/tools/data_source/biomart.xml

https://bitbucket.org/h_morita_dbcls/galaxy-central · 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. 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
  7. everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
  8. -->
  9. <tool name="BioMart" id="biomart" tool_type="data_source" version="1.0.1">
  10. <description>Central server</description>
  11. <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
  12. <inputs action="http://www.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
  13. <display>go to BioMart Central $GALAXY_URL</display>
  14. <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
  15. </inputs>
  16. <request_param_translation>
  17. <request_param galaxy_name="URL" remote_name="URL" missing="">
  18. <append_param separator="&amp;" first_separator="?" join="=">
  19. <value name="_export" missing="1" />
  20. <value name="GALAXY_URL" missing="0" />
  21. </append_param>
  22. </request_param>
  23. <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
  24. <value_translation>
  25. <value galaxy_value="tabular" remote_value="TSV" />
  26. </value_translation>
  27. </request_param>
  28. <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
  29. <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
  30. <request_param galaxy_name="organism" remote_name="organism" missing="" />
  31. <request_param galaxy_name="table" remote_name="table" missing="" />
  32. <request_param galaxy_name="description" remote_name="description" missing="" />
  33. <request_param galaxy_name="name" remote_name="name" missing="Biomart query" />
  34. <request_param galaxy_name="info" remote_name="info" missing="" />
  35. </request_param_translation>
  36. <uihints minwidth="800"/>
  37. <outputs>
  38. <data name="output" format="tabular" />
  39. </outputs>
  40. <options sanitize="False" refresh="True"/>
  41. </tool>