[2] | 1 | <display id="gbrowse_wig" version="1.0.0" name="display at GBrowse"> |
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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/gbrowse/gbrowse_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="gbrowse_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 $APP.config.gbrowse_display_sites}</filter> |
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| 10 | <filter>${dataset.dbkey in $builds}</filter> |
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| 11 | <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> |
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| 12 | <url>${gbrowse_link}/?${position}eurl=${wig_file.qp}</url> |
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| 13 | <param type="data" name="wig_file" url="galaxy_${DATASET_HASH}.wig" format="wig"/> |
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| 14 | <param type="template" name="position" strip="True" > |
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| 15 | #set chrom, start, end = $wig_file.datatype.get_estimated_display_viewport( $wig_file ) |
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| 16 | #if $chrom is not None: |
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| 17 | #if $chrom.startswith( 'chr' ): |
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| 18 | #set $chrom = $chrom[3:] |
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| 19 | #end if |
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| 20 | q=${chrom}:${start}..${end}& |
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| 21 | #end if |
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| 22 | </param> |
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| 23 | </dynamic_links> |
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| 24 | </display> |
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