Mercurial > repos > q2d2 > qiime2_core__tools__export
changeset 10:b6e4d26e4e7a draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 36ec48f8c55799a0c963733df13da30f19b1bdf3
| author | q2d2 |
|---|---|
| date | Wed, 28 Jan 2026 16:39:35 +0000 |
| parents | 6d6617a57925 |
| children | |
| files | qiime2_core__tools__export.xml |
| diffstat | 1 files changed, 168 insertions(+), 144 deletions(-) [+] |
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--- a/qiime2_core__tools__export.xml Sat Nov 01 17:33:56 2025 +0000 +++ b/qiime2_core__tools__export.xml Wed Jan 28 16:39:35 2026 +0000 @@ -1,22 +1,22 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2025, QIIME 2 development team. +Copyright (c) 2026, QIIME 2 development team. Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> <!-- This tool was automatically generated by: - q2galaxy (version: 2025.10.0) + q2galaxy (version: 2026.1.0) for: - qiime2 (version: 2025.10.0) + qiime2 (version: 2026.1.0) --> -<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2025.10.0+dist.hbfe50fe0" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2026.1.0+dist.h02a552c2" profile="22.05" license="BSD-3-Clause"> <description>Export data from a QIIME 2 artifact</description> <xrefs> <xref type="bio.tools">qiime2</xref> </xrefs> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2025.10</container> + <container type="docker">quay.io/qiime2/amplicon:2026.1</container> </requirements> <command>q2galaxy run tools export '$inputs'</command> <configfiles> @@ -80,7 +80,9 @@ <option value="FeatureData__ob__Sequence__cb__">FeatureData[Sequence]</option> <option value="FeatureData__ob__SingleBowtie2Index__cb__">FeatureData[SingleBowtie2Index]</option> <option value="FeatureData__ob__Taxonomy__cb__">FeatureData[Taxonomy]</option> + <option value="FeatureMap__ob__FunctionToContigs__cb__">FeatureMap[FunctionToContigs]</option> <option value="FeatureMap__ob__MAGtoContigs__cb__">FeatureMap[MAGtoContigs]</option> + <option value="FeatureMap__ob__TaxonomyToContigs__cb__">FeatureMap[TaxonomyToContigs]</option> <option value="FeatureTable__ob__Balance__cb__">FeatureTable[Balance]</option> <option value="FeatureTable__ob__Composition__cb__">FeatureTable[Composition]</option> <option value="FeatureTable__ob__Design__cb__">FeatureTable[Design]</option> @@ -419,12 +421,24 @@ <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> </param> </when> + <when value="FeatureMap__ob__FunctionToContigs__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="FeatureMapFormat">Feature Map Format</option> + </param> + </when> <when value="FeatureMap__ob__MAGtoContigs__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="MAGtoContigsFormat">MA Gto Contigs Format</option> </param> </when> + <when value="FeatureMap__ob__TaxonomyToContigs__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="FeatureMapFormat">Feature Map Format</option> + </param> + </when> <when value="FeatureTable__ob__Balance__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> @@ -891,7 +905,7 @@ </inputs> <outputs> <collection name="exported" type="list" label="${tool.name} on ${on_string} as ${fmt_peek}"> - <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'FastqGzFormat', 'BLAST6Format', 'TaxonomicClassiferTemporaryPickleDirFmt', 'ANCOMBC2OutputDirFmt', 'EggnogProteinSequencesDirFmt', 'PredictionsFormat', 'DataLoafPackageDirFmt', 'Kraken2DBReportDirectoryFormat', 'DeblurStatsDirFmt', 'OrthologAnnotationDirFmt', 'ImmutableMetadataDirectoryFormat', 'PressedProfileHmmsDirectoryFmt', 'LociDirectoryFormat', 