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/display_applications/ucsc/interval_as_bed.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 23 lines | 19 code | 0 blank | 4 comment | 0 complexity | ba51c213357e93834eaef9d9ed7092e7 MD5 | raw file
 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)}&amp;position=${position.qp}&amp;hgt.customText=${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}:${start}-${int( end ) + 1}
18#else:
19:-
20#end if
21        </param>
22    </dynamic_links>
23</display>