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/display_applications/ucsc/maf_customtrack.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 15 lines | 11 code | 0 blank | 4 comment | 0 complexity | b4c1fcc15783d0b82dfd6bce5713663e MD5 | raw file
 1<display id="ucsc_maf_customtrack" 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=${qp($maf_customtrack_file.dbkey)}&amp;position=${maf_customtrack_file.metadata.vp_chromosome}:${maf_customtrack_file.metadata.vp_start}-${maf_customtrack_file.metadata.vp_end}&amp;hgt.customText=${maf_customtrack_file.qp}</url>
13        <param type="data" name="maf_customtrack_file" url="galaxy_${DATASET_HASH}.maf" format="mafcustomtrack"/>
14    </dynamic_links>
15</display>