[2] | 1 | <display id="ensembl_bam" version="1.0.0" name="display at Ensembl"> |
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| 2 | <!-- Current Ensembl method of attaching user data via URL; archives older than ~November 2008 will use a different method --> |
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| 3 | <!-- Load links from file: one line to one link --> |
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| 4 | <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> |
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| 5 | |
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| 6 | <!-- Define parameters by column from file, allow splitting on builds --> |
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| 7 | <dynamic_param name="site_id" value="0"/> |
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| 8 | <dynamic_param name="site_name" value="1"/> |
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| 9 | <dynamic_param name="site_link" value="2"/> |
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| 10 | <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> |
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| 11 | <dynamic_param name="site_organisms" value="4" split="True" separator="," /> |
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| 12 | |
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| 13 | <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey --> |
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| 14 | <filter>${dataset.dbkey in $site_dbkeys}</filter> |
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| 15 | |
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| 16 | <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> |
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| 17 | <url>${site_link}${site_organism}/Location/View?contigviewbottom=bam:${bam_file.qp}=normal</url> |
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| 18 | |
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| 19 | <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" /> |
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| 20 | <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> |
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| 21 | <param type="template" name="site_organism" strip="True" > |
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| 22 | $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] |
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| 23 | </param> |
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| 24 | </dynamic_links> |
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| 25 | </display> |
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