1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/dc6fc958766f/ changeset: dc6fc958766f user: dan date: 2012-02-17 16:00:42 summary: Add RViewer external display application. affected #: 4 files
diff -r 4552fdcfce3aaf173a26c9fd0cab034e3c7b4df3 -r dc6fc958766f825d9aff62cc530231858480937c datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -93,6 +93,7 @@ <display file="genetrack.xml" inherit="True"/><display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/><display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/> + <display file="rviewer/bed.xml" inherit="True"/></datatype><datatype extension="picard_interval_list" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"><converter file="picard_interval_list_to_bed6_converter.xml" target_datatype="bed6"/> @@ -159,6 +160,7 @@ <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/><display file="ucsc/vcf.xml" /><display file="igv/vcf.xml" /> + <display file="rviewer/vcf.xml" inherit="True"/></datatype><datatype extension="bcf" type="galaxy.datatypes.binary:Binary" subclass="True"/><datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/>
diff -r 4552fdcfce3aaf173a26c9fd0cab034e3c7b4df3 -r dc6fc958766f825d9aff62cc530231858480937c display_applications/rviewer/bed.xml --- /dev/null +++ b/display_applications/rviewer/bed.xml @@ -0,0 +1,25 @@ +<?xml version="1.0"?> +<display id="rviewer_interval" version="1.0.0" name="display at RViewer"> + + <!-- Load links from file: one line to one link --> + <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_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_genome_versions" 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}/application/service/datasets/add?datasetName=${qp($bed_file.name)}&genomeVersion=${qp( $site_genome_versions[ $site_dbkeys.index( $bed_file.dbkey ) ] )}&dataFormat=bed&dataUrl=${bed_file.qp}</url> + + <param type="data" name="bed_file" format="bed" url="galaxy.bed" /> + + </dynamic_links> + + +</display>
diff -r 4552fdcfce3aaf173a26c9fd0cab034e3c7b4df3 -r dc6fc958766f825d9aff62cc530231858480937c display_applications/rviewer/vcf.xml --- /dev/null +++ b/display_applications/rviewer/vcf.xml @@ -0,0 +1,25 @@ +<?xml version="1.0"?> +<display id="rviewer_vcf" version="1.0.0" name="display at RViewer"> + + <!-- Load links from file: one line to one link --> + <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_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_genome_versions" 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}/application/service/datasets/add?datasetName=${qp($vcf_file.name)}&genomeVersion=${qp( $site_genome_versions[ $site_dbkeys.index( $vcf_file.dbkey ) ] )}&dataFormat=vcf&dataUrl=${vcf_file.qp}</url> + + <param type="data" name="vcf_file" url="galaxy.vcf" /> + + </dynamic_links> + + +</display>
diff -r 4552fdcfce3aaf173a26c9fd0cab034e3c7b4df3 -r dc6fc958766f825d9aff62cc530231858480937c tool-data/shared/rviewer/rviewer_build_sites.txt.sample --- /dev/null +++ b/tool-data/shared/rviewer/rviewer_build_sites.txt.sample @@ -0,0 +1,3 @@ +#site_id site_name site_url dbkey rviewer_genome_version +#lbl_test test http://127.0.0.1:8888 hg18,hg19 hg18,hg19 +lbl_main main http://rviewer.lbl.gov/rviewer hg18,hg19 hg18,hg19
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