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Add UCSC VCF external display application.

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This commit is contained in:
Daniel Blankenberg
2011-12-20 15:40:07 -05:00
parent 98264b4827
commit 08013f4ef1
2 changed files with 18 additions and 0 deletions
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datatypes_conf.xml.sample
+1
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@@ -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"/>
display_applications/ucsc/vcf.xml
+17
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@@ -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)}&amp;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>