LICENSE
README.md
pyproject.toml
bridges/AdmixtureCli.java
bridges/AmazingMetaCli.java
bridges/AssemblyRecommandCli.java
bridges/BamIndexCli.java
bridges/BamSortCli.java
bridges/BamStateCli.java
bridges/BarPlotterCli.java
bridges/BarplotCli.java
bridges/BatchVizMotifsCli.java
bridges/BlastXmlConvertCli.java
bridges/BlatExecutorCli.java
bridges/CalcRepeatCli.java
bridges/CalculateSimilarityCli.java
bridges/CddMotifCli.java
bridges/CircleGeneViewerCli.java
bridges/CircosCli.java
bridges/ColorSchemeCli.java
bridges/CtgGroupCli.java
bridges/CubeHeatmapCli.java
bridges/DeHistCli.java
bridges/DegramdomCli.java
bridges/DiffExpCli.java
bridges/DistanceCli.java
bridges/DualSynCli.java
bridges/EggnogCli.java
bridges/ExprCorrCli.java
bridges/FastaMergerCli.java
bridges/FastaTableConvertCli.java
bridges/FileCleanerCli.java
bridges/FileSplitCli.java
bridges/FindBlockDualCli.java
bridges/FindBlockMultipleCli.java
bridges/FindPathCli.java
bridges/GSEAWrapperCli.java
bridges/GenBank2FastaCli.java
bridges/GeneDensityCli.java
bridges/GeneLocGffCli.java
bridges/GeneStructureCli.java
bridges/GenericCli.java
bridges/GetENALinksCli.java
bridges/GetSubNewickTreeCli.java
bridges/GoEnrichCli.java
bridges/GoLevelCli.java
bridges/GroupedBarCli.java
bridges/GsaDiagCli.java
bridges/GxfFilterCli.java
bridges/GxfSortCli.java
bridges/HclustCli.java
bridges/HeatmapCli.java
bridges/HmmerSuiteCli.java
bridges/JgblocksCli.java
bridges/KeggEnrichCli.java
bridges/LayoutHeatmapCli.java
bridges/MCScanXCli.java
bridges/MCScanXFastCli.java
bridges/MSACli.java
bridges/MakeMotifCli.java
bridges/MarkerDesignCli.java
bridges/MarkerToolsCli.java
bridges/Mast2TabCli.java
bridges/MastCli.java
bridges/MastRunCli.java
bridges/Meme2TabCli.java
bridges/MemeCli.java
bridges/MemeRunCli.java
bridges/MgGxfCli.java
bridges/MicroSynCli.java
bridges/MirIdentifyCli.java
bridges/MotifCli.java
bridges/MotifPatternCli.java
bridges/MotifShiftCli.java
bridges/MountainPlotCli.java
bridges/MultiSuperHeatCli.java
bridges/NeedlemanWunschCli.java
bridges/PafGC.java
bridges/PafVizCli.java
bridges/PeakDistCli.java
bridges/Pep2CodonCli.java
bridges/PfamMotifCli.java
bridges/PhyloTreeCli.java
bridges/PileUpCli.java
bridges/PlantCAREResultClassifyCli.java
bridges/PubmedSearchCli.java
bridges/QpcrCli.java
bridges/QpcrDdctCli.java
bridges/QpcrProcCli.java
bridges/QuickGenomeDotCli.java
bridges/QuickProteinAnnoCli.java
bridges/QuickRunIQtreeCli.java
bridges/QuickTrimALCli.java
bridges/RNAplotCli.java
bridges/RegionBedToGFF3Cli.java
bridges/RegionDepthCli.java
bridges/SamBamCovCli.java
bridges/SeqConverterCli.java
bridges/SeqLenTrackCli.java
bridges/SeveralSpeciesCli.java
bridges/SimpleEnricherCli.java
bridges/SimpleHmmscanCli.java
bridges/SixFrameTranlaterCli.java
bridges/StructAnnoCompareCli.java
bridges/SubmitSMARTCli.java
bridges/SuperCircosCli.java
bridges/TableColManipCli.java
bridges/TableCollapseCli.java
bridges/TargetScoreCli.java
bridges/TauCalcCli.java
bridges/TaxonomyBatchCli.java
bridges/TreeCli.java
bridges/TreeRootingCli.java
bridges/TrimMSACli.java
bridges/UnrootedTreeCli.java
bridges/UpSetCli.java
bridges/Venn5Cli.java
bridges/Venn6Cli.java
bridges/ViolinCli.java
bridges/VisualizeCli.java
bridges/VizGFACli.java
tbtools_cli/__init__.py
tbtools_cli/auto_commands.py
tbtools_cli/cli.py
tbtools_cli/cli_load.py
tbtools_cli/cli_rpc.py
tbtools_cli/cli_tools_registry.py
tbtools_cli/cli_top.py
tbtools_cli/command_metadata.json
tbtools_cli/command_spec.py
tbtools_cli/config.example.toml
tbtools_cli/config.py
tbtools_cli/core.py
tbtools_cli/errors.py
tbtools_cli/mcp_server.py
tbtools_cli/presets.py
tbtools_cli/scenarios.py
tbtools_cli.egg-info/PKG-INFO
tbtools_cli.egg-info/SOURCES.txt
tbtools_cli.egg-info/dependency_links.txt
tbtools_cli.egg-info/entry_points.txt
tbtools_cli.egg-info/requires.txt
tbtools_cli.egg-info/top_level.txt
tests/test_cli.py
tests/test_command_spec.py
tests/test_contract.py
tests/test_i18n.py
tests/test_jobs.py
tests/test_metadata.py
tests/test_p0_protection.py