/display_applications/gbrowse/gbrowse_interval_as_bed.xml

 1<display id="gbrowse_interval_as_bed" version="1.0.0" name="display at GBrowse">
 2    <!-- Load links from file: one line to one link -->
 3    <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1">
 4        
 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        
12        <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
13        <filter>${site_id in $APP.config.gbrowse_display_sites}</filter>
14        <filter>${dataset.dbkey in $site_dbkeys}</filter>
15        
16        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
17        <url>${site_link}${site_organism}/?${position}eurl=${bed_file.qp}</url>
18        <param type="data" name="bed_file" url="galaxy_${DATASET_HASH}.bed" format="bedstrict"/> <!-- Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, gbrowse does not(?): force use of converter which will make strict BED6+ file -->
19        <param type="template" name="site_organism" strip="True" >
20            $site_organisms[ $site_dbkeys.index( $bed_file.dbkey ) ]
21        </param>
22        <param type="template" name="position" strip="True" >
23#set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file )
24#if $chrom is not None:
25#if $chrom.startswith( 'chr' ):
26    #set $chrom = $chrom[3:]
27#end if
28q=${chrom}:${start}..${end}&amp;
29#end if
30        </param>
31    </dynamic_links>
32</display>