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18 lines
1.4 KiB
XML
18 lines
1.4 KiB
XML
<display id="ucsc_bam" version="1.0.0" name="display at UCSC">
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<!-- Load links from file: one line to one link -->
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<dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0">
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<!-- Define parameters by column from file, allow splitting on builds -->
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<dynamic_param name="site_id" value="0"/>
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<dynamic_param name="ucsc_link" value="1"/>
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<dynamic_param name="builds" value="2" split="True" separator="," />
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<!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
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<filter>${site_id in $APP.datatypes_registry.get_display_sites('ucsc')}</filter>
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<filter>${dataset.dbkey in $builds}</filter>
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<!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
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<url>${ucsc_link}db=${qp($bam_file.dbkey)}&hgt.customText=${qp($track.url)}</url>
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<param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" />
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<param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
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<param type="template" name="track" viewable="True">track type="bam" name="${bam_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bam_file.url}" db="${bam_file.dbkey}" pairEndsByName="."</param>
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</dynamic_links>
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</display>
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