Data Sources

The Data Sources section is required in the Visualization XML to inform Galaxy of the compatible data types for your visualization.

xml

<data_sources>
    <data_source>
        <model_class>HistoryDatasetAssociation</model_class>
        <test test_attr="ext" result_type="datatype">{{ COMPATIBLE_EXTENSION }}</test>
        <to_param param_attr="id">dataset_id</to_param>
    </data_source>
</data_sources>
<params>
    <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
</params>

Galaxy supports a variety of datatype extensions: 4dn_pairs,4dn_pairsam,a3m,ab1,affybatch,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,agp,ampvis2,analyze75,arff,asn1,asn1-binary,augustus,avi,axt,bam,bcf,bcf_uncompressed,bcsl.model,bcsl.ts,bed,bed12,bed6,bed_tabix.gz,bedgraph,bedstrict,bgzip,bigbed,bigwig,bil,biom1,biom2,blastxml,blib,bref3,brukerbaf.d.tar,brukertdf.d.tar,bus,castep,cel,cell,chain,chira.sqlite,chrint,cif,cisml,ckpt,cmap,cml,cnn,cnr,cns,colab.tar,colab.tar.gz,consensusxml,cool,cps,cpt,cram,csfasta,csv,ct,ctl.result,cuffdiff.sqlite,cxb,d3_hierarchy,daa,dada2_dada,dada2_errorrates,dada2_mergepairs,dada2_sequencetable,dada2_uniques,dbn,dbnsfp.tabular,dcd,deeptools_compute_matrix_archive,deeptools_coverage_matrix,den_fmt,dlib,drf,dta,dta2d,dzi,edr,edta,eland,elandmulti,elib,embl,encodepeak,eset,excel.xls,expression.json,extxyz,fai,fast5.tar,fast5.tar.bz2,fast5.tar.gz,fast5.tar.xz,fasta,fasta.gz,fastg,fastk_hist,fastk_ktab,fastk_prof,fastq,fastq.bz2,fastq.gz,fastqcssanger,fastqcssanger.bz2,fastqcssanger.gz,fastqillumina,fastqillumina.bz2,fastqillumina.gz,fastqsanger,fastqsanger.bz2,fastqsanger.gz,fastqsolexa,fastqsolexa.bz2,fastqsolexa.gz,fcs,featurexml,ffdata,ffindex,fits,flowclr,flowframe,flowmfi,flowscore,flowset,flowstat1,flowstat2,flowstat3,flowtext,flv,fped,fphe,fps,fqtoc,fsom,gafa.sqlite,gal,gatk_dbsnp,gatk_interval,gatk_recal,gatk_report,gatk_tranche,gemini.sqlite,genbank,genbank.gz,genenotebook,geojson,gfa1,gfa1.gz,gfa2,gfa2.gz,gff,gff3,gff3.bz2,gff3.gz,gff_tabix.gz,gii,gii.gz,gmsh.geo,gmsh.msh,gpr,grd,grd.tgz,grib,gro,gtf,h5,h5ad,h5mlm,hdf4,hdr,hdt,hep.root,hexrd.accepted_orientations,hexrd.eta_ome.npz,hexrd.images.npz,hexrd.materials.h5,hexrd.scored_orientations.npz,hexrd.yml,hhr,hlf,hmm2,hmm3,icm,idat,ideaspre,idpdb,idxml,imgt.json,imzml,inchi,inp,inpcrd,intermine_tabular,interval,ipynb,isa-json,isa-tab,itp,jellyfish,jp2,json,jsonld,juicer_medium_tabix.gz,kallisto.idx,kroenik,lav,ldindep,len,loom,lped,ludwig_model,maf,magres,malist,mascotxml,maskinfo-asn1,maskinfo-asn1-binary,mcool,mdp,memepsp,memexml,meryldb,metacyto_clr.