mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Daniel Blankenberg
d1c905f78d
Applications are assigned to specific datatypes (i.e. on an extension basis) via the datatypes_conf.xml file. View the sample display applications at /display_applications/[ucsc/]*.xml for examples of usage. Provided sample display applications: View BAM files (with bai indexes) at UCSC using BigDataUrl support. ucsc interval as bed viewer - not enabled by default (the old style display app is still used by default; both can be used simultaneously - but this would likely be confusing) GeneTrack viewer - any interval datatype can now be viewed at GeneTrack, if the application is enabled for a particular datatype; also a valid display application for genetrack datatype. Display applications can make full use of datatype converters, even allowing explicitly defined multi-step conversions, e.g. interval --> bed --> genetrack; the datatype conversion framework will need to be enhanced to natively support multi-step conversions before this can be done implicitly. A new datatype, bedstrict, has been defined, the only way to have an item with this datatype is to be created by a tool; metadata cannot be edited; and sniffing this datatype would require aggressively parsing the entirety of the file. A bedstrict file must conform exactly to the BED specification (whereas Galaxy allows BED files to have non-standard columns). These files are suitable e.g. for display at the UCSC genome browser and is used by the new ucsc interval display application. Add a bed to bedstrict converter, this is used by the ucsc interval display application. Add a bed to genetrack converter, this is used by the new GeneTrack display application. TODO: If the GeneTrack indexer can be enhanced to accept column assignments, this should be an interval to genetrack converter. Several performance enhancements available for the ucsc tools, such as bigurl support, potential speed improvement when loading a user's history than the old style for certain displays, e.g. ucsc interval display no longer requires the viewport (position) to be calculated for each relevant history item in a users history; this calculation now occurs on a separate page after the user clicks a view link. Non-strict BED files no longer have their content calculated on the fly and then streamed, etc. Refer to additional comments in code.
242 lines
17 KiB
XML
242 lines
17 KiB
XML
<?xml version="1.0"?>
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<datatypes>
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<registration converters_path="lib/galaxy/datatypes/converters">
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<datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/>
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<datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/>
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<datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true">
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<converter file="bam_to_bai.xml" target_datatype="bai"/>
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<display file="ucsc/bam.xml" />
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</datatype>
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<datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">
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<converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
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<converter file="interval_to_coverage.xml" target_datatype="coverage"/>
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<converter file="bed_to_interval_index_converter.xml" target_datatype="interval_index"/>
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<converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/>
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<!-- <display file="ucsc/interval_as_bed.xml" /> -->
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<display file="genetrack.xml" />
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</datatype>
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<datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict">
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<display file="ucsc/interval_as_bed.xml" />
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<display file="genetrack.xml" />
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</datatype>
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<datatype extension="binseq.zip" type="galaxy.datatypes.binary:Binseq" mimetype="application/zip" display_in_upload="true"/>
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<datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true">
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<!-- no converters yet -->
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</datatype>
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<datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true">
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<indexer file="coverage.xml" />
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</datatype>
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<datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
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<datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>
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<datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/>
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<datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true">
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<converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/>
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</datatype>
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<datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/>
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<datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/>
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<datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack">
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<!-- <display file="genetrack.xml" /> -->
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</datatype>
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<datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true">
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<converter file="gff_to_bed_converter.xml" target_datatype="bed"/>
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</datatype>
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<datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/>
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<datatype extension="gif" type="galaxy.datatypes.images:Image" mimetype="image/gif"/>
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<datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
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<datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/>
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<datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true">
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<converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
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<converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/>
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<indexer file="interval_awk.xml" />
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<!-- <display file="ucsc/interval_as_bed.xml" /> -->
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<display file="genetrack.xml" />
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</datatype>
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<datatype extension="jpg" type="galaxy.datatypes.images:Image" mimetype="image/jpeg"/>
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<datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
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<datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true"/>
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<datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true">
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<converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/>
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<converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
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</datatype>
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<datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
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<datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
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<datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
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<datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/>
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<datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
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<datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"/>
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<datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
