HISTORY.rst
LICENSE
Makefile
README.rst
dev-requirements.txt
mypy.ini
pyproject.toml
pytest.ini
setup.cfg
scripts/commit_version.py
scripts/new_version.py
scripts/print_version_for_release.py
src/galaxy/datatypes/__init__.py
src/galaxy/datatypes/_schema.py
src/galaxy/datatypes/annotation.py
src/galaxy/datatypes/anvio.py
src/galaxy/datatypes/assembly.py
src/galaxy/datatypes/binary.py
src/galaxy/datatypes/blast.py
src/galaxy/datatypes/chain.py
src/galaxy/datatypes/checkers.py
src/galaxy/datatypes/chrominfo.py
src/galaxy/datatypes/constructive_solid_geometry.py
src/galaxy/datatypes/coverage.py
src/galaxy/datatypes/data.py
src/galaxy/datatypes/flow.py
src/galaxy/datatypes/genetics.py
src/galaxy/datatypes/gis.py
src/galaxy/datatypes/goldenpath.py
src/galaxy/datatypes/graph.py
src/galaxy/datatypes/hdf5.py
src/galaxy/datatypes/images.py
src/galaxy/datatypes/interval.py
src/galaxy/datatypes/isa.py
src/galaxy/datatypes/larch.py
src/galaxy/datatypes/media.py
src/galaxy/datatypes/metacyto.py
src/galaxy/datatypes/metadata.py
src/galaxy/datatypes/microarrays.py
src/galaxy/datatypes/molecules.py
src/galaxy/datatypes/mothur.py
src/galaxy/datatypes/msa.py
src/galaxy/datatypes/neo4j.py
src/galaxy/datatypes/ngsindex.py
src/galaxy/datatypes/phylip.py
src/galaxy/datatypes/plant_tribes.py
src/galaxy/datatypes/proteomics.py
src/galaxy/datatypes/protocols.py
src/galaxy/datatypes/py.typed
src/galaxy/datatypes/qiime2.py
src/galaxy/datatypes/qualityscore.py
src/galaxy/datatypes/registry.py
src/galaxy/datatypes/sequence.py
src/galaxy/datatypes/set_metadata_tool.xml
src/galaxy/datatypes/sniff.py
src/galaxy/datatypes/spaln.py
src/galaxy/datatypes/speech.py
src/galaxy/datatypes/tabular.py
src/galaxy/datatypes/text.py
src/galaxy/datatypes/tracks.py
src/galaxy/datatypes/triples.py
src/galaxy/datatypes/upload_util.py
src/galaxy/datatypes/xml.py
src/galaxy/datatypes/converters/.tt_skip
src/galaxy/datatypes/converters/__init__.py
src/galaxy/datatypes/converters/archive_to_directory.xml
src/galaxy/datatypes/converters/bam_to_bai.xml
src/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
src/galaxy/datatypes/converters/bcf_bcf_uncompressed_converter.xml
src/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
src/galaxy/datatypes/converters/bed_to_fli_converter.xml
src/galaxy/datatypes/converters/bed_to_gff_converter.py
src/galaxy/datatypes/converters/bed_to_gff_converter.xml
src/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
src/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
src/galaxy/datatypes/converters/bigbed_to_bed_converter.xml
src/galaxy/datatypes/converters/bigwig_to_wig_converter.xml
src/galaxy/datatypes/converters/biom.xml
src/galaxy/datatypes/converters/bz2_to_uncompressed.xml
src/galaxy/datatypes/converters/cml_to_smi_converter.xml
src/galaxy/datatypes/converters/cram_to_bam_converter.xml
src/galaxy/datatypes/converters/csv_to_tabular.xml
src/galaxy/datatypes/converters/dbkeys.loc.test
src/galaxy/datatypes/converters/fasta_to_2bit.xml
src/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
src/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
src/galaxy/datatypes/converters/fasta_to_fai.xml
src/galaxy/datatypes/converters/fasta_to_len.py
src/galaxy/datatypes/converters/fasta_to_len.xml
src/galaxy/datatypes/converters/fasta_to_tabular_converter.py
src/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
src/galaxy/datatypes/converters/fastq_to_fqtoc.py
src/galaxy/datatypes/converters/fastq_to_fqtoc.xml
src/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
src/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
src/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
src/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
src/galaxy/datatypes/converters/gff_to_bed_converter.py
src/galaxy/datatypes/converters/gff_to_bed_converter.xml
src/galaxy/datatypes/converters/gff_to_fli_converter.xml
src/galaxy/datatypes/converters/gff_to_interval_index_converter.py
src/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
src/galaxy/datatypes/converters/gro_to_pdb.xml
src/galaxy/datatypes/converters/gz_to_uncompressed.xml
src/galaxy/datatypes/converters/hg17.len
