/tools/data_source/biomart.xml

 1<?xml version="1.0"?>
 2<!--
 3    If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
 4    the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
 5    initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
 6
 7    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
 8    everything including and beyond the first '&' is truncated from URL.  They said they'll let us know when this is fixed at their end.
 9-->
10<tool name="BioMart" id="biomart" tool_type="data_source" version="1.0.1">
11	<description>Central server</description>
12	<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
13	<inputs action="http://www.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
14		<display>go to BioMart Central $GALAXY_URL</display>
15		<param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
16    </inputs>
17    <request_param_translation>
18        <request_param galaxy_name="URL" remote_name="URL" missing="">
19            <append_param separator="&amp;" first_separator="?" join="=">
20                <value name="_export" missing="1" />
21                <value name="GALAXY_URL" missing="0" />
22            </append_param>
23        </request_param>
24        <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
25            <value_translation>
26                <value galaxy_value="tabular" remote_value="TSV" />
27            </value_translation>
28        </request_param>
29        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
30        <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
31        <request_param galaxy_name="organism" remote_name="organism" missing="" />
32        <request_param galaxy_name="table" remote_name="table" missing="" />
33        <request_param galaxy_name="description" remote_name="description" missing="" />
34        <request_param galaxy_name="name" remote_name="name" missing="Biomart query" />
35        <request_param galaxy_name="info" remote_name="info" missing="" />
36    </request_param_translation>
37	<uihints minwidth="800"/>
38	<outputs>
39		<data name="output" format="tabular" />
40	</outputs>
41	<options sanitize="False" refresh="True"/>
42</tool>