/display_applications/ucsc/interval_as_bed.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 23 lines · 19 code · 0 blank · 4 comment · 0 complexity · ba51c213357e93834eaef9d9ed7092e7 MD5 · raw file

  1. <display id="ucsc_interval_as_bed" version="1.0.0" name="display at UCSC" inherit="True">
  2. <!-- Load links from file: one line to one link -->
  3. <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
  4. <!-- Define parameters by column from file, allow splitting on builds -->
  5. <dynamic_param name="site_id" value="0"/>
  6. <dynamic_param name="ucsc_link" value="1"/>
  7. <dynamic_param name="builds" value="2" split="True" separator="," />
  8. <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
  9. <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
  10. <filter>${dataset.dbkey in $builds}</filter>
  11. <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
  12. <url>${ucsc_link}db=${qp($bed_file.dbkey)}&amp;position=${position.qp}&amp;hgt.customText=${bed_file.qp}</url>
  13. <param type="data" name="bed_file" url="galaxy_${DATASET_HASH}.bed" format="bedstrict"/> <!-- Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, UCSC does not: force use of converter which will make strict BED6+ file -->
  14. <param type="template" name="position" strip="True" >
  15. #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file )
  16. #if $chrom is not None:
  17. ${chrom}:${start}-${int( end ) + 1}
  18. #else:
  19. :-
  20. #end if
  21. </param>
  22. </dynamic_links>
  23. </display>