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

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
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="GrameneMart" id="gramenemart" 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.gramene.org/biomart/martview" check_values="false" method="get" target="_top">
14 <display>go to GrameneMart 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>