<?xml version="1.0"?>
<datatypes>
  <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
    <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/>
    <datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false"/>
    <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/>
    <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/>
    <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true">
      <converter file="bam_to_bai.xml" target_datatype="bai"/>
      <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
      <!--
        Caution: (a) this converter requires bedtools to be installed and (b) it is very memory intensive and
        is not recommended for most laptops/desktops.
        <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
      -->
      <display file="ucsc/bam.xml" />
      <display file="ensembl/ensembl_bam.xml" />
      <display file="igv/bam.xml" />
      <display file="igb/bam.xml" />
    </datatype>
    <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">
      <converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
      <converter file="interval_to_coverage.xml" target_datatype="coverage"/>
      <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/>
      <converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
      <converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
      <converter file="bed_to_fli_converter.xml" target_datatype="fli"/>
      <!-- <display file="ucsc/interval_as_bed.xml" /> -->
      <display file="genetrack.xml" />
      <display file="igb/bed.xml" />
    </datatype>
    <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true">
      <converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/>
    </datatype>
    <datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" />
    <datatype extension="bed6" type="galaxy.datatypes.interval:Bed6">
      <converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/>
    </datatype>
    <datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" />
    <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true">
      <converter file="len_to_linecount.xml" target_datatype="linecount" />
    </datatype>
    <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true">
      <display file="ucsc/bigbed.xml" />
      <display file="igb/bb.xml" />
    </datatype>
    <datatype extension="bigwig" type="galaxy.datatypes.binary:BigWig" mimetype="application/octet-stream" display_in_upload="true">
      <display file="ucsc/bigwig.xml" />
      <display file="igb/bigwig.xml" />
    </datatype>
    <datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="True">
      <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
      <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
      <converter file="interval_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
    </datatype>
    <!-- MSI added Datatypes -->
    <datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /> <!-- FIXME: csv is 'tabular'ized data, but not 'tab-delimited'; the class used here is intended for 'tab-delimited' -->
    <!-- End MSI added Datatypes -->
    <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
    <datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="False"/>
    <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="False"/>
    <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>
    <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" />
    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true">
      <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/>
      <converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/>
      <converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/>
      <converter file="fasta_to_2bit.xml" target_datatype="twobit"/>
      <converter file="fasta_to_len.xml" target_datatype="len"/>
    </datatype>
    <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true">
        <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
    </datatype>
    <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true">
        <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
    </datatype>
    <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true">
        <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
    </datatype>
    <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true">
        <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
    </datatype>
    <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true">
        <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
    </datatype>
    <datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/>
    <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/>
    <datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/>
    <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack">
      <!-- <display file="genetrack.xml" /> -->
    </datatype>
    <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true">
      <converter file="gff_to_bed_converter.xml" target_datatype="bed"/>
      <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
      <converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
      <converter file="gff_to_fli_converter.xml" target_datatype="fli"/>
      <display file="ensembl/ensembl_gff.xml" inherit="True"/>
      <!-- <display file="gbrowse/gbrowse_gff.xml" inherit="True" /> -->
    </datatype>
    <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/>
    <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/>
    <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
    <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true">
        <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
        <converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
    </datatype>
    <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" />
    <datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" />
    <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/>
    <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true">
      <converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
      <converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/>
      <converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/>
      <converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/>
      <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
      <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
	  <converter file="interval_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
      <!-- <display file="ucsc/interval_as_bed.xml" inherit="True" /> -->
      <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"/>
    </datatype>
    <datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/>
    <datatype extension="gatk_report" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/>
    <datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/>
    <datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/>
    <datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/>
    <datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/>
    <datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff"/>
    <datatype extension="bmp" type="galaxy.datatypes.images:Bmp" mimetype="image/bmp"/>
    <datatype extension="im" type="galaxy.datatypes.images:Im" mimetype="image/im"/>
    <datatype extension="pcd" type="galaxy.datatypes.images:Pcd" mimetype="image/pcd"/>
    <datatype extension="pcx" type="galaxy.datatypes.images:Pcx" mimetype="image/pcx"/>
    <datatype extension="ppm" type="galaxy.datatypes.images:Ppm" mimetype="image/ppm"/>