'ArtificialGroupingFormat', 'SRAMetadataFormat', 'PlacementsFormat', 'MAGtoContigsFormat', 'ImportanceFormat', 'DifferentialDirectoryFormat', 'EMPSingleEndDirFmt', 'SeppReferenceDirFmt', 'NewickFormat', 'BooleanSeriesFormat', 'ProteinsDirectoryFormat', 'ErrorCorrectionDetailsFmt', 'PredictionsDirectoryFormat', 'ProcrustesStatisticsFmt', 'MultiBAMDirFmt', 'ProteinSequencesDirectoryFormat', 'FirstDifferencesFormat', 'DNASequencesDirectoryFormat', 'DADA2StatsFormat', 'AlphaDiversityDirectoryFormat', 'ProteinFASTAFormat', 'DADA2BaseTransitionStatsFormat', 'RNAMultipleProfileHmmDirectoryFmt', 'ArtificialGroupingDirectoryFormat', 'KaijuDBDirectoryFormat', 'QualityFilterStatsFmt', 'BIOMV210DirFmt', 'UchimeStatsDirFmt', 'Kraken2DBReportFormat', 'SeedOrthologDirFmt', 'FirstDifferencesDirectoryFormat', 'DifferentialFormat', 'TrueTargetsDirectoryFormat', 'Kraken2DBDirectoryFormat', 'BLAST6DirectoryFormat', 'OrdinationDirectoryFormat', 'Kraken2OutputDirectoryFormat', 'BIOMV210Format', 'AlignedProteinSequencesDirectoryFormat', 'MAGtoContigsDirFmt', 'DecontamScoreDirFmt', 'RNAFASTAFormat', 'DistanceMatrixDirectoryFormat', 'SequenceCharacteristicsDirectoryFormat', 'QualityFilterStatsDirFmt', 'ProbabilitiesFormat', 'DADA2StatsDirFmt', 'Kraken2ReportDirectoryFormat', 'SingleLanePerSamplePairedEndFastqDirFmt', 'ErrorCorrectionDetailsDirFmt', 'SILVATaxidMapDirectoryFormat', 'SRAMetadataDirFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'AlignedRNAFASTAFormat', 'SequenceCharacteristicsFormat', 'MultiBowtie2IndexDirFmt', 'LSMatFormat', 'PlacementsDirFmt', 'BooleanSeriesDirectoryFormat', 'ProteinSingleProfileHmmDirectoryFmt', 'AlignedRNASequencesDirectoryFormat', 'GenomeSequencesDirectoryFormat', 'ContigSequencesDirFmt', 'SILVATaxidMapFormat', 'ImmutableMetadataFormat', 'DiamondDatabaseFileFmt', 'BLASTDBDirFmtV5', 'NCBITaxonomyDirFmt', 'SRAFailedIDsDirFmt', 'NCBIAccessionIDsFormat', 'QIIME1DemuxFormat', 'NCBIAccessionIDsDirFmt', 'RNASequencesDirectoryFormat', 'OrdinationFormat', 'DeblurStatsFmt', 'NewickDirectoryFormat', 'AlignedDNASequencesDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'DNAFASTAFormat', 'AlphaDiversityFormat', 'MultiFASTADirectoryFormat', 'PairedDNASequencesDirectoryFormat', 'SILVATaxonomyDirectoryFormat', 'EggnogRefDirFmt', 'GenesDirectoryFormat', 'SILVATaxonomyFormat', 'UchimeStatsFmt', 'TSVTaxonomyDirectoryFormat', 'DecontamScoreFormat', 'RNASingleProfileHmmDirectoryFmt', 'TableJSONLFileFormat', 'MAGSequencesDirFmt', 'AlignedDNAFASTAFormat', 'AlignedProteinFASTAFormat', 'TableJSONLDirFmt', 'SampleEstimatorDirFmt', 'DADA2BaseTransitionStatsDirFmt', 'ImportanceDirectoryFormat', 'BAMDirFmt', 'TSVTaxonomyFormat', 'PairedRNASequencesDirectoryFormat', 'SRAFailedIDsFormat', 'ProcrustesStatisticsDirFmt', 'ProbabilitiesDirectoryFormat', 'EMPPairedEndDirFmt', 'BrackenDBDirectoryFormat', 'ProteinMultipleProfileHmmDirectoryFmt', 'DiamondDatabaseDirFmt', 'MultiMAGSequencesDirFmt', 'DNAMultipleProfileHmmDirectoryFmt', 'DNASingleProfileHmmDirectoryFmt', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'Bowtie2IndexDirFmt', 'QIIME1DemuxDirFmt'}</filter> + <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'ProteinSingleProfileHmmDirectoryFmt', 'RNAMultipleProfileHmmDirectoryFmt', 'ProbabilitiesDirectoryFormat', 'SingleLanePerSampleSingleEndFastqDirFmt', 'Kraken2OutputDirectoryFormat', 'SILVATaxidMapDirectoryFormat', 'BLAST6DirectoryFormat', 'MultiFASTADirectoryFormat', 'AlphaDiversityFormat', 'BLASTDBDirFmtV5', 'TaxonomicClassiferTemporaryPickleDirFmt', 'OrdinationFormat', 'RNASingleProfileHmmDirectoryFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'PairedRNASequencesDirectoryFormat', 'AlignedProteinFASTAFormat', 'ArtificialGroupingFormat', 'SequenceCharacteristicsDirectoryFormat', 'NewickDirectoryFormat', 'NCBITaxonomyDirFmt', 'OrthologAnnotationDirFmt', 'TableJSONLDirFmt', 'UchimeStatsFmt', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'ContigSequencesDirFmt', 'TSVTaxonomyDirectoryFormat', 'ProcrustesStatisticsFmt', 'SILVATaxonomyFormat', 'EggnogRefDirFmt', 'EggnogProteinSequencesDirFmt', 'FirstDifferencesDirectoryFormat', 'DNASequencesDirectoryFormat', 'NewickFormat', 'SRAMetadataFormat', 'MultiMAGSequencesDirFmt', 'RNAFASTAFormat', 'DiamondDatabaseDirFmt', 'BLAST6Format', 'LSMatFormat', 'FeatureMapDirFmt', 'QualityFilterStatsDirFmt', 'AlignedRNAFASTAFormat', 'RNASequencesDirectoryFormat', 'TableJSONLFileFormat', 'BooleanSeriesDirectoryFormat', 'AlignedDNAFASTAFormat', 'ImmutableMetadataFormat', 'PressedProfileHmmsDirectoryFmt', 'PairedDNASequencesDirectoryFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'MAGSequencesDirFmt', 'Bowtie2IndexDirFmt', 'OrdinationDirectoryFormat', 'SRAMetadataDirFmt', 'Kraken2DBReportFormat', 'ImportanceFormat', 'DecontamScoreDirFmt', 'EMPSingleEndDirFmt', 'SRAFailedIDsFormat', 'QualityFilterStatsFmt', 'SILVATaxidMapFormat', 'UchimeStatsDirFmt', 'SequenceCharacteristicsFormat', 'Kraken2DBReportDirectoryFormat', 'DNAMultipleProfileHmmDirectoryFmt', 'DifferentialDirectoryFormat', 'GenesDirectoryFormat', 'MultiBowtie2IndexDirFmt', 'BIOMV210Format', 'ErrorCorrectionDetailsDirFmt', 'ProteinSequencesDirectoryFormat', 'QIIME1DemuxFormat', 'DADA2BaseTransitionStatsFormat', 'BooleanSeriesFormat', 'SampleEstimatorDirFmt', 'ProteinMultipleProfileHmmDirectoryFmt', 'DataLoafPackageDirFmt', 'AlignedRNASequencesDirectoryFormat', 'PlacementsDirFmt', 'PlacementsFormat', 'DNAFASTAFormat', 'FirstDifferencesFormat', 'ArtificialGroupingDirectoryFormat', 'DNASingleProfileHmmDirectoryFmt', 'DecontamScoreFormat', 'BAMDirFmt', 'ProcrustesStatisticsDirFmt', 'MAGtoContigsFormat', 'ProteinFASTAFormat', 'EMPPairedEndDirFmt', 'ImmutableMetadataDirectoryFormat', 'ANCOMBC2OutputDirFmt', 'FeatureMapFormat', 'ImportanceDirectoryFormat', 'SRAFailedIDsDirFmt', 'AlignedDNASequencesDirectoryFormat', 'ErrorCorrectionDetailsFmt', 'PredictionsDirectoryFormat', 'ProbabilitiesFormat', 'DeblurStatsFmt', 'DADA2StatsDirFmt', 'KaijuDBDirectoryFormat', 'DADA2BaseTransitionStatsDirFmt', 'NCBIAccessionIDsDirFmt', 'QIIME1DemuxDirFmt', 'DiamondDatabaseFileFmt', 'DifferentialFormat', 'MAGtoContigsDirFmt', 'BIOMV210DirFmt', 'SingleLanePerSamplePairedEndFastqDirFmt', 'FastqGzFormat', 'TrueTargetsDirectoryFormat', 'SeppReferenceDirFmt', 'DistanceMatrixDirectoryFormat', 'AlphaDiversityDirectoryFormat', 'TSVTaxonomyFormat', 'PredictionsFormat', 'MultiBAMDirFmt', 'Kraken2DBDirectoryFormat', 'SILVATaxonomyDirectoryFormat', 'LociDirectoryFormat', 'AlignedProteinSequencesDirectoryFormat', 'GenomeSequencesDirectoryFormat', 'DeblurStatsDirFmt', 'ProteinsDirectoryFormat', 'DADA2StatsFormat', 'NCBIAccessionIDsFormat', 'SeedOrthologDirFmt', 'Kraken2ReportDirectoryFormat', 'BrackenDBDirectoryFormat'}</filter> <discover_datasets pattern="__designation_and_ext__" visible="false"/> </collection> <data name="ANCOMBC2OutputDirFmt" label="${tool.name} on ${on_string} as ANCOMBC2OutputDirFmt"> @@ -1113,6 +1127,14 @@ <filter>fmt_finder['output_format'] == 'FastqGzFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'FastqGzFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <data name="FeatureMapDirFmt" label="${tool.name} on ${on_string} as FeatureMapDirFmt"> + <filter>fmt_finder['output_format'] == 'FeatureMapDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'FeatureMapDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>feature-map)\.