/tools/data_source/hapmapmart.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 46 lines · 34 code · 0 blank · 12 comment · 0 complexity · d7ab1df975be1b5a1ba76d2ee9f3f505 MD5 · raw file

  1. <?xml version="1.0"?>
  2. <!--
  3. hacked from biomart.xml - testing hapmap biomart - problem is going to be converting these to lped/pbed
  4. the data returned will be in all sorts of different shapes - and the sample ids need to be obtained separately
  5. to create reliable pedigrees. eesh...
  6. If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
  7. the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
  8. initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
  9. 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
  10. everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
  11. -->
  12. <tool name="HapMapMart" id="hapmapmart" tool_type="data_source" version="0.0.01">
  13. <description>HapMap Biomart</description>
  14. <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
  15. <inputs action="http://hapmap.ncbi.nlm.nih.gov/biomart/martview" check_values="false" method="get" target="_top">
  16. <display>go to HapMap BioMart $GALAXY_URL</display>
  17. <param name="GALAXY_URL" type="baseurl" value="/tool_runner/hapmapmart" />
  18. </inputs>
  19. <request_param_translation>
  20. <request_param galaxy_name="URL" remote_name="URL" missing="">
  21. <append_param separator="&amp;" first_separator="?" join="=">
  22. <value name="_export" missing="1" />
  23. <value name="GALAXY_URL" missing="0" />
  24. </append_param>
  25. </request_param>
  26. <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
  27. <value_translation>
  28. <value galaxy_value="tabular" remote_value="TSV" />
  29. </value_translation>
  30. </request_param>
  31. <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
  32. <request_param galaxy_name="dbkey" remote_name="dbkey" missing="hg18" />
  33. <request_param galaxy_name="organism" remote_name="organism" missing="human" />
  34. <request_param galaxy_name="table" remote_name="table" missing="" />
  35. <request_param galaxy_name="description" remote_name="description" missing="" />
  36. <request_param galaxy_name="name" remote_name="name" missing="HapMap query" />
  37. <request_param galaxy_name="info" remote_name="info" missing="" />
  38. </request_param_translation>
  39. <uihints minwidth="800"/>
  40. <outputs>
  41. <data name="output" format="tabular" />
  42. </outputs>
  43. <options sanitize="False" refresh="True"/>
  44. </tool>