/display_applications/ensembl/ensembl_bam.xml

 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        
 6        <!-- Define parameters by column from file, allow splitting on builds -->
 7        <dynamic_param name="site_id" value="0"/>
 8        <dynamic_param name="site_name" value="1"/>
 9        <dynamic_param name="site_link" value="2"/>
10        <dynamic_param name="site_dbkeys" value="3" split="True" separator="," />
11        <dynamic_param name="site_organisms" value="4" split="True" separator="," />
12        
13        <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
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}${site_organism}/Location/View?contigviewbottom=bam:${bam_file.qp}=normal</url>
18        
19        <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" />
20        <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" />
21        <param type="template" name="site_organism" strip="True" >
22            $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ]
23        </param>
24    </dynamic_links>
25</display>