From 8a207dcd87d3bbc4c73a9351dc9c04e15e86de20 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 21 Mar 2007 19:52:01 +0000
Subject: [PATCH] Update UCSC direct connection to use main ucsc site. Add
 direct test connection.

---
 tool_conf.xml.sample                         |  5 ++--
 tools/data_source/ucsc_proxy.xml             |  2 +-
 tools/data_source/ucsc_tablebrowser.xml      |  6 ++---
 tools/data_source/ucsc_tablebrowser_test.xml | 25 ++++++++++++++++++++
 tools/data_source/ucsc_testproxy.xml         |  2 +-
 5 files changed, 33 insertions(+), 7 deletions(-)
 create mode 100644 tools/data_source/ucsc_tablebrowser_test.xml

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 076917c4259..54ecf03cf81 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -3,8 +3,9 @@
   <section name="Get Data" id="getext">
     <tool file="data_source/upload.xml"/>
     <tool file="data_source/ucsc_tablebrowser.xml" />
-    <tool file="data_source/ucsc_proxy.xml"/> 
-    <tool file="data_source/ucsc_testproxy.xml" />
+    <tool file="data_source/ucsc_tablebrowser_test.xml" />
+<!--    <tool file="data_source/ucsc_proxy.xml"/> 
+    <tool file="data_source/ucsc_testproxy.xml" /> -->
     <tool file="data_source/ucsc_archaea.xml" />
     <tool file="data_source/microbial_import.xml" />
     <tool file="data_source/biomart.xml" />
diff --git a/tools/data_source/ucsc_proxy.xml b/tools/data_source/ucsc_proxy.xml
index 20034266321..65c9c5c5db2 100644
--- a/tools/data_source/ucsc_proxy.xml
+++ b/tools/data_source/ucsc_proxy.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool name="UCSC Main" id="ucsc_proxy">
 	
-	<description>table browser</description>
+	<description>table browser proxy</description>
 	
 	<command interpreter="python">
 		ucsc_proxy.py $param_file $output
diff --git a/tools/data_source/ucsc_tablebrowser.xml b/tools/data_source/ucsc_tablebrowser.xml
index 8058ad484cf..3f7bc45f4a8 100644
--- a/tools/data_source/ucsc_tablebrowser.xml
+++ b/tools/data_source/ucsc_tablebrowser.xml
@@ -1,11 +1,11 @@
 <?xml version="1.0"?>
-<tool name="UCSC Table Browser" id="ucsc_table_direct1">
+<tool name="UCSC Main" id="ucsc_table_direct1">
 	
-	<description>direct connection</description>
+	<description>table browser</description>
 	
 	<command interpreter="python2.4">ucsc_tablebrowser.py $output</command>
 	
-	<inputs action="http://genome-test.cse.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
+	<inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
 		<display>go to UCSC Table Browser $GALAXY_URL</display>
 		<param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
 		<param name="tool_id" type="hidden" value="ucsc_table_direct1" />
diff --git a/tools/data_source/ucsc_tablebrowser_test.xml b/tools/data_source/ucsc_tablebrowser_test.xml
new file mode 100644
index 00000000000..58d1083f90a
--- /dev/null
+++ b/tools/data_source/ucsc_tablebrowser_test.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<tool name="UCSC Test" id="ucsc_table_direct_test1">
+	
+	<description>table browser</description>
+	
+	<command interpreter="python2.4">ucsc_tablebrowser.py $output</command>
+	
+	<inputs action="http://genome-test.cse.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
+		<display>go to UCSC Table Browser $GALAXY_URL</display>
+		<param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
+		<param name="tool_id" type="hidden" value="ucsc_table_direct1" />
+		<param name="sendToGalaxy" type="hidden" value="1" />
+		<param name="hgta_compressType" type="hidden" value="none" />
+		<param name="hgta_outputType" type="hidden" value="bed" />
+	</inputs>
+	
+	<code file="ucsc_tablebrowser_code.py"/>
+	
+	<outputs>
+		<data name="output" format="bed" />
+	</outputs>
+	<options sanitize="False" refresh="True"/>
+
+</tool>
+
diff --git a/tools/data_source/ucsc_testproxy.xml b/tools/data_source/ucsc_testproxy.xml
index cf917b24fd7..af6e96f83c9 100644
--- a/tools/data_source/ucsc_testproxy.xml
+++ b/tools/data_source/ucsc_testproxy.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool name="UCSC Test" id="ucsc_testproxy">
 	
-	<description>table browser</description>
+	<description>table browser proxy</description>
 	
 	<command interpreter="python">
 		ucsc_proxy.py $param_file $output