txt,metacyto_stats.txt,metacyto_summary.txt,mgf,mkv,mol,mol2,mongodb,mothur.accnos,mothur.align,mothur.align.check,mothur.align.report,mothur.axes,mothur.cons.taxonomy,mothur.count_table,mothur.design,mothur.dist,mothur.filter,mothur.filtered.masked.quan,mothur.filtered.quan,mothur.freq,mothur.groups,mothur.list,mothur.lower.dist,mothur.map,mothur.masked.quan,mothur.names,mothur.oligos,mothur.otu,mothur.otu.corr,mothur.otulabels,mothur.pair.dist,mothur.quan,mothur.rabund,mothur.rdp.taxonomy,mothur.ref.taxonomy,mothur.relabund,mothur.sabund,mothur.seq.taxonomy,mothur.sff.flow,mothur.shared,mothur.square.dist,mothur.summary,mothur.tax.summary,mothur.tre,mov,mp3,mp4,mpg,mrc,mrm,ms2,msh,msp,mtx,mz.sqlite,mz5,mzdata,mzid,mzml,mzq,mzqc,mztab,mztab2,mzxml,n3,ncbi_genome_dataset.zip,ncbitaxonomy.sqlite,ndx,neostore.zip,neper.mscell,neper.points,neper.points.tsv,neper.tesr,neper.tess,netcdf,newick,nex,nhx,nii1,nii1.gz,nii2,nii2.gz,nmrml,npy,npz,nt,obfs,obo,odgi,ogg,ome.tiff,onnx,osw,owl,oxlicg,oxligl,oxling,oxliss,oxlist,oxlits,paf,paf.gz,par,param,paramxml,parquet,pbed,pdb,pdbqt,pdf,peff,peplist,peptideshaker_archive,pepxml,pepxml.tsv,phar,phylip,phyloseq,phyloxml,picard_interval_list,pileup,pithya.model,pithya.property,pithya.result,plyascii,plybinary,png,pod5,postgresql,pov,pphe,pqp,pqr,pretext,prj,prmtop,probam,probed,protobuf2,protobuf3,protxml,protxml.tsv,psl,psms,pssm-asn1,ptkscmp,qcml,qiime2.tabular,qname_sorted.bam,qual454,qualillumina,qualsolexa,qualsolid,qza,qzv,rdata,rdata.camera.negative,rdata.camera.positive,rdata.camera.quick,rdata.msnbase.raw,rdata.sce,rdata.se,rdata.xcms.fillpeaks,rdata.xcms.findchrompeaks,rdata.xcms.group,rdata.xcms.raw,rdata.xcms.retcor,rdf,rdock_as,rds,rma6,rna_eps,sam,sbml,sbol,scf,scidx,scool,sdf,searchgui_archive,sf3,sff,shp,sif,smat,smi,snaphmm,snpeffdb,snpmatrix,snpsiftdbnsfp,snptest,source.c,source.cpp,source.cs,source.go,source.h,source.py,source.rs,spalndba,spalndbnp,spec.xml,splib,splib_noindex,sqlite,sqmass,sra,sra_manifest.tabular,star,stl,stockholm,storm.check,storm.sample,tabular,tabular.gz,tandem,tar,taxonomy,tck,textgrid,tgz,thermo.raw,tiff,toml,top,tpr,trackhub,trafoxml,traml,trk,trr,tsv,ttl,twobit,txt,ucsc.net,uniprotxml,unsorted.bam,vcf,vcf_bgzip,vel,velvet,vg,visium.tar.gz,vtkascii,vtkbinary,watersmasslynx.raw.tar,wav,webm,wiff,wiff.tar,wiff2,wiff2.tar,wig,wma,wmv,xg,xgmml,xlsx,xmfa,xml,xquest.xml,xsd,xtc,xvg,xyz,yaml,zip,zset.geof.

For more information on datatypes please refer to the Galaxy Documentation at: https://docs.galaxyproject.org/en/master/dev/data_types.html.

Data Sources ​

Data Sources