mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Daniel Blankenberg
db737b3003
More work is required to allow the one-off indexes built by bowtie to become Galaxy datasets; alternatively, the custom genome selection could be limited to the index datatype for input (and not allow fasta directly), which would allow implicit datatype conversion to occur when a fasta file is selected as input, but this would prevent the index tuning that is currently available when currently selecting a fasta file.
304 lines
22 KiB
XML
304 lines
22 KiB
XML
<?xml version="1.0"?>
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<datatypes>
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<registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
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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="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false"/>
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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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<converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/>
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<display file="ucsc/bam.xml" />
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<display file="ensembl/ensembl_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_summary_tree_converter.xml" target_datatype="summary_tree"/>
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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="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true">
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<converter file="bedgraph_to_array_tree_converter.xml" target_datatype="array_tree"/>
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</datatype>
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<datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" />
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<datatype extension="bed6" type="galaxy.datatypes.interval:Bed6">
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<converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/>
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</datatype>
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<datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" />
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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="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true">
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<display file="ucsc/bigbed.xml" />
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</datatype>
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<datatype extension="bigwig" type="galaxy.datatypes.binary:BigWig" mimetype="application/octet-stream" display_in_upload="true">
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<display file="ucsc/bigwig.xml" />
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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="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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<!-- MSI added Datatypes -->
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<datatype extension="csv" type="galaxy.datatypes.tabular:Tabular"/>
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<!-- End MSI added Datatypes -->
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<datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
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<datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="False"/>
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<datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="False"/>
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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" max_optional_metadata_filesize="1048576" />
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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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<converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/>
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<converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/>
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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="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"/>
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<datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"/>
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<datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"/>
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<datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/>
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<datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" 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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<converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
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<converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
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<display file="ensembl/ensembl_gff.xml" inherit="True"/>
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<!-- <display file="gbrowse/gbrowse_gff.xml" inherit="True" /> -->
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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="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"/>
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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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<converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/>
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<converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/>
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<indexer file="interval_awk.xml" />
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<!-- <display file="ucsc/interval_as_bed.xml" inherit="True" /> -->
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<display file="genetrack.xml" inherit="True"/>
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<display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/>
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<display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/>
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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="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack">
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<display file="ucsc/maf_customtrack.xml" />
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</datatype>
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<datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/>
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<datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" />
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<datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
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<datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" />
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<datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
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<datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" 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="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/>
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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="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
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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="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/>
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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="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true">
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<converter file="vcf_to_interval_index_converter.xml" target_datatype="interval_index"/>
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<converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
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</datatype>
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<datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/>
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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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<!-- <display file="gbrowse/gbrowse_wig.xml" /> -->
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</datatype>
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<datatype extension="array_tree" type="galaxy.datatypes.data:Data" />
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<datatype extension="summary_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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<!-- information redundancy (LD) filtered plink pbed -->
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<datatype extension="ldindep" type="galaxy.datatypes.genetics:ldIndep" display_in_upload="true">
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</datatype>
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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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<converter file="pbed_ldreduced_converter.xml" target_datatype="ldindep"/>
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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"/>
|
|
<datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/>
|
|
<datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/>
|
|
<datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/>
|
|
<datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/>
|
|
<datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/>
|
|
<!-- End RGenetics Datatypes -->
|
|
</registration>
|
|
<sniffers>
|
|
<!--
|
|
The order in which Galaxy attempts to determine data types is
|
|
important because some formats are much more loosely defined
|
|
than others. The following list should be the most rigidly
|
|
defined format first, followed by next-most rigidly defined,
|
|
and so on.
|
|
-->
|
|
<sniffer type="galaxy.datatypes.binary:Bam"/>
|
|
<sniffer type="galaxy.datatypes.binary:Sff"/>
|
|
<sniffer type="galaxy.datatypes.xml:BlastXml"/>
|
|
<sniffer type="galaxy.datatypes.sequence:Maf"/>
|
|
<sniffer type="galaxy.datatypes.sequence:Lav"/>
|
|
<sniffer type="galaxy.datatypes.sequence:csFasta"/>
|
|
<sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
|
|
<sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
|
|
<sniffer type="galaxy.datatypes.sequence:Fasta"/>
|
|
<sniffer type="galaxy.datatypes.sequence:Fastq"/>
|
|
<sniffer type="galaxy.datatypes.interval:Wiggle"/>
|
|
<sniffer type="galaxy.datatypes.images:Html"/>
|
|
<sniffer type="galaxy.datatypes.images:Pdf"/>
|
|
<sniffer type="galaxy.datatypes.sequence:Axt"/>
|
|
<sniffer type="galaxy.datatypes.interval:Bed"/>
|
|
<sniffer type="galaxy.datatypes.interval:CustomTrack"/>
|
|
<sniffer type="galaxy.datatypes.interval:Gff"/>
|
|
<sniffer type="galaxy.datatypes.interval:Gff3"/>
|
|
<sniffer type="galaxy.datatypes.tabular:Pileup"/>
|
|
<sniffer type="galaxy.datatypes.interval:Interval"/>
|
|
<sniffer type="galaxy.datatypes.tabular:Sam"/>
|
|
<sniffer type="galaxy.datatypes.tabular:Vcf"/>
|
|
<!--
|
|
Keep this commented until the sniff method in the assembly.py
|
|
module is fixed to not read the entire file.
|
|
<sniffer type="galaxy.datatypes.assembly:Amos"/>
|
|
-->
|
|
</sniffers>
|
|
</datatypes>
|