/display_applications/ensembl/ensembl_bam.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 25 lines · 16 code · 4 blank · 5 comment · 0 complexity · 8a888fc02e4bc0ae64c9a1edc052c94c MD5 · raw file

  1. <display id="ensembl_bam" version="1.0.0" name="display at Ensembl">
  2. <!-- Current Ensembl method of attaching user data via URL; archives older than ~November 2008 will use a different method -->
  3. <!-- Load links from file: one line to one link -->
  4. <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1">
  5. <!-- Define parameters by column from file, allow splitting on builds -->
  6. <dynamic_param name="site_id" value="0"/>
  7. <dynamic_param name="site_name" value="1"/>
  8. <dynamic_param name="site_link" value="2"/>
  9. <dynamic_param name="site_dbkeys" value="3" split="True" separator="," />
  10. <dynamic_param name="site_organisms" value="4" split="True" separator="," />
  11. <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
  12. <filter>${dataset.dbkey in $site_dbkeys}</filter>
  13. <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
  14. <url>${site_link}${site_organism}/Location/View?contigviewbottom=bam:${bam_file.qp}=normal</url>
  15. <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" />
  16. <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" />
  17. <param type="template" name="site_organism" strip="True" >
  18. $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ]
  19. </param>
  20. </dynamic_links>
  21. </display>