p> <b>%s<b>' % (base_url, exc)
-                return msg
-
-# HTML for generating the proxy page.
-beginning = '''<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-
-<head>
-<title>Galaxy</title>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<link href="/static/style/base.css" rel="stylesheet" type="text/css" />
-<script language="javascript" type="text/javascript">
-function changeTarget(target)
-{
-    document.forms['mainForm'].target = target;
-}
-</script>
-</head>
-
-<body>
-<div class="toolForm" id="ucsc_proxy">
-  <div class="toolFormTitle">UCSC Table Browser</div>
-
-  <div class="toolFormBody">
- '''
-ending = '''
-<P>This is a proxy to the data services provided by the <a href=\"http://genome.ucsc.edu\" target=\"_blank\">UCSC Genome Browser</a>'s <a href=\"http://genome.ucsc.edu/cgi-bin/hgTables\" target=\"_blank\">Table Browser.</a></P>
-  </div>
-</div>
-</body>
-</html>'''
-
-# This is a mess of mappings of text to make the proxy friendlier to
-# galaxy users.
-altered_regions = {
-    '"../cgi-bin/hgTables' : '"/ucsc_proxy/index',
-    '<TR><TD>\n<B>output file:</B>&nbsp;<INPUT TYPE=TEXT NAME="hgta_outFileName" SIZE=29 VALUE="">&nbsp;(leave blank to keep output in browser)</TD></TR>\n<TR><TD>\n<B>file type returned:&nbsp;</B><INPUT TYPE=RADIO NAME="hgta_compressType" VALUE="none" CHECKED>&nbsp;plain text&nbsp&nbsp<INPUT TYPE=RADIO NAME="hgta_compressType" VALUE="gzip" >&nbsp;gzip compressed</TD></TR>' : '<INPUT TYPE=HIDDEN NAME="hgta_compressType" VALUE="none" /><INPUT TYPE=HIDDEN NAME="hgta_outFileName" VALUE="" />',
-    ' <P>To reset <B>all</B> user cart settings (including custom tracks), \n<A HREF="/cgi-bin/cartReset?destination=/cgi-bin/hgTables">click here</A>.' : '',
-    'ACTION="../cgi-bin/hgTables"' : 'ACTION="/ucsc_proxy/index"',
-    '<A HREF="/goldenPath/help/customTrack.html" TARGET=_blank>custom track</A>' : '<A HREF="http://genome.ucsc.edu/goldenPath/help/customTrack.html" TARGET=_blank>custom track</A>',
-    '<INPUT TYPE=RADIO NAME="hgta_regionType" VALUE="genome" onClick="regionType=\'genome\';" CHECKED>' : '<INPUT TYPE=RADIO NAME="hgta_regionType" VALUE="genome" onClick="regionType=\'genome\';">',
-    '<INPUT TYPE=RADIO NAME="hgta_regionType" VALUE="range" onClick="regionType=\'range\';">' : '<INPUT TYPE=RADIO NAME="hgta_regionType" VALUE="range" onClick="regionType=\'range\';" CHECKED>',
-    "<OPTION VALUE=bed>" : "<OPTION VALUE=bed SELECTED>" ,
-    '<INPUT TYPE=SUBMIT NAME="hgta_doSchema" VALUE="describe table schema">' : '<INPUT TYPE=SUBMIT NAME="hgta_doSchema" VALUE="describe table schema" onClick="changeTarget(\'_blank\')" onMouseOut="changeTarget(\'_self\')">'
-}
diff --git a/tools/data_source/ucsc_archaea.xml b/tools/data_source/ucsc_archaea.xml
deleted file mode 100644
index 4a55acfcd51..00000000000
--- a/tools/data_source/ucsc_archaea.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0"?>
-<tool name="UCSC Archaea" id="ucsc_proxy" version="1.0.0">
-	
-	<description>table browser</description>
-	
-	<command interpreter="python">
-		ucsc_proxy.py $param_file $output
-	</command>
-	
-	<inputs action="/ucsc_proxy/index" check_values="false">
-		<display>go to UCSC $init $hgta_outputType</display>
-		<param type="hidden" name="init" value="3"/>
-		<param type="hidden" name="hgta_outputType" value="bed"/>
-	</inputs>
-	
-	<code file="ucsc_filter.py"/>
-	
-	<outputs>
-		<data name="output" format="bed" />
-	</outputs>
-
-</tool>
-
diff --git a/tools/data_source/ucsc_filter.py b/tools/data_source/ucsc_filter.py
deleted file mode 100644
index 5d10527ddc8..00000000000
--- a/tools/data_source/ucsc_filter.py
+++ /dev/null
@@ -1,68 +0,0 @@
-# runs after the job (and after the default post-filter)
-from galaxy import datatypes, jobs
-
-def validate(incoming):
-    """Validator"""
-    #raise Exception, 'not quite right'
-    pass
-
-def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
-    """Sets the name of the data"""
-    outputType = param_dict.get( 'hgta_outputType', None )
-    if isinstance(outputType, list) and len(outputType)>0: outputType = outputType[-1]
-    items = out_data.items()
-    
-    for name, data in items:
-        data.name  = param_dict.get('display', data.name)
-        data.dbkey = param_dict.get('dbkey', '???')
