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/tools/data_source/flymine.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 35 lines | 29 code | 1 blank | 5 comment | 0 complexity | 022bafe5c669bb66dcd21f682e0f5468 MD5 | raw file
 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<tool name="Flymine" id="flymine" tool_type="data_source">
 8    <description>server</description>
 9    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
10    <inputs action="http://www.flymine.org" check_values="false" method="get"> 
11        <display>go to Flymine server $GALAXY_URL</display>
12        <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
13    </inputs>
14    <request_param_translation>
15        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
16        <request_param galaxy_name="URL" remote_name="URL" missing="" />
17        <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
18        <request_param galaxy_name="organism" remote_name="organism" missing="" />
19        <request_param galaxy_name="table" remote_name="table" missing="" />
20        <request_param galaxy_name="description" remote_name="description" missing="" />
21        <request_param galaxy_name="name" remote_name="name" missing="FlyMine query" />
22        <request_param galaxy_name="info" remote_name="info" missing="" />
23        <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
24            <value_translation>
25                <value galaxy_value="auto" remote_value="txt" /> <!-- intermine currently always provides 'txt', make this auto detect -->
26            </value_translation>
27        </request_param>
28    </request_param_translation>
29    <uihints minwidth="800"/>
30    <outputs>
31        <data name="output" format="txt" />
32    </outputs>
33    <options sanitize="False" refresh="True"/>
34</tool>
35