    <datatype extension="psd" type="galaxy.datatypes.images:Psd" mimetype="image/psd"/>
    <datatype extension="xbm" type="galaxy.datatypes.images:Xbm" mimetype="image/xbm"/>
    <datatype extension="xpm" type="galaxy.datatypes.images:Xpm" mimetype="image/xpm"/>
    <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/>
    <datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/>
    <datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/>
    <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/>
    <datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/>
    <datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
    <datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true"/>
    <datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true">
      <converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/>
      <converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
    </datatype>
    <datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack">
      <display file="ucsc/maf_customtrack.xml" />
    </datatype>
	<datatype extension="encodepeak" type="galaxy.datatypes.interval:ENCODEPeak" display_in_upload="True">
	  <converter file="encodepeak_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
	  <converter file="encodepeak_to_bgzip_converter.xml" target_datatype="bgzip"/>
	  <converter file="encodepeak_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
	</datatype>
    <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/>
    <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" />
    <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/>
    <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" />
    <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
    <datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/>
    <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/>
    <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
    <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/>
    <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true">
    	<converter file="sam_to_bam.xml" target_datatype="bam"/>
    	<converter file="sam_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
	</datatype>
    <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
    <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
    <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/>
    <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/>
    <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
    <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
    <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
    <datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/>
    <datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/>
    <datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/>
    <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" display_in_upload="true"/>
    <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true">
      <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/>
      <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" />
      <display file="rviewer/vcf.xml" inherit="True"/>
    </datatype>
    <datatype extension="bcf" type="galaxy.datatypes.binary:Binary" subclass="True" display_in_upload="True"/>
    <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/>
    <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true">
      <converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/>
      <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/>
      <!-- <display file="gbrowse/gbrowse_wig.xml" /> -->
      <display file="igb/wig.xml" />
    </datatype>
    <datatype extension="summary_tree" type="galaxy.datatypes.binary:Binary" subclass="True" />
    <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="True" />
    <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="True" />
    <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="True" />
    <datatype extension="vcf_bgzip" type_extension="bgzip" subclass="True" >
      <display file="igv/vcf.xml" />
      <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/>
    </datatype>
    <!-- Phylogenetic tree datatypes -->
    <datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true" />
    <datatype extension="nhx" type="galaxy.datatypes.data:Newick" display_in_upload="true" />
    <datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true" />
    <!-- Start RGenetics Datatypes -->
    <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/>
    <!-- eigenstrat pedigree input file -->
    <datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/>
    <!-- eigenstrat pca output file for adjusted eigenQTL eg -->
    <datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/>
    <datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true" />
    <!-- fbat/pbat format pedigree (header row of marker names) -->
    <datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/>
    <!-- phenotype file - fbat format -->
    <datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/>
    <!-- genome graphs ucsc file - first col is always marker then numeric values to plot -->
    <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>
    <!-- part of linkage format pedigree -->
    <!-- information redundancy (LD) filtered plink pbed -->
    <datatype extension="ldindep" type="galaxy.datatypes.genetics:ldIndep" display_in_upload="true">
    </datatype>
    <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/>
    <!-- linkage format pedigree (separate .map file) -->
    <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true">
      <converter file="lped_to_fped_converter.xml" target_datatype="fped"/>
      <converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/>
    </datatype>
    <!-- plink compressed file - has bed extension unfortunately -->
    <datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true">
      <converter file="pbed_to_lped_converter.xml" target_datatype="lped"/>
      <converter file="pbed_ldreduced_converter.xml" target_datatype="ldindep"/>
    </datatype>
    <datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/>
    <!-- phenotype file - plink format -->
    <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.tabular:Vcf"/>
    <sniffer type="galaxy.datatypes.binary:TwoBit"/>
    <sniffer type="galaxy.datatypes.binary:Bam"/>
    <sniffer type="galaxy.datatypes.binary:Sff"/>
    <sniffer type="galaxy.datatypes.xml:Phyloxml"/>
    <sniffer type="galaxy.datatypes.xml:GenericXml"/>
    <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:Gtf"/>
    <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.data:Newick"/>
    <sniffer type="galaxy.datatypes.data:Nexus"/>
    <sniffer type="galaxy.datatypes.images:Jpg"/>
    <sniffer type="galaxy.datatypes.images:Png"/>
    <sniffer type="galaxy.datatypes.images:Tiff"/>
    <sniffer type="galaxy.datatypes.images:Bmp"/>
    <sniffer type="galaxy.datatypes.images:Gif"/>
    <sniffer type="galaxy.datatypes.images:Im"/>
    <sniffer type="galaxy.datatypes.images:Pcd"/>
    <sniffer type="galaxy.datatypes.images:Pcx"/>
    <sniffer type="galaxy.datatypes.images:Ppm"/>
    <sniffer type="galaxy.datatypes.images:Psd"/>
    <sniffer type="galaxy.datatypes.images:Xbm"/>
    <sniffer type="galaxy.datatypes.images:Rgb"/>
    <sniffer type="galaxy.datatypes.images:Pbm"/>
    <sniffer type="galaxy.datatypes.images:Pgm"/>
    <sniffer type="galaxy.datatypes.images:Xpm"/>
    <sniffer type="galaxy.datatypes.images:Eps"/>
    <sniffer type="galaxy.datatypes.images:Rast"/>
    <!--
    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>