root/galaxy-central/display_applications/gbrowse/gbrowse_interval_as_bed.xml

リビジョン 2, 1.5 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<display id="gbrowse_interval_as_bed" version="1.0.0" name="display at GBrowse">
2    <!-- Load links from file: one line to one link -->
3    <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_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="gbrowse_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 $APP.config.gbrowse_display_sites}</filter>
10        <filter>${dataset.dbkey in $builds}</filter>
11        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
12        <url>${gbrowse_link}/?${position}eurl=${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, gbrowse 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#if $chrom.startswith( 'chr' ):
18    #set $chrom = $chrom[3:]
19#end if
20q=${chrom}:${start}..${end}&amp;
21#end if
22        </param>
23    </dynamic_links>
24</display>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。