HISTORY.rst
LICENSE
MANIFEST.in
README.rst
dev-requirements.txt
pyproject.toml
setup.cfg
test-requirements.txt
galaxy/__init__.py
galaxy/py.typed
galaxy/datatypes/__init__.py
galaxy/datatypes/_schema.py
galaxy/datatypes/annotation.py
galaxy/datatypes/anvio.py
galaxy/datatypes/assembly.py
galaxy/datatypes/binary.py
galaxy/datatypes/blast.py
galaxy/datatypes/chain.py
galaxy/datatypes/checkers.py
galaxy/datatypes/chrominfo.py
galaxy/datatypes/constructive_solid_geometry.py
galaxy/datatypes/coverage.py
galaxy/datatypes/data.py
galaxy/datatypes/flow.py
galaxy/datatypes/genetics.py
galaxy/datatypes/gis.py
galaxy/datatypes/goldenpath.py
galaxy/datatypes/graph.py
galaxy/datatypes/hdf5.py
galaxy/datatypes/images.py
galaxy/datatypes/interval.py
galaxy/datatypes/isa.py
galaxy/datatypes/larch.py
galaxy/datatypes/media.py
galaxy/datatypes/metacyto.py
galaxy/datatypes/metadata.py
galaxy/datatypes/microarrays.py
galaxy/datatypes/molecules.py
galaxy/datatypes/mothur.py
galaxy/datatypes/msa.py
galaxy/datatypes/neo4j.py
galaxy/datatypes/ngsindex.py
galaxy/datatypes/phylip.py
galaxy/datatypes/plant_tribes.py
galaxy/datatypes/proteomics.py
galaxy/datatypes/protocols.py
galaxy/datatypes/qiime2.py
galaxy/datatypes/qualityscore.py
galaxy/datatypes/registry.py
galaxy/datatypes/sequence.py
galaxy/datatypes/set_metadata_tool.xml
galaxy/datatypes/sniff.py
galaxy/datatypes/spaln.py
galaxy/datatypes/speech.py
galaxy/datatypes/tabular.py
galaxy/datatypes/text.py
galaxy/datatypes/tracks.py
galaxy/datatypes/triples.py
galaxy/datatypes/upload_util.py
galaxy/datatypes/xml.py
galaxy/datatypes/converters/__init__.py
galaxy/datatypes/converters/bam_to_bai.xml
galaxy/datatypes/converters/bam_to_bigwig_converter.xml
galaxy/datatypes/converters/bcf_bcf_uncompressed_converter.xml
galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
galaxy/datatypes/converters/bed_to_fli_converter.xml
galaxy/datatypes/converters/bed_to_gff_converter.py
galaxy/datatypes/converters/bed_to_gff_converter.xml
galaxy/datatypes/converters/bed_to_interval_index_converter.xml
galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
galaxy/datatypes/converters/bigwig_to_wig_converter.xml
galaxy/datatypes/converters/biom.xml
galaxy/datatypes/converters/bz2_to_uncompressed.xml
galaxy/datatypes/converters/cml_to_smi_converter.xml
galaxy/datatypes/converters/cram_to_bam_converter.xml
galaxy/datatypes/converters/csv_to_tabular.xml
galaxy/datatypes/converters/fasta_to_2bit.xml
galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
galaxy/datatypes/converters/fasta_to_fai.xml
galaxy/datatypes/converters/fasta_to_len.py
galaxy/datatypes/converters/fasta_to_len.xml
galaxy/datatypes/converters/fasta_to_tabular_converter.py
galaxy/datatypes/converters/fasta_to_tabular_converter.xml
galaxy/datatypes/converters/fastq_to_fqtoc.py
galaxy/datatypes/converters/fastq_to_fqtoc.xml
galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
galaxy/datatypes/converters/gff_to_bed_converter.py
galaxy/datatypes/converters/gff_to_bed_converter.xml
galaxy/datatypes/converters/gff_to_fli_converter.xml
galaxy/datatypes/converters/gff_to_interval_index_converter.py
galaxy/datatypes/converters/gff_to_interval_index_converter.xml
galaxy/datatypes/converters/gro_to_pdb.xml
galaxy/datatypes/converters/gz_to_uncompressed.xml
galaxy/datatypes/converters/inchi_to_mol_converter.xml
galaxy/datatypes/converters/interval_to_bed12_converter.xml
galaxy/datatypes/converters/interval_to_bed6_converter.xml
galaxy/datatypes/converters/interval_to_bed_converter.py
galaxy/datatypes/converters/interval_to_bed_converter.xml
galaxy/datatypes/converters/interval_to_bedstrict_converter.py
galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
galaxy/datatypes/converters/interval_to_bgzip_converter.xml
galaxy/datatypes/converters/interval_to_bigwig_converter.xml
galaxy/datatypes/converters/interval_to_fli.py
galaxy/datatypes/converters/interval_to_interval_index_converter.py
galaxy/datatypes/converters/interval_to_interval_index_converter.xml
galaxy/datatypes/converters/interval_to_tabix_converter.xml
galaxy/datatypes/converters/len_to_linecount.xml
galaxy/datatypes/converters/lped_to_fped_converter.py
galaxy/datatypes/converters/lped_to_fped_converter.xml
galaxy/datatypes/converters/lped_to_pbed_converter.py
galaxy/datatypes/converters/lped_to_pbed_converter.xml
galaxy/datatypes/converters/maf_to_fasta_converter.py
galaxy/datatypes/converters/maf_to_fasta_converter.xml
galaxy/datatypes/converters/maf_to_interval_converter.py
galaxy/datatypes/converters/maf_to_interval_converter.xml
galaxy/datatypes/converters/mdconvert.xml
galaxy/datatypes/converters/mol2_to_mol_converter.xml
galaxy/datatypes/converters/molecules_converter.xml
galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml
galaxy/datatypes/converters/parquet_to_csv_converter.py
galaxy/datatypes/converters/parquet_to_csv_converter.xml
galaxy/datatypes/converters/pbed_ldreduced_converter.py
galaxy/datatypes/converters/pbed_ldreduced_converter.xml
galaxy/datatypes/converters/pbed_to_lped_converter.py
galaxy/datatypes/converters/pbed_to_lped_converter.xml
galaxy/datatypes/converters/pdb_to_gro.xml
galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
galaxy/datatypes/converters/pileup_to_interval_index_converter.py
galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
galaxy/datatypes/converters/sam_to_bigwig_converter.xml
galaxy/datatypes/converters/sam_to_unsorted_bam.xml
galaxy/datatypes/converters/smi_to_mol_converter.xml
galaxy/datatypes/converters/smi_to_smi_converter.xml
galaxy/datatypes/converters/tabular_csv.py
galaxy/datatypes/converters/tabular_to_csv.xml
galaxy/datatypes/converters/tabular_to_dbnsfp.xml
galaxy/datatypes/converters/tar_to_directory.xml
galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
galaxy/datatypes/converters/to_qname_sorted_bam.xml
galaxy/datatypes/converters/uncompressed_to_gz.xml
galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
galaxy/datatypes/converters/vcf_to_interval_index_converter.py
galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
galaxy/datatypes/converters/wig_to_bigwig_converter.xml
galaxy/datatypes/converters/wiggle_to_simple_converter.py
galaxy/datatypes/converters/wiggle_to_simple_converter.xml
galaxy/datatypes/dataproviders/__init__.py
galaxy/datatypes/dataproviders/base.py
galaxy/datatypes/dataproviders/chunk.py
galaxy/datatypes/dataproviders/column.py
galaxy/datatypes/dataproviders/dataset.py
galaxy/datatypes/dataproviders/decorators.py
galaxy/datatypes/dataproviders/exceptions.py
galaxy/datatypes/dataproviders/external.py
galaxy/datatypes/dataproviders/hierarchy.py
galaxy/datatypes/dataproviders/line.py
galaxy/datatypes/display_applications/__init__.py
galaxy/datatypes/display_applications/application.py
galaxy/datatypes/display_applications/parameters.py
galaxy/datatypes/display_applications/util.py
galaxy/datatypes/display_applications/configs/biom/biom_simple.xml
galaxy/datatypes/display_applications/configs/ensembl/ensembl_bam.xml
galaxy/datatypes/display_applications/configs/ensembl/ensembl_gff.xml
galaxy/datatypes/display_applications/configs/ensembl/ensembl_interval_as_bed.xml
galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_gff.xml
galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_interval_as_bed.xml
galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_wig.xml
galaxy/datatypes/display_applications/configs/icn3d/icn3d_simple.xml
galaxy/datatypes/display_applications/configs/igb/bam.xml
galaxy/datatypes/display_applications/configs/igb/bb.xml
galaxy/datatypes/display_applications/configs/igb/bed.xml
galaxy/datatypes/display_applications/configs/igb/bedgraph.xml
galaxy/datatypes/display_applications/configs/igb/bigwig.xml
galaxy/datatypes/display_applications/configs/igb/gtf.xml
galaxy/datatypes/display_applications/configs/igb/wig.xml
galaxy/datatypes/display_applications/configs/igv/bam.xml
galaxy/datatypes/display_applications/configs/igv/bigwig.xml
galaxy/datatypes/display_applications/configs/igv/genbank.xml
galaxy/datatypes/display_applications/configs/igv/genome_fasta.xml
galaxy/datatypes/display_applications/configs/igv/gff.xml
galaxy/datatypes/display_applications/configs/igv/interval_as_bed.xml
galaxy/datatypes/display_applications/configs/igv/vcf.xml
galaxy/datatypes/display_applications/configs/image/avivator.xml
galaxy/datatypes/display_applications/configs/intermine/intermine_simple.xml
galaxy/datatypes/display_applications/configs/iobio/bam.xml
galaxy/datatypes/display_applications/configs/iobio/vcf.xml
galaxy/datatypes/display_applications/configs/minerva/tabular.xml
galaxy/datatypes/display_applications/configs/qiime/qiime2/q2view.xml
galaxy/datatypes/display_applications/configs/rviewer/bed.xml
galaxy/datatypes/display_applications/configs/rviewer/vcf.xml
galaxy/datatypes/display_applications/configs/ucsc/bam.xml
galaxy/datatypes/display_applications/configs/ucsc/bigbed.xml
galaxy/datatypes/display_applications/configs/ucsc/bigwig.xml
galaxy/datatypes/display_applications/configs/ucsc/interval_as_bed.xml
galaxy/datatypes/display_applications/configs/ucsc/maf_customtrack.xml
galaxy/datatypes/display_applications/configs/ucsc/trackhub.xml
galaxy/datatypes/display_applications/configs/ucsc/vcf.xml
galaxy/datatypes/display_applications/xsd/geda.xsd
galaxy/datatypes/util/__init__.py
galaxy/datatypes/util/generic_util.py
galaxy/datatypes/util/gff_util.py
galaxy/datatypes/util/maf_utilities.py
galaxy/model/__init__.py
galaxy/model/base.py
galaxy/model/custom_types.py
galaxy/model/database_heartbeat.py
galaxy/model/database_object_names.py
galaxy/model/database_utils.py
galaxy/model/deferred.py
galaxy/model/index_filter_util.py
galaxy/model/item_attrs.py
galaxy/model/mapping.py
galaxy/model/metadata.py
galaxy/model/none_like.py
galaxy/model/scoped_session.py
galaxy/model/security.py
galaxy/model/tags.py
galaxy/model/dataset_collections/__init__.py
galaxy/model/dataset_collections/builder.py
galaxy/model/dataset_collections/matching.py
galaxy/model/dataset_collections/registry.py
galaxy/model/dataset_collections/structure.py
galaxy/model/dataset_collections/subcollections.py
galaxy/model/dataset_collections/type_description.py
galaxy/model/dataset_collections/types/__init__.py
galaxy/model/dataset_collections/types/list.py
galaxy/model/dataset_collections/types/paired.py
galaxy/model/migrations/README.md
galaxy/model/migrations/__init__.py
galaxy/model/migrations/alembic.ini
galaxy/model/migrations/base.py
galaxy/model/migrations/dbscript.py
galaxy/model/migrations/exceptions.py
galaxy/model/migrations/scripts.py
galaxy/model/migrations/util.py
galaxy/model/migrations/alembic/env.py
galaxy/model/migrations/alembic/script.py.mako
galaxy/model/migrations/alembic/versions_gxy/186d4835587b_drop_job_state_history_update_time_.py
galaxy/model/migrations/alembic/versions_gxy/2d749563e1fe_add_notification_system_tables.py