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<datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/>
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<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
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<datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
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<datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
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<datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" display_in_upload="true"/>
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<datatype extension="txtseq.zip" type="galaxy.datatypes.data:Txtseq" mimetype="application/zip" display_in_upload="true"/>
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<datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true">
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<converter file="wiggle_to_array_tree_converter.xml" target_datatype="array_tree"/>
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<converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/>
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</datatype>
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<datatype extension="array_tree" type="galaxy.datatypes.data:Data" />
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<datatype extension="interval_index" type="galaxy.datatypes.data:Data" />
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<!-- Start EMBOSS tools -->
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<datatype extension="acedb" type="galaxy.datatypes.data:Text"/>
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<datatype extension="asn1" type="galaxy.datatypes.data:Text"/>
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<datatype extension="btwisted" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cai" type="galaxy.datatypes.data:Text"/>
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<datatype extension="charge" type="galaxy.datatypes.data:Text"/>
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<datatype extension="checktrans" type="galaxy.datatypes.data:Text"/>
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<datatype extension="chips" type="galaxy.datatypes.data:Text"/>
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<datatype extension="clustal" type="galaxy.datatypes.data:Text"/>
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<datatype extension="codata" type="galaxy.datatypes.data:Text"/>
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<datatype extension="codcmp" type="galaxy.datatypes.data:Text"/>
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<datatype extension="coderet" type="galaxy.datatypes.data:Text"/>
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<datatype extension="compseq" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cpgplot" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cpgreport" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cusp" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cut" type="galaxy.datatypes.data:Text"/>
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<datatype extension="dan" type="galaxy.datatypes.data:Text"/>
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<datatype extension="dbmotif" type="galaxy.datatypes.data:Text"/>
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<datatype extension="diffseq" type="galaxy.datatypes.data:Text"/>
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<datatype extension="digest" type="galaxy.datatypes.data:Text"/>
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<datatype extension="dreg" type="galaxy.datatypes.data:Text"/>
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<datatype extension="einverted" type="galaxy.datatypes.data:Text"/>
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<datatype extension="embl" type="galaxy.datatypes.data:Text"/>
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<datatype extension="epestfind" type="galaxy.datatypes.data:Text"/>
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<datatype extension="equicktandem" type="galaxy.datatypes.data:Text"/>
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<datatype extension="est2genome" type="galaxy.datatypes.data:Text"/>
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<datatype extension="etandem" type="galaxy.datatypes.data:Text"/>
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<datatype extension="excel" type="galaxy.datatypes.data:Text"/>
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<datatype extension="feattable" type="galaxy.datatypes.data:Text"/>
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<datatype extension="fitch" type="galaxy.datatypes.data:Text"/>
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<datatype extension="freak" type="galaxy.datatypes.data:Text"/>
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<datatype extension="fuzznuc" type="galaxy.datatypes.data:Text"/>
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<datatype extension="fuzzpro" type="galaxy.datatypes.data:Text"/>
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<datatype extension="fuzztran" type="galaxy.datatypes.data:Text"/>
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<datatype extension="garnier" type="galaxy.datatypes.data:Text"/>
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<datatype extension="gcg" type="galaxy.datatypes.data:Text"/>
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<datatype extension="geecee" type="galaxy.datatypes.data:Text"/>
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<datatype extension="genbank" type="galaxy.datatypes.data:Text"/>
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<datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text"/>
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<datatype extension="hennig86" type="galaxy.datatypes.data:Text"/>
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<datatype extension="hmoment" type="galaxy.datatypes.data:Text"/>
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<datatype extension="ig" type="galaxy.datatypes.data:Text"/>
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<datatype extension="isochore" type="galaxy.datatypes.data:Text"/>
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<datatype extension="jackknifer" type="galaxy.datatypes.data:Text"/>
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<datatype extension="jackknifernon" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx10" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx1" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx0" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx3" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx2" type="galaxy.datatypes.data:Text"/>
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<datatype extension="match" type="galaxy.datatypes.data:Text"/>
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<datatype extension="mega" type="galaxy.datatypes.data:Text"/>
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<datatype extension="meganon" type="galaxy.datatypes.data:Text"/>
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<datatype extension="motif" type="galaxy.datatypes.data:Text"/>
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<datatype extension="msf" type="galaxy.datatypes.data:Text"/>
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<datatype extension="nametable" type="galaxy.datatypes.data:Text"/>
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<datatype extension="ncbi" type="galaxy.datatypes.data:Text"/>
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<datatype extension="needle" type="galaxy.datatypes.data:Text"/>
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<datatype extension="newcpgreport" type="galaxy.datatypes.data:Text"/>
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<datatype extension="newcpgseek" type="galaxy.datatypes.data:Text"/>
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<datatype extension="nexus" type="galaxy.datatypes.data:Text"/>
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<datatype extension="nexusnon" type="galaxy.datatypes.data:Text"/>
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<datatype extension="noreturn" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pair" type="galaxy.datatypes.data:Text"/>
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<datatype extension="palindrome" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pepcoil" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pepinfo" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pepstats" type="galaxy.datatypes.data:Text"/>
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<datatype extension="phylip" type="galaxy.datatypes.data:Text"/>
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<datatype extension="phylipnon" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pir" type="galaxy.datatypes.data:Text"/>
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<datatype extension="polydot" type="galaxy.datatypes.data:Text"/>
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<datatype extension="preg" type="galaxy.datatypes.data:Text"/>
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<datatype extension="prettyseq" type="galaxy.datatypes.data:Text"/>