(?P<ext>json)" visible="true"/> + </data> + <data name="FeatureMapFormat" label="${tool.name} on ${on_string} as FeatureMapFormat"> + <filter>fmt_finder['output_format'] == 'FeatureMapFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'FeatureMapFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> <data name="FirstDifferencesDirectoryFormat" label="${tool.name} on ${on_string} as FirstDifferencesDirectoryFormat"> <filter>fmt_finder['output_format'] == 'FirstDifferencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'FirstDifferencesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>FirstDifferences)\.(?P<ext>tsv)" visible="true"/> @@ -1493,20 +1515,20 @@ -------- These formats have documentation available. -SRAFailedIDsFormat -****************** +TSVTaxonomyFormat +***************** +Format for a 2+ column TSV file with an expected minimal header. -This is a "fake" format only used to store a list of failed SRA IDs, -which can be converted to QIIME's metadata and input into any fondue -action. +The only header recognized by this format is: -NCBIAccessionIDsFormat -********************** + Feature ID<tab>Taxon + +Optionally followed by other arbitrary columns. -This is a format used to store a list of SRA accession IDs (run, -study, BioProject, sample and experiment IDs), which can be converted -to QIIME's metadata. Artifacts containing of run, study and BioProject -IDs can be input into any fondue action. +This format supports blank lines. The expected header must be the first +non-blank line. In addition to the header, there must be at least one line +of data. + SequenceCharacteristicsFormat ***************************** @@ -1522,6 +1544,14 @@ "FeatureData[SequenceCharacteristics % Properties("length")]" adds validation for a numerical column called "length". +NCBIAccessionIDsFormat +********************** + +This is a format used to store a list of SRA accession IDs (run, +study, BioProject, sample and experiment IDs), which can be converted +to QIIME's metadata. Artifacts containing of run, study and BioProject +IDs can be input into any fondue action. + ANCOMBC2OutputDirFmt ******************** @@ -1537,22 +1567,6 @@ - diff: differentially abundant boolean (i.e. q < alpha) - passed_ss: whether sensitivity analysis was passed -FastqGzFormat -************* - -A gzipped fastq file. - - -PressedProfileHmmsDirectoryFmt -****************************** - -The <hmmfile>.h3m file contains the profile HMMs -and their annotation in a binary format. The <hmmfile>.h3i file is an -SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains -precomputed data structures for the fast heuristic filter -(the MSV filter). The <hmmfile>.h3p file contains precomputed data -structures for the rest of each profile. - QIIME1DemuxFormat ***************** QIIME 1 demultiplexed FASTA format. @@ -1587,143 +1601,153 @@ - Each sequence must be DNA and cannot be empty. -TSVTaxonomyFormat -***************** -Format for a 2+ column TSV file with an expected minimal header. +PressedProfileHmmsDirectoryFmt +****************************** -The only header recognized by this format is: +The <hmmfile>.h3m file contains the profile HMMs +and their annotation in a binary format. The <hmmfile>.h3i file is an +SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains +precomputed data structures for the fast heuristic filter +(the MSV filter). The <hmmfile>.h3p file contains precomputed data +structures for the rest of each profile. - Feature ID<tab>Taxon - -Optionally followed by other arbitrary columns. +SRAFailedIDsFormat +****************** -This format supports blank lines. The expected header must be the first -non-blank line. In addition to the header, there must be at least one line -of data. +This is a "fake" format only used to store a list of failed SRA IDs, +which can be converted to QIIME's metadata and input into any fondue +action. + +FastqGzFormat +************* + +A gzipped fastq file. Additional formats without documentation: ***************************************** - - ContigSequencesDirFmt - - BrackenDBDirectoryFormat - - SILVATaxidMapFormat - - ErrorCorrectionDetailsDirFmt - - EggnogRefDirFmt - - SRAFailedIDsDirFmt - - CasavaOneEightSingleLanePerSampleDirFmt + - ArtificialGroupingFormat + - AlignedRNAFASTAFormat + - SILVATaxonomyFormat - RNAMultipleProfileHmmDirectoryFmt - - BLAST6Format - - LSMatFormat - - RNAFASTAFormat - - PlacementsDirFmt + - SeppReferenceDirFmt - NewickFormat - - BooleanSeriesDirectoryFormat - - MAGSequencesDirFmt - - TSVTaxonomyDirectoryFormat - - DiamondDatabaseFileFmt - - MAGtoContigsDirFmt - - DADA2BaseTransitionStatsDirFmt - - BLAST6DirectoryFormat - - QIIME1DemuxDirFmt - - Kraken2DBReportDirectoryFormat - - RNASequencesDirectoryFormat - - NewickDirectoryFormat - - ProteinSequencesDirectoryFormat - - OrthologAnnotationDirFmt - - FirstDifferencesDirectoryFormat - - BAMDirFmt - - DeblurStatsFmt - - AlignedRNAFASTAFormat - - DiamondDatabaseDirFmt - - ProteinsDirectoryFormat - - MAGtoContigsFormat + - ContigSequencesDirFmt + - ProteinFASTAFormat + - QualityFilterStatsFmt + - AlignedRNASequencesDirectoryFormat + - SILVATaxonomyDirectoryFormat + - CasavaOneEightSingleLanePerSampleDirFmt + - SequenceCharacteristicsDirectoryFormat + - OrdinationFormat + - FirstDifferencesFormat + - PredictionsFormat + - TableJSONLFileFormat + - Kraken2ReportDirectoryFormat + - BIOMV210DirFmt - UchimeStatsDirFmt - NCBIAccessionIDsDirFmt - - DecontamScoreFormat - - DADA2StatsDirFmt - - EMPSingleEndDirFmt - - ProteinSingleProfileHmmDirectoryFmt + - GenesDirectoryFormat + - MAGSequencesDirFmt - ProbabilitiesFormat - - ProteinFASTAFormat - - MultiBAMDirFmt - - BIOMV210Format - - AlignedRNASequencesDirectoryFormat - - Kraken2DBReportFormat - - ImportanceFormat - - SeedOrthologDirFmt - - SequenceCharacteristicsDirectoryFormat - - EMPPairedEndDirFmt - - MultiplexedSingleEndBarcodeInSequenceDirFmt - - ArtificialGroupingFormat - - ProteinMultipleProfileHmmDirectoryFmt - - ProbabilitiesDirectoryFormat - - SampleEstimatorDirFmt - - DistanceMatrixDirectoryFormat - - Kraken2OutputDirectoryFormat + - SILVATaxidMapFormat - EggnogProteinSequencesDirFmt - - DecontamScoreDirFmt - DNAFASTAFormat + - ImmutableMetadataFormat + - BooleanSeriesDirectoryFormat + - ErrorCorrectionDetailsFmt + - BrackenDBDirectoryFormat + - FeatureMapFormat + - DADA2StatsDirFmt + - OrdinationDirectoryFormat + - BooleanSeriesFormat + - QIIME1DemuxDirFmt + - DataLoafPackageDirFmt + - ProteinSingleProfileHmmDirectoryFmt + - AlphaDiversityFormat + - PairedDNASequencesDirectoryFormat + - TableJSONLDirFmt - ImportanceDirectoryFormat - - OrdinationFormat - - DNASingleProfileHmmDirectoryFmt - - TrueTargetsDirectoryFormat - - SingleLanePerSamplePairedEndFastqDirFmt - - PairedDNASequencesDirectoryFormat - - DeblurStatsDirFmt - - ImmutableMetadataFormat - - AlphaDiversityFormat + - Kraken2DBReportFormat + - BAMDirFmt - AlignedProteinFASTAFormat - - GenesDirectoryFormat - - DADA2BaseTransitionStatsFormat - - AlphaDiversityDirectoryFormat - - TaxonomicClassiferTemporaryPickleDirFmt - - SILVATaxonomyFormat - - OrdinationDirectoryFormat - - DNAMultipleProfileHmmDirectoryFmt - - BLASTDBDirFmtV5 - - PlacementsFormat - - MultiFASTADirectoryFormat + - ProteinsDirectoryFormat + - ProcrustesStatisticsFmt + - ErrorCorrectionDetailsDirFmt + - FeatureMapDirFmt + - MAGtoContigsFormat + - QualityFilterStatsDirFmt + - ProteinMultipleProfileHmmDirectoryFmt + - ArtificialGroupingDirectoryFormat + - SRAMetadataFormat - PairedRNASequencesDirectoryFormat - - BooleanSeriesFormat - - SRAMetadataFormat + - Kraken2DBReportDirectoryFormat + - MAGtoContigsDirFmt + - BIOMV210Format + - MultiBAMDirFmt - AlignedProteinSequencesDirectoryFormat - - RNASingleProfileHmmDirectoryFmt + - ImportanceFormat - DifferentialFormat - DNASequencesDirectoryFormat - - GenomeSequencesDirectoryFormat - - QualityFilterStatsDirFmt - - ProcrustesStatisticsFmt - - MultiMAGSequencesDirFmt - - AlignedDNAFASTAFormat - - SILVATaxonomyDirectoryFormat - - DADA2StatsFormat + - ProcrustesStatisticsDirFmt + - FirstDifferencesDirectoryFormat + - KaijuDBDirectoryFormat + - DNASingleProfileHmmDirectoryFmt - SILVATaxidMapDirectoryFormat - - MultiplexedPairedEndBarcodeInSequenceDirFmt - - TableJSONLFileFormat + - AlignedDNAFASTAFormat + - DecontamScoreFormat + - LociDirectoryFormat - DifferentialDirectoryFormat - - BIOMV210DirFmt - - PredictionsFormat - - Kraken2ReportDirectoryFormat - - SeppReferenceDirFmt - - LociDirectoryFormat + - DecontamScoreDirFmt + - ImmutableMetadataDirectoryFormat + - SingleLanePerSamplePairedEndFastqDirFmt + - EMPSingleEndDirFmt + - AlignedDNASequencesDirectoryFormat + - Kraken2OutputDirectoryFormat + - AlphaDiversityDirectoryFormat + - GenomeSequencesDirectoryFormat + - LSMatFormat + - MultiFASTADirectoryFormat + - DiamondDatabaseFileFmt + - NewickDirectoryFormat + - MultiplexedSingleEndBarcodeInSequenceDirFmt + - DeblurStatsDirFmt + - BLASTDBDirFmtV5 + - EMPPairedEndDirFmt + - DADA2BaseTransitionStatsFormat + - DNAMultipleProfileHmmDirectoryFmt + - DiamondDatabaseDirFmt + - TaxonomicClassiferTemporaryPickleDirFmt + - BLAST6Format + - EggnogRefDirFmt + - UchimeStatsFmt + - SeedOrthologDirFmt + - DistanceMatrixDirectoryFormat + - RNAFASTAFormat + - SRAFailedIDsDirFmt + - ProbabilitiesDirectoryFormat + - TrueTargetsDirectoryFormat + - PlacementsDirFmt + - MultiMAGSequencesDirFmt - Bowtie2IndexDirFmt - - UchimeStatsFmt - - ProcrustesStatisticsDirFmt - - MultiBowtie2IndexDirFmt - - AlignedDNASequencesDirectoryFormat - - ErrorCorrectionDetailsFmt - - ImmutableMetadataDirectoryFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt - NCBITaxonomyDirFmt + - TSVTaxonomyDirectoryFormat + - PredictionsDirectoryFormat + - Kraken2DBDirectoryFormat + - DADA2BaseTransitionStatsDirFmt - SRAMetadataDirFmt - - TableJSONLDirFmt - - QualityFilterStatsFmt - - Kraken2DBDirectoryFormat - - DataLoafPackageDirFmt + - RNASingleProfileHmmDirectoryFmt + - BLAST6DirectoryFormat + - DADA2StatsFormat + - PlacementsFormat + - OrthologAnnotationDirFmt - SingleLanePerSampleSingleEndFastqDirFmt - - PredictionsDirectoryFormat - - FirstDifferencesFormat - - ArtificialGroupingDirectoryFormat - - KaijuDBDirectoryFormat + - RNASequencesDirectoryFormat + - MultiBowtie2IndexDirFmt + - ProteinSequencesDirectoryFormat + - DeblurStatsFmt + - SampleEstimatorDirFmt </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>