src/galaxy/datatypes/converters/inchi_to_mol_converter.xml
src/galaxy/datatypes/converters/interval_to_bed12_converter.xml
src/galaxy/datatypes/converters/interval_to_bed6_converter.xml
src/galaxy/datatypes/converters/interval_to_bed_converter.py
src/galaxy/datatypes/converters/interval_to_bed_converter.xml
src/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
src/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
src/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
src/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
src/galaxy/datatypes/converters/interval_to_fli.py
src/galaxy/datatypes/converters/interval_to_interval_index_converter.py
src/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
src/galaxy/datatypes/converters/interval_to_tabix_converter.xml
src/galaxy/datatypes/converters/len_to_linecount.xml
src/galaxy/datatypes/converters/lped_to_fped_converter.py
src/galaxy/datatypes/converters/lped_to_fped_converter.xml
src/galaxy/datatypes/converters/lped_to_pbed_converter.py
src/galaxy/datatypes/converters/lped_to_pbed_converter.xml
src/galaxy/datatypes/converters/maf_to_fasta_converter.py
src/galaxy/datatypes/converters/maf_to_fasta_converter.xml
src/galaxy/datatypes/converters/maf_to_interval_converter.py
src/galaxy/datatypes/converters/maf_to_interval_converter.xml
src/galaxy/datatypes/converters/mdconvert.xml
src/galaxy/datatypes/converters/mol2_to_mol_converter.xml
src/galaxy/datatypes/converters/molecules_converter.xml
src/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml
src/galaxy/datatypes/converters/parquet_to_csv_converter.py
src/galaxy/datatypes/converters/parquet_to_csv_converter.xml
src/galaxy/datatypes/converters/pbed_ldreduced_converter.py
src/galaxy/datatypes/converters/pbed_ldreduced_converter.xml
src/galaxy/datatypes/converters/pbed_to_lped_converter.py
src/galaxy/datatypes/converters/pbed_to_lped_converter.xml
src/galaxy/datatypes/converters/pdb_to_gro.xml
src/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
src/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
src/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
src/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
src/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
src/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
src/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
src/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
src/galaxy/datatypes/converters/smi_to_mol_converter.xml
src/galaxy/datatypes/converters/smi_to_smi_converter.xml
src/galaxy/datatypes/converters/tabular_csv.py
src/galaxy/datatypes/converters/tabular_to_csv.xml
src/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
src/galaxy/datatypes/converters/tar_to_directory.xml
src/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
src/galaxy/datatypes/converters/to_qname_sorted_bam.xml
src/galaxy/datatypes/converters/tool_data_table_conf.xml.test
src/galaxy/datatypes/converters/uncompressed_to_gz.xml
src/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
src/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
src/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
src/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
src/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
src/galaxy/datatypes/converters/wiggle_to_simple_converter.py
src/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
src/galaxy/datatypes/dataproviders/__init__.py
src/galaxy/datatypes/dataproviders/base.py
src/galaxy/datatypes/dataproviders/chunk.py
src/galaxy/datatypes/dataproviders/column.py
src/galaxy/datatypes/dataproviders/dataset.py
src/galaxy/datatypes/dataproviders/decorators.py
src/galaxy/datatypes/dataproviders/exceptions.py
src/galaxy/datatypes/dataproviders/external.py
src/galaxy/datatypes/dataproviders/hierarchy.py
src/galaxy/datatypes/dataproviders/line.py
src/galaxy/datatypes/display_applications/__init__.py
src/galaxy/datatypes/display_applications/application.py
src/galaxy/datatypes/display_applications/parameters.py
src/galaxy/datatypes/display_applications/util.py
src/galaxy/datatypes/display_applications/configs/biom/biom_simple.xml