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<datatype extension="primersearch" type="galaxy.datatypes.data:Text"/>
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<datatype extension="regions" type="galaxy.datatypes.data:Text"/>
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<datatype extension="score" type="galaxy.datatypes.data:Text"/>
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<datatype extension="selex" type="galaxy.datatypes.data:Text"/>
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<datatype extension="seqtable" type="galaxy.datatypes.data:Text"/>
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<datatype extension="showfeat" type="galaxy.datatypes.data:Text"/>
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<datatype extension="showorf" type="galaxy.datatypes.data:Text"/>
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<datatype extension="simple" type="galaxy.datatypes.data:Text"/>
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<datatype extension="sixpack" type="galaxy.datatypes.data:Text"/>
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<datatype extension="srs" type="galaxy.datatypes.data:Text"/>
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<datatype extension="srspair" type="galaxy.datatypes.data:Text"/>
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<datatype extension="staden" type="galaxy.datatypes.data:Text"/>
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<datatype extension="strider" type="galaxy.datatypes.data:Text"/>
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<datatype extension="supermatcher" type="galaxy.datatypes.data:Text"/>
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<datatype extension="swiss" type="galaxy.datatypes.data:Text"/>
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<datatype extension="syco" type="galaxy.datatypes.data:Text"/>
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<datatype extension="table" type="galaxy.datatypes.data:Text"/>
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<datatype extension="textsearch" type="galaxy.datatypes.data:Text"/>
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<datatype extension="vectorstrip" type="galaxy.datatypes.data:Text"/>
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<datatype extension="wobble" type="galaxy.datatypes.data:Text"/>
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<datatype extension="wordcount" type="galaxy.datatypes.data:Text"/>
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<datatype extension="tagseq" type="galaxy.datatypes.data:Text"/>
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<!-- End EMBOSS tools -->
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<!-- Start RGenetics Datatypes -->
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<datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/>
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<!-- eigenstrat pedigree input file -->
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<datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/>
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<!-- eigenstrat pca output file for adjusted eigenQTL eg -->
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<datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/>
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<datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true" />
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<!-- fbat/pbat format pedigree (header row of marker names) -->
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<datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/>
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<!-- phenotype file - fbat format -->
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<datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/>
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<!-- genome graphs ucsc file - first col is always marker then numeric values to plot -->
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<datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>
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<!-- part of linkage format pedigree -->
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<datatype extension="lmap" type="galaxy.datatypes.genetics:Lmap" display_in_upload="true"/>
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<datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/>
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<!-- linkage format pedigree (separate .map file) -->
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<datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true">
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<converter file="lped_to_fped_converter.xml" target_datatype="fped"/>
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<converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/>
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</datatype>
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<!-- plink compressed file - has bed extension unfortunately -->
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<datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true">
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<converter file="pbed_to_lped_converter.xml" target_datatype="lped"/>
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</datatype>
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<datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/>
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<!-- phenotype file - plink format -->
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<datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/>
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<datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/>
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<datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/>
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<datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/>
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<datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/>
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<datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/>
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<!-- End RGenetics Datatypes -->
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</registration>
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<sniffers>
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<!--
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The order in which Galaxy attempts to determine data types is
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important because some formats are much more loosely defined
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than others. The following list should be the most rigidly
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defined format first, followed by next-most rigidly defined,
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and so on.
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-->
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<sniffer type="galaxy.datatypes.binary:Bam"/>
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<sniffer type="galaxy.datatypes.binary:Sff"/>
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<sniffer type="galaxy.datatypes.xml:BlastXml"/>
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<sniffer type="galaxy.datatypes.sequence:Maf"/>
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<sniffer type="galaxy.datatypes.sequence:Lav"/>
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<sniffer type="galaxy.datatypes.sequence:csFasta"/>
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<sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
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<sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
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<sniffer type="galaxy.datatypes.sequence:Fasta"/>
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<sniffer type="galaxy.datatypes.sequence:Fastq"/>
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<sniffer type="galaxy.datatypes.interval:Wiggle"/>
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<sniffer type="galaxy.datatypes.images:Html"/>
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<sniffer type="galaxy.datatypes.sequence:Axt"/>
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<sniffer type="galaxy.datatypes.interval:Bed"/>
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<sniffer type="galaxy.datatypes.interval:CustomTrack"/>
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<sniffer type="galaxy.datatypes.interval:Gff"/>
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<sniffer type="galaxy.datatypes.interval:Gff3"/>
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<sniffer type="galaxy.datatypes.interval:Interval"/>
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<sniffer type="galaxy.datatypes.tabular:Sam"/>
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</sniffers>
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</datatypes>
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