/tools/data_source/biomart.xml
XML | 42 lines | 34 code | 0 blank | 8 comment | 0 complexity | d56ab5d90c0836302c17ec94c73d1de2 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 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="&" 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>