-
-        if outputType == 'wigData':
-            ext = "wig"
-        elif outputType == 'maf':
-            ext = "maf"
-        elif outputType == 'gff':
-            ext = "gff"
-        elif outputType == 'gff3':
-            ext = "gff3"
-        else:
-            if 'hgta_doPrintSelectedFields' in param_dict:
-                ext = "interval"
-            elif 'hgta_doGetBed' in param_dict:
-                ext = "bed"
-            elif 'hgta_doGenomicDna' in param_dict:
-                ext = "fasta"
-            elif 'hgta_doGenePredSequence' in param_dict:
-                ext = "fasta"
-            else:
-                ext = "interval"
-        
-        data = app.datatypes_registry.change_datatype(data, ext)
-        out_data[name] = data
-        
-def exec_after_process( app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
-    """Verifies the data after the run"""
-    items = out_data.items()
-    for name, data in items:
-        data.set_size()
-        try:            
-            err_msg, err_flag = 'Errors:', False
-            line_count = 0
-            num_lines = len(file(data.file_name).readlines())
-            for line in file(data.file_name):
-                line_count += 1
-                if line and line[0] == '-':
-                    if line_count + 3 == num_lines and not err_flag:
-                        err_flag = True
-                        err_msg = "Warning: It appears that your results have been truncated by UCSC. View the bottom of your result file for details."
-                        break
-                    err_flag = True
-                    err_msg = err_msg +" (line "+str(line_count)+")"+line
-            data.set_peek()
-            if isinstance(data.datatype, datatypes.interval.Interval) and data.missing_meta():
-                data = app.datatypes_registry.change_datatype(data, 'tabular')
-                out_data[name] = data
-            if err_flag:
-                raise Exception(err_msg)
-        except Exception, exc:
-            data.info  = data.info + "\n" + str(exc)
-            data.blurb = "error"
diff --git a/tools/data_source/ucsc_proxy.py b/tools/data_source/ucsc_proxy.py
deleted file mode 100644
index d8111799062..00000000000
--- a/tools/data_source/ucsc_proxy.py
+++ /dev/null
@@ -1,65 +0,0 @@
-#!/usr/bin/env python
-import urllib
-import sys, os
-
-assert sys.version_info[:2] >= ( 2, 4 )
-
-CHUNK   = 2**20 # 1Mb 
-MAXSIZE = CHUNK * 100
-if __name__ == '__main__':
-
-    if len(sys.argv) != 3:
-        print 'Usage ucsc.py input_params output_file'
-        sys.exit()
-
-    inp_file = sys.argv[1]
-    out_file = sys.argv[2]
-
-    DEFAULT_URL = "http://genome.ucsc.edu/hgTables?"
