diff tools/data_source/gramene_mart.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/data_source/gramene_mart.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,42 @@
+<?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" version="1.0.1">
+    <description> Central server</description>
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</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="">
+            <append_param separator="&amp;" first_separator="?" join="=">
+                <value name="_export" missing="1" />
+                <value name="GALAXY_URL" missing="0" />
+            </append_param>
+        </request_param>
+        <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular">
+            <value_translation>
+                <value galaxy_value="tabular" remote_value="TSV" />
+            </value_translation> 
+        </request_param>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
+        <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>