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Add support for displaying BAM files at Ensembl

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This commit is contained in:
Brad Chapman
2010-10-06 11:03:28 -04:00
parent a889f76076
commit 8679ac8442
3 changed files with 27 additions and 0 deletions
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datatypes_conf.xml.sample
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@@ -8,6 +8,7 @@
<converter file="bam_to_bai.xml" target_datatype="bai"/>
<converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/>
<display file="ucsc/bam.xml" />
<display file="ensembl/ensembl_bam.xml" />
</datatype>
<datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">
<converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
display_applications/ensembl/ensembl_bam.xml
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@@ -0,0 +1,25 @@
<display id="ensembl_bam" version="1.0.0" name="display at Ensembl">
<!-- Current Ensembl method of attaching user data via URL; archives older than ~November 2008 will use a different method -->
<!-- Load links from file: one line to one link -->
<dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1">
<!-- Define parameters by column from file, allow splitting on builds -->
<dynamic_param name="site_id" value="0"/>
<dynamic_param name="site_name" value="1"/>
<dynamic_param name="site_link" value="2"/>
<dynamic_param name="site_dbkeys" value="3" split="True" separator="," />
<dynamic_param name="site_organisms" value="4" split="True" separator="," />
<!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
<filter>${dataset.dbkey in $site_dbkeys}</filter>
<!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
<url>${site_link}${site_organism}/Location/View?contigviewbottom=bam:${bam_file.qp}=normal</url>
<param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" />
<param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" />
<param type="template" name="site_organism" strip="True" >
$site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ]
</param>
</dynamic_links>
</display>
tool-data/shared/ensembl/ensembl_sites.txt
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@@ -2,3 +2,4 @@
#http://www.ensembl.org/info/docs/webcode/linking.html
ensembl_Current Current http://www.ensembl.org/ hg19,felCat3,galGal3,bosTau4,canFam2,loxAfr3,cavPor3,equCab2,anoCar1,oryLat2,mm9,monDom5,ponAbe2,susScr2,ornAna1,oryCun2,rn4,rheMac2,gasAcu1,tetNig2,xenTro2,taeGut1,danRer5,ci2,dm3,ce6,sacCer2 Homo_sapiens,Felis_catus,Gallus_gallus,Bos_taurus,Canis_familiaris,Loxodonta_africana,Cavia_porcellus,Equus_caballus,Anolis_carolinensis,Oryzias_latipes,Mus_musculus,Monodelphis_domestica,Pongo_pygmaeus,Sus_scrofa,Ornithorhynchus_anatinus,Oryctolagus_cuniculus,Rattus_norvegicus,Macaca_mulatta,Gasterosteus_aculeatus,Tetraodon_nigroviridis,Xenopus_tropicalis,Taeniopygia_guttata,Danio_rerio,Ciona_intestinalis,Drosophila_melanogaster,Caenorhabditis_elegans,Saccharomyces_cerevisiae
ensembl_May_2009 May 2009 http://may2009.archive.ensembl.org/ hg18 Homo_sapiens
ensembl_plants Plants http://plants.ensembl.org/ araTha_tair9 Arabidopsis_thaliana