From dfd5e9827f86cdfec5d4cc04e4e93162b685917e Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Mon, 15 Dec 2008 10:37:39 -0500
Subject: [PATCH] Rename gbrowse_elegans to wormbase_test, add a config for the
 wormbase production server.

---
 tool_conf.xml.sample                          |  3 ++-
 tools/data_source/wormbase.xml                | 26 +++++++++++++++++++
 ...{gbrowse_elegans.xml => wormbase_test.xml} | 11 ++++----
 3 files changed, 33 insertions(+), 7 deletions(-)
 create mode 100644 tools/data_source/wormbase.xml
 rename tools/data_source/{gbrowse_elegans.xml => wormbase_test.xml} (81%)

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index f50684cc4c0..977d56293b7 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -9,7 +9,8 @@
     <tool file="data_source/microbial_import.xml" />
     <tool file="data_source/biomart.xml" />
     <tool file="data_source/biomart_test.xml" />
-    <tool file="data_source/gbrowse_elegans.xml" />
+    <tool file="data_source/wormbase.xml" />
+    <tool file="data_source/wormbase_test.xml" />
     <tool file="data_source/flymine.xml" />
     <tool file="data_source/encode_db.xml" />
     <tool file="data_source/epigraph_import.xml" />
diff --git a/tools/data_source/wormbase.xml b/tools/data_source/wormbase.xml
new file mode 100644
index 00000000000..d437c1d9c80
--- /dev/null
+++ b/tools/data_source/wormbase.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0"?>
+<tool name="Wormbase" id="wormbase" tool_type="data_source" URL_method="get">
+    <description>server</description>
+    <command interpreter="python">data_source.py $output</command>
+    <inputs action="http://www.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top"> 
+        <display>go to Wormbase server $GALAXY_URL</display>
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase" />
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL" remote_name="URL" missing="">
+            <add_to_url>
+                <param_from_source name="d" missing="" />
+                <param_from_source name="dbkey" missing="" />
+                <param_from_source name="q" missing="" />
+                <param_from_source name="s" missing="" />
+                <param_from_source name="t" missing="" />
+            </add_to_url>
+        </request_param>
+        <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" />
+    </request_param_translation>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+</tool>
diff --git a/tools/data_source/gbrowse_elegans.xml b/tools/data_source/wormbase_test.xml
similarity index 81%
rename from tools/data_source/gbrowse_elegans.xml
rename to tools/data_source/wormbase_test.xml
index dab815f8f99..9242840d77f 100644
--- a/tools/data_source/gbrowse_elegans.xml
+++ b/tools/data_source/wormbase_test.xml
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
-<tool name="C. Elegans" id="gbrowse_elegans" tool_type="data_source" URL_method="get">
-	<description>server</description>
+<tool name="Wormbase" id="wormbase_test" tool_type="data_source" URL_method="get">
+	<description>test server</description>
 	<command interpreter="python">data_source.py $output</command>
 	<inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top"> 
-		<display>go to C. Elegans server $GALAXY_URL</display>
-		<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=gbrowse_elegans" />
+		<display>go to Wormbase test server $GALAXY_URL</display>
+		<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase_test" />
 	</inputs>
     <request_param_translation>
         <request_param galaxy_name="URL" remote_name="URL" missing="">
@@ -16,7 +16,7 @@
                 <param_from_source name="t" missing="" />
             </add_to_url>
         </request_param>
-        <request_param galaxy_name="data_type" remote_name="data_type" missing="gff3" />
+        <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" />
     </request_param_translation>
 	<uihints minwidth="800"/>
 	<outputs>
@@ -24,4 +24,3 @@
 	</outputs>
 	<options sanitize="False" refresh="True"/>
 </tool>
-