diff pride_biomart.xml @ 0:ff9c373bf26f draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pride_biomart.xml	Tue Dec 18 23:57:43 2012 -0500
@@ -0,0 +1,39 @@
+<?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="PRIDE BioMart" id="pride_biomart" tool_type="data_source" version="0.1.0">
+    <description>Download proteomic data from the EBI Pride BioMart.</description>
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <inputs action="http://www.ebi.ac.uk/pride/biomart/martview" check_values="false" method="get" target="_top">
+        <display>$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="Rice mart 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>