1 | <display id="ucsc_bam" version="1.0.0" name="display at UCSC"> |
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2 | <!-- Load links from file: one line to one link --> |
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3 | <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> |
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4 | <!-- Define parameters by column from file, allow splitting on builds --> |
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5 | <dynamic_param name="site_id" value="0"/> |
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6 | <dynamic_param name="ucsc_link" value="1"/> |
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7 | <dynamic_param name="builds" value="2" split="True" separator="," /> |
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8 | <!-- 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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9 | <filter>${site_id in $APP.config.ucsc_display_sites}</filter> |
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10 | <filter>${dataset.dbkey in $builds}</filter> |
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11 | <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> |
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12 | <url>${ucsc_link}db=${qp($bam_file.dbkey)}&hgt.customText=${qp($track.url)}</url> |
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13 | <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" /> |
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14 | <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /><!-- UCSC expects index file to exist as bam_file_name.bai --> |
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15 | <param type="template" name="track" viewable="True" strip_https="True">track type=bam name="${bam_file.name}" bigDataUrl=${bam_file.url} db=${bam_file.dbkey}</param> |
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16 | </dynamic_links> |
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17 | </display> |
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