1 | <display id="ucsc_interval_as_bed" version="1.0.0" name="display at UCSC" inherit="True"> |
---|
2 | <!-- Load links from file: one line to one link --> |
---|
3 | <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> |
---|
4 | <!-- Define parameters by column from file, allow splitting on builds --> |
---|
5 | <dynamic_param name="site_id" value="0"/> |
---|
6 | <dynamic_param name="ucsc_link" value="1"/> |
---|
7 | <dynamic_param name="builds" value="2" split="True" separator="," /> |
---|
8 | <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey --> |
---|
9 | <filter>${site_id in $APP.config.ucsc_display_sites}</filter> |
---|
10 | <filter>${dataset.dbkey in $builds}</filter> |
---|
11 | <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> |
---|
12 | <url>${ucsc_link}db=${qp($bed_file.dbkey)}&position=${position.qp}&hgt.customText=${bed_file.qp}</url> |
---|
13 | <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, UCSC does not: force use of converter which will make strict BED6+ file --> |
---|
14 | <param type="template" name="position" strip="True" > |
---|
15 | #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file ) |
---|
16 | #if $chrom is not None: |
---|
17 | ${chrom}:${start}-${end + 1} |
---|
18 | #else: |
---|
19 | :- |
---|
20 | #end if |
---|
21 | </param> |
---|
22 | </dynamic_links> |
---|
23 | </display> |
---|