/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>