|
0
|
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="UCSC Archaea" id="ucsc_table_direct_archaea1" tool_type="data_source">
|
|
|
8 <description>table browser</description>
|
|
|
9 <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
|
|
10 <inputs action="http://archaea.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
|
|
|
11 <display>go to UCSC Table Browser $GALAXY_URL</display>
|
|
|
12 <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
|
|
|
13 <param name="tool_id" type="hidden" value="ucsc_table_direct_archaea1" />
|
|
|
14 <param name="sendToGalaxy" type="hidden" value="1" />
|
|
|
15 <param name="hgta_compressType" type="hidden" value="none" />
|
|
|
16 <param name="hgta_outputType" type="hidden" value="bed" />
|
|
|
17 </inputs>
|
|
|
18 <request_param_translation>
|
|
|
19 <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
|
|
|
20 <request_param galaxy_name="URL" remote_name="URL" missing="" />
|
|
|
21 <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
|
|
|
22 <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
|
|
|
23 <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
|
|
|
24 <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
|
|
|
25 <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="auto" >
|
|
|
26 <value_translation>
|
|
|
27 <value galaxy_value="auto" remote_value="primaryTable" />
|
|
|
28 <value galaxy_value="auto" remote_value="selectedFields" />
|
|
|
29 <value galaxy_value="wig" remote_value="wigData" />
|
|
|
30 <value galaxy_value="interval" remote_value="tab" />
|
|
|
31 <value galaxy_value="html" remote_value="hyperlinks" />
|
|
|
32 <value galaxy_value="fasta" remote_value="sequence" />
|
|
|
33 <value galaxy_value="gtf" remote_value="gff" />
|
|
|
34 </value_translation>
|
|
|
35 </request_param>
|
|
|
36 </request_param_translation>
|
|
|
37 <uihints minwidth="800"/>
|
|
|
38 <outputs>
|
|
|
39 <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/>
|
|
|
40 </outputs>
|
|
|
41 <options sanitize="False" refresh="True"/>
|
|
|
42 </tool>
|
