1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bb5e05256c29/ changeset: bb5e05256c29 user: dan date: 2011-12-20 21:40:07 summary: Add UCSC VCF external display application. affected #: 2 files diff -r f22a8a7bd077a118bcfa71430f345ff46873757f -r bb5e05256c2997892f5cac6b1998bbe90896372d datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -162,6 +162,7 @@ <converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/><converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/><converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <display file="ucsc/vcf.xml" /><display file="igv/vcf.xml" /></datatype><datatype extension="bcf" type="galaxy.datatypes.binary:Binary" subclass="True"/> diff -r f22a8a7bd077a118bcfa71430f345ff46873757f -r bb5e05256c2997892f5cac6b1998bbe90896372d display_applications/ucsc/vcf.xml --- /dev/null +++ b/display_applications/ucsc/vcf.xml @@ -0,0 +1,17 @@ +<display id="ucsc_vcf" version="1.0.0" name="display at UCSC"> + <!-- Load links from file: one line to one link --> + <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <!-- Define parameters by column from file, allow splitting on builds --> + <dynamic_param name="site_id" value="0"/> + <dynamic_param name="ucsc_link" value="1"/> + <dynamic_param name="builds" value="2" split="True" separator="," /> + <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey --> + <filter>${site_id in $APP.config.ucsc_display_sites}</filter> + <filter>${dataset.dbkey in $builds}</filter> + <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> + <url>${ucsc_link}db=${qp($bgzip_file.dbkey)}&hgt.customText=${qp($track.url)}</url> + <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" /> + <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" /> + <param type="template" name="track" viewable="True">track type="vcfTabix" name="${bgzip_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bgzip_file.url}" db="${bgzip_file.dbkey}"</param> + </dynamic_links> +</display> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.