From 3f78f9a449d624f3d7136f9a796646a95bf11044 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Fri, 27 Jun 2014 14:44:55 -0400
Subject: [PATCH] Re-add InterMine tools removed in
 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.

---
 tool_conf.xml.main                  |  5 +++++
 tool_conf.xml.sample                |  7 ++++++
 tools/data_source/flymine.xml       | 35 +++++++++++++++++++++++++++++
 tools/data_source/flymine_test.xml  | 31 +++++++++++++++++++++++++
 tools/data_source/metabolicmine.xml | 13 +++++++++++
 tools/data_source/modmine.xml       | 19 ++++++++++++++++
 tools/data_source/mousemine.xml     | 35 +++++++++++++++++++++++++++++
 tools/data_source/ratmine.xml       | 34 ++++++++++++++++++++++++++++
 tools/data_source/yeastmine.xml     | 20 +++++++++++++++++
 9 files changed, 199 insertions(+)
 create mode 100644 tools/data_source/flymine.xml
 create mode 100644 tools/data_source/flymine_test.xml
 create mode 100644 tools/data_source/metabolicmine.xml
 create mode 100644 tools/data_source/modmine.xml
 create mode 100644 tools/data_source/mousemine.xml
 create mode 100644 tools/data_source/ratmine.xml
 create mode 100644 tools/data_source/yeastmine.xml

diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 485b9b16576..5c66e2c0ffa 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -7,7 +7,12 @@
     <tool file="data_source/ebi_sra.xml" />
     <tool file="data_source/biomart.xml" />
     <tool file="data_source/gramene_mart.xml" />
+    <tool file="data_source/flymine.xml" />
     <tool file="data_source/fly_modencode.xml" />
+    <tool file="data_source/modmine.xml" />
+    <tool file="data_source/mousemine.xml" />
+    <tool file="data_source/ratmine.xml" />
+    <tool file="data_source/yeastmine.xml" />
     <tool file="data_source/worm_modencode.xml" />
     <tool file="data_source/wormbase.xml" />
     <tool file="data_source/eupathdb.xml" />
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 447b73b7268..76f4187f613 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -12,6 +12,13 @@
     <tool file="data_source/cbi_rice_mart.xml" />
     <tool file="data_source/gramene_mart.xml" />
     <tool file="data_source/fly_modencode.xml" />
+    <tool file="data_source/flymine.xml" />
+    <tool file="data_source/flymine_test.xml" />
+    <tool file="data_source/modmine.xml" />
+    <tool file="data_source/mousemine.xml" />
+    <tool file="data_source/ratmine.xml" />
+    <tool file="data_source/yeastmine.xml" />
+    <tool file="data_source/metabolicmine.xml" />
     <tool file="data_source/worm_modencode.xml" />
     <tool file="data_source/wormbase.xml" />
     <tool file="data_source/wormbase_test.xml" />
diff --git a/tools/data_source/flymine.xml b/tools/data_source/flymine.xml
new file mode 100644
index 00000000000..cb9253ab157
--- /dev/null
+++ b/tools/data_source/flymine.xml
@@ -0,0 +1,35 @@
+<?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="Flymine" id="flymine" tool_type="data_source">
+    <description>server</description>
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <inputs action="http://www.flymine.org" check_values="false" method="get"> 
+        <display>go to Flymine server $GALAXY_URL</display>
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
+        <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="FlyMine query" />
+        <request_param galaxy_name="info" remote_name="info" missing="" />
+        <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
+            <value_translation>
+                <value galaxy_value="auto" remote_value="txt" /> <!-- intermine currently always provides 'txt', make this auto detect -->
+            </value_translation>
+        </request_param>
+    </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/flymine_test.xml b/tools/data_source/flymine_test.xml
new file mode 100644
index 00000000000..f66259c694c
--- /dev/null
+++ b/tools/data_source/flymine_test.xml
@@ -0,0 +1,31 @@
+<?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="Flymine test" id="flymine_test" tool_type="data_source">
+    <description>server</description>
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get"> 
+        <display>go to Flymine server $GALAXY_URL</display>
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
+        <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="FlyMine 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/metabolicmine.xml b/tools/data_source/metabolicmine.xml
new file mode 100644
index 00000000000..206bb4aa33b
--- /dev/null
+++ b/tools/data_source/metabolicmine.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<tool name="metabolicMine" id="metabolicmine" tool_type="data_source">
+    <description>server</description>
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <inputs action="http://www.metabolicmine.org/beta/begin.do" check_values="false" method="get"> 
+        <display>go to metabolicMine server $GALAXY_URL</display>
+    </inputs>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+</tool>
diff --git a/tools/data_source/modmine.xml b/tools/data_source/modmine.xml
new file mode 100644
index 00000000000..0d5b043dad1
--- /dev/null
+++ b/tools/data_source/modmine.xml
@@ -0,0 +1,19 @@
+<?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="modENCODE modMine" id="modmine" tool_type="data_source">
+    <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"> 
+        <display>go to modENCODE modMine server $GALAXY_URL</display>
+    </inputs>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+</tool>
+
diff --git a/tools/data_source/mousemine.xml b/tools/data_source/mousemine.xml
new file mode 100644
index 00000000000..e372d0d10f9
--- /dev/null
+++ b/tools/data_source/mousemine.xml
@@ -0,0 +1,35 @@
+<?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="MouseMine" id="mousemine" tool_type="data_source">
+    <description>server</description>
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <inputs action="http://www.mousemine.org/mousemine/begin.do" check_values="false" method="get"> 
+        <display>go to MouseMine server $GALAXY_URL</display>
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=mousemine" />
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
+        <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="MouseMine query" />
+        <request_param galaxy_name="info" remote_name="info" missing="" />
+        <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
+            <value_translation>
+                <value galaxy_value="auto" remote_value="txt" /> <!-- intermine currently always provides 'txt', make this auto detect -->
+            </value_translation>
+        </request_param>
+    </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..7ef3c69ef5d
--- /dev/null
+++ b/tools/data_source/ratmine.xml
@@ -0,0 +1,34 @@
+<?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">
+    <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"> 
+        <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_method" remote_name="URL_method" missing="post" />
+        <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="auto" >
+            <value_translation>
+                <value galaxy_value="auto" remote_value="txt" /> <!-- intermine currently always provides 'txt', make this auto detect -->
+            </value_translation>
+        </request_param>
+    </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/yeastmine.xml b/tools/data_source/yeastmine.xml
new file mode 100644
index 00000000000..9c82ca39364
--- /dev/null
+++ b/tools/data_source/yeastmine.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<tool name="YeastMine" id="yeastmine" tool_type="data_source">
+    <description>server</description>
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <inputs action="http://yeastmine.yeastgenome.org/yeastmine/begin.do" check_values="false" method="get"> 
+        <display>go to yeastMine server $GALAXY_URL</display>
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
+            <value_translation>
+                <value galaxy_value="auto" remote_value="txt" /> <!-- intermine currently always provides 'txt', make this auto detect -->
+            </value_translation>
+        </request_param>
+    </request_param_translation>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+</tool>