galaxy/model/migrations/alembic/versions_gxy/2dc3386d091f_add_indexes_for_workflow_comment_.py
galaxy/model/migrations/alembic/versions_gxy/3100452fa030_add_workflow_invocation_message_table.py
galaxy/model/migrations/alembic/versions_gxy/3356bc2ecfc4_drop_view.py
galaxy/model/migrations/alembic/versions_gxy/3a2914d703ca_add_index_wf_r_s_s__workflow_invocation_.py
galaxy/model/migrations/alembic/versions_gxy/460d0ecd1dd8_.py
galaxy/model/migrations/alembic/versions_gxy/518c8438a91b_add_when_expression_column.py
galaxy/model/migrations/alembic/versions_gxy/55f02fd8ab6c_add_index_on_hda_extension.py
galaxy/model/migrations/alembic/versions_gxy/59e024ceaca1_add_export_association_table.py
galaxy/model/migrations/alembic/versions_gxy/6a67bf27e6a6_deferred_data_tables.py
galaxy/model/migrations/alembic/versions_gxy/8a19186a6ee7_add_columns_to_interactivetool_entry_point.py
galaxy/model/migrations/alembic/versions_gxy/92fb564c7095_.py
galaxy/model/migrations/alembic/versions_gxy/9540a051226e_preferred_object_store_ids.py
galaxy/model/migrations/alembic/versions_gxy/987ce9839ecb_create_celery_user_rate_limit_table.py
galaxy/model/migrations/alembic/versions_gxy/b182f655505f_add_workflow_source_metadata_column.py
galaxy/model/migrations/alembic/versions_gxy/b855b714e8b8_make_api_keys_deleted_non_nullable.py
galaxy/model/migrations/alembic/versions_gxy/c39f1de47a04_add_skipped_state_to_collection_job_.py
galaxy/model/migrations/alembic/versions_gxy/caa7742f7bca_add_index_wf_r_i_p__workflow_invocation_.py
galaxy/model/migrations/alembic/versions_gxy/d0583094c8cd_add_quota_source_labels.py
galaxy/model/migrations/alembic/versions_gxy/ddbdbc40bdc1_add_workflow_comment_table.py
galaxy/model/migrations/alembic/versions_gxy/e0561d5fc8c7_add_archived_columns_to_history.py
galaxy/model/migrations/alembic/versions_gxy/e0e3bb173ee6_add_column_deleted_to_api_keys.py
galaxy/model/migrations/alembic/versions_gxy/e7b6dcb09efd_create_gxy_branch.py
galaxy/model/migrations/alembic/versions_gxy/e93c5d0b47a9_alter_column_external_user_id.py
galaxy/model/migrations/alembic/versions_tsi/d4a650f47a3c_create_tsi_branch.py
galaxy/model/orm/__init__.py
galaxy/model/orm/engine_factory.py
galaxy/model/orm/now.py
galaxy/model/orm/scripts.py
galaxy/model/orm/util.py
galaxy/model/store/__init__.py
galaxy/model/store/_bco_convert_utils.py
galaxy/model/store/build_objects.py
galaxy/model/store/discover.py
galaxy/model/store/load_objects.py
galaxy/model/store/ro_crate_utils.py
galaxy/model/tool_shed_install/__init__.py
galaxy/model/tool_shed_install/mapping.py
galaxy/model/triggers/__init__.py
galaxy/model/triggers/history_update_time_field.py
galaxy/model/triggers/update_audit_table.py
galaxy/model/triggers/utils.py
galaxy/model/unittest_utils/__init__.py
galaxy/model/unittest_utils/beaker_testing_utils.py
galaxy/model/unittest_utils/data_app.py
galaxy/model/unittest_utils/gxy_model_fixtures.py
galaxy/model/unittest_utils/mapping_testing_utils.py
galaxy/model/unittest_utils/migration_scripts_testing_utils.py
galaxy/model/unittest_utils/model_testing_utils.py
galaxy/model/unittest_utils/store_fixtures.py
galaxy/model/unittest_utils/tsi_model_fixtures.py
galaxy/quota/__init__.py
galaxy/quota/_schema.py
galaxy/security/__init__.py
galaxy/security/idencoding.py
galaxy/security/object_wrapper.py
galaxy/security/passwords.py
galaxy/security/ssh_util.py
galaxy/security/validate_user_input.py
galaxy/security/vault.py
galaxy_data.egg-info/PKG-INFO
galaxy_data.egg-info/SOURCES.txt
galaxy_data.egg-info/dependency_links.txt
galaxy_data.egg-info/entry_points.txt
galaxy_data.egg-info/requires.txt
galaxy_data.egg-info/top_level.txt