/display_applications/ensembl/ensembl_interval_as_bed.xml

<display id="ensembl_interval" 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=${position};contigviewbottom=url:${bed_file.qp}=normal</url>
        
        <param type="data" name="bed_file" url="galaxy_${DATASET_HASH}.bed" format="bedstrict"/>
        <param type="template" name="site_organism" strip="True" >
            $site_organisms[ $site_dbkeys.index( $bed_file.dbkey ) ]
        </param>
        <param type="template" name="position" strip="True" >
#set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_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
${chrom}:${int( start ) + 1}-${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=${bed_file.qp}${position}</url>
        
        <param type="data" name="bed_file" url="galaxy_${DATASET_HASH}.bed" format="bedstrict"/>
        <param type="template" name="site_organism" strip="True" >
            $site_organisms[ $site_dbkeys.index( $bed_file.dbkey ) ]
        </param>
        <param type="template" name="position" strip="True" >
            #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_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 = $chrom[3:]
            #end if
            &amp;chr=${chrom}&amp;start=${int( start ) + 1}&amp;end=${end}
            #end if
        </param>
    </dynamic_links>

</display>