/display_applications/ensembl/ensembl_gff.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 79 lines · 59 code · 10 blank · 10 comment · 0 complexity · 38e2a71483ba24901b5e0809df036a20 MD5 · raw file
- <display id="ensembl_gff" version="1.0.0" name="display at Ensembl">
- <!-- Current Ensembl method of attaching user data via URL; archives older than ~November 2008 will use a different method -->
- <!-- Load links from file: one line to one link -->
- <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1">
-
- <!-- Define parameters by column from file, allow splitting on builds -->
- <dynamic_param name="site_id" value="0"/>
- <dynamic_param name="site_name" value="1"/>
- <dynamic_param name="site_link" value="2"/>
- <dynamic_param name="site_dbkeys" value="3" split="True" separator="," />
- <dynamic_param name="site_organisms" value="4" split="True" separator="," />
-
- <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
- <filter>${dataset.dbkey in $site_dbkeys}</filter>
-
- <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
- <url>${site_link}${site_organism}/Location/View?r=${position};contigviewbottom=url:${gff_file.qp}=normal</url>
-
- <param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.gff" />
- <param type="template" name="site_organism" strip="True" >
- $site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ]
- </param>
- <param type="template" name="position" strip="True" >
- #set chrom, start, end = $gff_file.datatype.get_estimated_display_viewport( $gff_file )
- #if $chrom is not None:
- ##The difference between chr1 and 1 is handled by Ensembl, except for the viewport, we need to provide e.g. '1' instead of 'chr1' here
- ##This is rather naive, it would be more ideal to have actual mappings
- #if $chrom == 'chrM':
- #set $chrom = 'MT'
- #end if
- #if $chrom.startswith( 'chr' ):
- #set $chrom = $chrom[3:]
- #end if
- ${chrom}:${start}-${end}
- #else:
- ##default view is of '1'
- 1
- #end if
- </param>
- </dynamic_links>
- <!-- Old Ensembl method of attaching user data via URL -->
- <!-- Load links from file: one line to one link -->
- <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1">
-
- <!-- Define parameters by column from file, allow splitting on builds -->
- <dynamic_param name="site_id" value="0"/>
- <dynamic_param name="site_name" value="1"/>
- <dynamic_param name="site_link" value="2"/>
- <dynamic_param name="site_dbkeys" value="3" split="True" separator="," />
- <dynamic_param name="site_organisms" value="4" split="True" separator="," />
-
- <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
- <filter>${dataset.dbkey in $site_dbkeys}</filter>
-
- <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
- <url>${site_link}${site_organism}/contigview?data_URL=${gff_file.qp}${position}</url>
-
- <param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.gff" />
- <param type="template" name="site_organism" strip="True" >
- $site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ]
- </param>
- <param type="template" name="position" strip="True" >
- #set chrom, start, end = $gff_file.datatype.get_estimated_display_viewport( $gff_file )
- #if $chrom is not None:
- ##The difference between chr1 and 1 is handled by Ensembl, except for the viewport, we need to provide e.g. '1' instead of 'chr1' here
- ##This is rather naive, it would be more ideal to have actual mappings
- #if $chrom == 'chrM':
- #set $chrom = 'MT'
- #end if
- #if $chrom.startswith( 'chr' ):
- #set $chrom = $chrom[3:]
- #end if
- &chr=${chrom}&start=${start}&end=${end}
- #end if
- </param>
- </dynamic_links>
- </display>