src/galaxy/datatypes/display_applications/configs/ensembl/ensembl_bam.xml
src/galaxy/datatypes/display_applications/configs/ensembl/ensembl_gff.xml
src/galaxy/datatypes/display_applications/configs/ensembl/ensembl_interval_as_bed.xml
src/galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_gff.xml
src/galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_interval_as_bed.xml
src/galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_wig.xml
src/galaxy/datatypes/display_applications/configs/icn3d/icn3d_simple.xml
src/galaxy/datatypes/display_applications/configs/igb/bam.xml
src/galaxy/datatypes/display_applications/configs/igb/bb.xml
src/galaxy/datatypes/display_applications/configs/igb/bed.xml
src/galaxy/datatypes/display_applications/configs/igb/bedgraph.xml
src/galaxy/datatypes/display_applications/configs/igb/bigwig.xml
src/galaxy/datatypes/display_applications/configs/igb/cram.xml
src/galaxy/datatypes/display_applications/configs/igb/gtf.xml
src/galaxy/datatypes/display_applications/configs/igb/wig.xml
src/galaxy/datatypes/display_applications/configs/igv/bam.xml
src/galaxy/datatypes/display_applications/configs/igv/bigwig.xml
src/galaxy/datatypes/display_applications/configs/igv/genbank.xml
src/galaxy/datatypes/display_applications/configs/igv/genome_fasta.xml
src/galaxy/datatypes/display_applications/configs/igv/gff.xml
src/galaxy/datatypes/display_applications/configs/igv/interval_as_bed.xml
src/galaxy/datatypes/display_applications/configs/igv/vcf.xml
src/galaxy/datatypes/display_applications/configs/image/avivator.xml
src/galaxy/datatypes/display_applications/configs/intermine/intermine_simple.xml
src/galaxy/datatypes/display_applications/configs/iobio/bam.xml
src/galaxy/datatypes/display_applications/configs/iobio/vcf.xml
src/galaxy/datatypes/display_applications/configs/minerva/tabular.xml
src/galaxy/datatypes/display_applications/configs/qiime/qiime2/q2view.xml
src/galaxy/datatypes/display_applications/configs/rviewer/bed.xml
src/galaxy/datatypes/display_applications/configs/rviewer/vcf.xml
src/galaxy/datatypes/display_applications/configs/ucsc/bam.xml
src/galaxy/datatypes/display_applications/configs/ucsc/bigbed.xml
src/galaxy/datatypes/display_applications/configs/ucsc/bigwig.xml
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src/galaxy/datatypes/display_applications/configs/ucsc/maf_customtrack.xml
src/galaxy/datatypes/display_applications/configs/ucsc/trackhub.xml
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src/galaxy/datatypes/display_applications/xsd/geda.xsd
src/galaxy/datatypes/test/0.txt
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src/galaxy/datatypes/test/1.4dn_pairs
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src/galaxy/datatypes/test/1.cytoscapejson
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src/galaxy/datatypes/test/1.excel.xls
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src/galaxy/datatypes/test/1.mrc
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src/galaxy/datatypes/test/1.phyloxml
src/galaxy/datatypes/test/1.psl
src/galaxy/datatypes/test/1.ptkscmp
src/galaxy/datatypes/test/1.qname_sorted.bam
src/galaxy/datatypes/test/1.sam
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src/galaxy/datatypes/test/10col.pileup
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src/galaxy/datatypes/test/1_1119_2_22_001.textgrid
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src/galaxy/datatypes/test/Accuri_C6_A01_H2O.fcs
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src/galaxy/datatypes/test/IIT2mean_top_2000bytes.trk
src/galaxy/datatypes/test/Images.zarr.zip
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src/galaxy/datatypes/test/NuBBE_1_obabel_3D.pdbqt
src/galaxy/datatypes/test/Si.castep
src/galaxy/datatypes/test/Si.cif
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src/galaxy/datatypes/test/Si.extxyz
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src/galaxy/datatypes/test/big.gfa1
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src/galaxy/datatypes/test/brukerbaf.d.tar
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