/display_applications/ensembl/ensembl_gff.xml

 1<display id="ensembl_gff" 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}${site_organism}/Location/View?r=${position};contigviewbottom=url:${gff_file.qp}=normal</url>
18        
19        <param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.gff" />
20        <param type="template" name="site_organism" strip="True" >
21            $site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ]
22        </param>
23        <param type="template" name="position" strip="True" >
24#set chrom, start, end = $gff_file.datatype.get_estimated_display_viewport( $gff_file )
25#if $chrom is not None:
26##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
27##This is rather naive, it would be more ideal to have actual mappings
28#if $chrom == 'chrM':
29    #set $chrom = 'MT'
30#end if
31#if $chrom.startswith( 'chr' ):
32    #set $chrom = $chrom[3:]
33#end if
34${chrom}:${start}-${end}
35#else:
36##default view is of '1'
371
38#end if
39        </param>
40    </dynamic_links>
41
42    <!-- Old Ensembl method of attaching user data via URL -->
43    <!-- Load links from file: one line to one link -->
44    <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1">
45        
46        <!-- Define parameters by column from file, allow splitting on builds -->
47        <dynamic_param name="site_id" value="0"/>
48        <dynamic_param name="site_name" value="1"/>
49        <dynamic_param name="site_link" value="2"/>
50        <dynamic_param name="site_dbkeys" value="3" split="True" separator="," />
51        <dynamic_param name="site_organisms" value="4" split="True" separator="," />
52        
53        <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
54        <filter>${dataset.dbkey in $site_dbkeys}</filter>
55        
56        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
57        <url>${site_link}${site_organism}/contigview?data_URL=${gff_file.qp}${position}</url>
58        
59        <param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.gff" />
60        <param type="template" name="site_organism" strip="True" >
61            $site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ]
62        </param>
63        <param type="template" name="position" strip="True" >
64            #set chrom, start, end = $gff_file.datatype.get_estimated_display_viewport( $gff_file )
65            #if $chrom is not None:
66            ##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
67            ##This is rather naive, it would be more ideal to have actual mappings
68            #if $chrom == 'chrM':
69                #set $chrom = 'MT'
70            #end if
71            #if $chrom.startswith( 'chr' ):
72                #set $chrom = $chrom[3:]
73            #end if
74            &amp;chr=${chrom}&amp;start=${start}&amp;end=${end}
75            #end if
76        </param>
77    </dynamic_links>
78
79</display>