-    
-    # this must stay a list to allow multiple selections for the same widget name (checkboxes)
-    params  = []
-    for line in file(inp_file):
-        line = line.strip()
-        if line:
-            parts = line.split('=')
-            if len(parts) == 0:
-                key = ""
-                value = ""
-            elif len(parts) == 1:
-                key = parts[0]
-                value = ""
-            else:
-                key = parts[0]
-                value = parts[1]
-            if key == 'display':
-                print value
-            # get url from params, refered from proxy.py, initialized by the tool xml
-            elif key == 'proxy_url':
-                DEFAULT_URL = value
-            else:
-                params.append( (key, value) )
-    
-    #print params
-    
-    encoded_params = urllib.urlencode(params)
-    url = DEFAULT_URL + encoded_params
-
-    #print url
-
-    page = urllib.urlopen(url)
-
-    fp = open(out_file, 'wt')
-    size = 0
-    while 1:
-        data = page.read(CHUNK)
-        if not data:
-            break
-        if size > MAXSIZE:
-            fp.write('----- maximum datasize exceeded ---\n')
-            break
-        size += len(data)
-        fp.write(data)
-
-    fp.close()
-
diff --git a/tools/data_source/ucsc_proxy.xml b/tools/data_source/ucsc_proxy.xml
deleted file mode 100644
index 1459b198797..00000000000
--- a/tools/data_source/ucsc_proxy.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0"?>
-<tool name="UCSC Main" id="ucsc_proxy" version="1.0.0">
-	
-	<description>table browser proxy</description>
-	
-	<command interpreter="python">
-		ucsc_proxy.py $param_file $output
-	</command>
-	
-	<inputs action="/ucsc_proxy/index" check_values="false">
-		<display>go to UCSC $init $hgta_outputType</display>
-		<param type="hidden" name="init" value="1"/>
-		<param type="hidden" name="hgta_outputType" value="bed"/>
-	</inputs>
-	
-	<code file="ucsc_filter.py"/>
-	
-	<outputs>
-		<data name="output" format="bed" />
-	</outputs>
-
-</tool>
-
diff --git a/tools/data_source/ucsc_tablebrowser.xml b/tools/data_source/ucsc_tablebrowser.xml
index 649c9d1d8f5..f93aca6081e 100644
--- a/tools/data_source/ucsc_tablebrowser.xml
+++ b/tools/data_source/ucsc_tablebrowser.xml
@@ -39,4 +39,8 @@
         <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/>
     </outputs>
     <options sanitize="False" refresh="True"/>
+    <citations>
+        <citation type="doi">10.1093/database/bar011</citation>
+        <citation type="doi">10.1101/gr.229102</citation>
+    </citations>
 </tool>
diff --git a/tools/data_source/ucsc_tablebrowser_archaea.xml b/tools/data_source/ucsc_tablebrowser_archaea.xml
index 3a352034b41..271b232f0a0 100644
--- a/tools/data_source/ucsc_tablebrowser_archaea.xml
+++ b/tools/data_source/ucsc_tablebrowser_archaea.xml
@@ -39,4 +39,9 @@
         <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/>
     </outputs>
     <options sanitize="False" refresh="True"/>
+    <citations>
+        <citation type="doi">10.1093/database/bar011</citation>
+        <citation type="doi">10.1101/gr.229102</citation>
+        <citation type="doi">10.1093/nar/gkj134</citation>
+    </citations>
 </tool>
diff --git a/tools/data_source/ucsc_tablebrowser_test.xml b/tools/data_source/ucsc_tablebrowser_test.xml
index 43eacdcf083..ced94288060 100644
--- a/tools/data_source/ucsc_tablebrowser_test.xml
+++ b/tools/data_source/ucsc_tablebrowser_test.xml
@@ -39,4 +39,8 @@
         <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/>
     </outputs>
     <options sanitize="False" refresh="True"/>
+    <citations>
+        <citation type="doi">10.1093/database/bar011</citation>
+        <citation type="doi">10.1101/gr.229102</citation>
+    </citations>
 </tool>
diff --git a/tools/data_source/ucsc_testproxy.xml b/tools/data_source/ucsc_testproxy.xml
deleted file mode 100644
index 46b534d9189..00000000000
--- a/tools/data_source/ucsc_testproxy.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0"?>
-<tool name="UCSC Test" id="ucsc_testproxy" version="1.0.0">
-	
-	<description>table browser proxy</description>
-	
-	<command interpreter="python">
-		ucsc_proxy.py $param_file $output
-	</command>
-	
-	<inputs action="/ucsc_proxy/index" check_values="false">
-		<display>go to UCSC genome-test $init $hgta_outputType</display>
-		<param type="hidden" name="init" value="2"/>
-		<param type="hidden" name="hgta_outputType" value="bed"/>
-	</inputs>
-	
-	<code file="ucsc_filter.py"/>
-	
-	<outputs>
-		<data name="output" format="bed" />
-	</outputs>
-
-</tool>
-