From e608f904ee9500ae49b1ede9fcc924e512849fbf Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wed, 27 May 2009 14:19:59 -0400
Subject: [PATCH] Add tool config for GrameneMart data source.

---
 tool_conf.xml.main                 |  1 +
 tool_conf.xml.sample               |  1 +
 tools/data_source/gramene_mart.xml | 41 ++++++++++++++++++++++++++++++
 3 files changed, 43 insertions(+)
 create mode 100644 tools/data_source/gramene_mart.xml

diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index c1f37307c6b..e8aeb52a709 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -6,6 +6,7 @@
     <tool file="data_source/ucsc_tablebrowser_archaea.xml" />
     <tool file="data_source/microbial_import.xml" />
     <tool file="data_source/biomart.xml" />
+    <tool file="data_source/gramene_mart.xml" />
     <tool file="data_source/flymine.xml" />
     <tool file="data_source/encode_db.xml" />
     <tool file="data_source/epigraph_import.xml" />
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index ae07d21a938..84e267155f1 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -8,6 +8,7 @@
     <tool file="data_source/microbial_import.xml" />
     <tool file="data_source/biomart.xml" />
     <tool file="data_source/biomart_test.xml" />
+    <tool file="data_source/gramene_mart.xml" />
     <tool file="data_source/wormbase.xml" />
     <tool file="data_source/wormbase_test.xml" />
     <tool file="data_source/flymine.xml" />
diff --git a/tools/data_source/gramene_mart.xml b/tools/data_source/gramene_mart.xml
new file mode 100644
index 00000000000..3eed0531048
--- /dev/null
+++ b/tools/data_source/gramene_mart.xml
@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<!--
+    If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
+    the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
+    initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
+
+    TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile
+    everything including and beyond the first '&' is truncated from URL.  They said they'll let us know when this is fixed at their end.
+-->
+<tool name="GrameneMart" id="gramenemart" tool_type="data_source" URL_method="get" version="1.0.1">
+    <description> Central server</description>
+    <command interpreter="python">data_source.py $output</command>
+    <inputs action="http://www.gramene.org/biomart/martview" check_values="false" method="get" target="_top">
+        <display>go to GrameneMart Central $GALAXY_URL</display>
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL" remote_name="URL" missing="">
+            <add_to_url>
+                <param_from_source name="_export" missing="1" />
+                <param_from_source name="GALAXY_URL" missing="0" />
+            </add_to_url>
+        </request_param>
+        <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular">
+            <data_type_translation>
+                <format galaxy_format="tabular" remote_format="TSV" />
+            </data_type_translation> 
+        </request_param>
+        <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
+        <request_param galaxy_name="organism" remote_name="organism" missing="" />
+        <request_param galaxy_name="table" remote_name="table" missing="" />
+        <request_param galaxy_name="description" remote_name="description" missing="" />
+        <request_param galaxy_name="name" remote_name="name" missing="Biomart query" />
+        <request_param galaxy_name="info" remote_name="info" missing="" />
+    </request_param_translation>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="tabular" />
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+</tool>