From 8e9b070fac96dba93687d385fbb1a8792e704931 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 3 Jul 2007 17:15:06 +0000
Subject: [PATCH] Add direct connection to ucsc archaea browser.  We should no
 longer need the proxy.

---
 tool_conf.xml.sample                          |  5 ++--
 .../data_source/ucsc_tablebrowser_archaea.xml | 25 +++++++++++++++++++
 2 files changed, 28 insertions(+), 2 deletions(-)
 create mode 100644 tools/data_source/ucsc_tablebrowser_archaea.xml

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index c11542eeabb..fc8ff6038a1 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -4,9 +4,10 @@
     <tool file="data_source/upload.xml"/>
     <tool file="data_source/ucsc_tablebrowser.xml" />
     <tool file="data_source/ucsc_tablebrowser_test.xml" />
+    <tool file="data_source/ucsc_tablebrowser_archaea.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/ucsc_testproxy.xml" />
+    <tool file="data_source/ucsc_archaea.xml" /> -->
     <tool file="data_source/microbial_import.xml" />
     <tool file="data_source/biomart.xml" />
     <tool file="data_source/biomart_test.xml" />
diff --git a/tools/data_source/ucsc_tablebrowser_archaea.xml b/tools/data_source/ucsc_tablebrowser_archaea.xml
new file mode 100644
index 00000000000..e0d26585c6c
--- /dev/null
+++ b/tools/data_source/ucsc_tablebrowser_archaea.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<tool name="UCSC Archaea" id="ucsc_table_direct_archaea1">
+	
+	<description>table browser</description>
+	
+	<command interpreter="python2.4">ucsc_tablebrowser.py $output</command>
+	
+	<inputs action="http://archaea.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_direct_archaea1" />
+		<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>
+