1 | <display id="gbrowse_gff" 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}/?${position}eurl=${gff_file.qp}</url> |
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13 | <param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.gff" /> |
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14 | <param type="template" name="position" strip="True" > |
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15 | #set chrom, start, end = $gff_file.datatype.get_estimated_display_viewport( $gff_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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