From f16d27c2d4d3f339c2988f8c9ecbddce4e1864fb Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 3 Dec 2009 15:33:15 -0500
Subject: [PATCH] Add datasource tool configs for modMine and Ratmine.

---
 tool_conf.xml.main            |  2 ++
 tool_conf.xml.sample          |  6 ++++--
 tools/data_source/modmine.xml | 30 ++++++++++++++++++++++++++++++
 tools/data_source/ratmine.xml | 29 +++++++++++++++++++++++++++++
 4 files changed, 65 insertions(+), 2 deletions(-)
 create mode 100644 tools/data_source/modmine.xml
 create mode 100644 tools/data_source/ratmine.xml

diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index ee76623594d..28119c56039 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -8,6 +8,8 @@
     <tool file="data_source/biomart.xml" />
     <tool file="data_source/gramene_mart.xml" />
     <tool file="data_source/flymine.xml" />
+    <tool file="data_source/modmine.xml" />
+    <tool file="data_source/ratmine.xml" />
     <tool file="data_source/eupathdb.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 7c62f97a9be..9b8eae0f1c5 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -9,10 +9,12 @@
     <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" />
     <tool file="data_source/flymine_test.xml" />
+    <tool file="data_source/modmine.xml" />
+    <tool file="data_source/ratmine.xml" />
+    <tool file="data_source/wormbase.xml" />
+    <tool file="data_source/wormbase_test.xml" />
     <tool file="data_source/eupathdb.xml" />
     <tool file="data_source/encode_db.xml" />
     <tool file="data_source/epigraph_import.xml" />
diff --git a/tools/data_source/modmine.xml b/tools/data_source/modmine.xml
new file mode 100644
index 00000000000..c66d08a4f78
--- /dev/null
+++ b/tools/data_source/modmine.xml
@@ -0,0 +1,30 @@
+<?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.
+-->
+<tool name="modMine" id="modmine" tool_type="data_source" URL_method="post">
+    <description>server</description>
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <inputs action="http://intermine.modencode.org/" check_values="false" method="get" target="_top"> 
+        <display>go to modMine server $GALAXY_URL</display>
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modmine" />
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL" remote_name="URL" missing="" />
+        <request_param galaxy_name="dbkey" remote_name="db" 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="modMine query" />
+        <request_param galaxy_name="info" remote_name="info" missing="" />
+        <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/ratmine.xml b/tools/data_source/ratmine.xml
new file mode 100644
index 00000000000..f8db5cd3f31
--- /dev/null
+++ b/tools/data_source/ratmine.xml
@@ -0,0 +1,29 @@
+<?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.
+-->
+<tool name="Ratmine" id="ratmine" tool_type="data_source" URL_method="post">
+    <description>server</description>
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get" target="_top"> 
+        <display>go to Ratmine server $GALAXY_URL</display>
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=ratmine" />
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL" remote_name="URL" missing="" />
+        <request_param galaxy_name="dbkey" remote_name="db" 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="Ratmine query" />
+        <request_param galaxy_name="info" remote_name="info" missing="" />
+        <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>