Mercurial > repos > q2d2 > qiime2_core__tools__export
changeset 7:f83fcc984626 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit b1fccfb38b4873cd4699743033449014a2978e7d
| author | q2d2 |
|---|---|
| date | Mon, 05 May 2025 19:06:10 +0000 |
| parents | 40bcc0e139fa |
| children | |
| files | qiime2_core__tools__export.xml |
| diffstat | 1 files changed, 169 insertions(+), 136 deletions(-) [+] |
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--- a/qiime2_core__tools__export.xml Wed Oct 30 20:00:17 2024 +0000 +++ b/qiime2_core__tools__export.xml Mon May 05 19:06:10 2025 +0000 @@ -1,22 +1,22 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2024, QIIME 2 development team. +Copyright (c) 2025, 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: 2024.10.0) + q2galaxy (version: 2025.4.0) for: - qiime2 (version: 2024.10.1) + qiime2 (version: 2025.4.0) --> -<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2024.10.0+dist.h3d8a7e27" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2025.4.0+dist.h1147124e" 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:2024.10</container> + <container type="docker">quay.io/qiime2/amplicon:2025.4</container> </requirements> <command>q2galaxy run tools export '$inputs'</command> <configfiles> @@ -55,6 +55,7 @@ <option value="EMPPairedEndSequences">EMPPairedEndSequences</option> <option value="EMPSingleEndSequences">EMPSingleEndSequences</option> <option value="ErrorCorrectionDetails">ErrorCorrectionDetails</option> + <option value="FeatureData__ob__ANCOMBC2Output__cb__">FeatureData[ANCOMBC2Output]</option> <option value="FeatureData__ob__AlignedProteinSequence__cb__">FeatureData[AlignedProteinSequence]</option> <option value="FeatureData__ob__AlignedRNASequence__cb__">FeatureData[AlignedRNASequence]</option> <option value="FeatureData__ob__AlignedSequence__cb__">FeatureData[AlignedSequence]</option> @@ -263,6 +264,12 @@ <option value="ErrorCorrectionDetailsFmt">Error Correction Details Format</option> </param> </when> + <when value="FeatureData__ob__ANCOMBC2Output__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="ANCOMBC2OutputDirFmt">ANCOMBC2 Output Directory Format</option> + </param> + </when> <when value="FeatureData__ob__AlignedProteinSequence__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> @@ -855,9 +862,20 @@ </inputs> <outputs> <collection name="exported" type="list" label="${tool.name} on ${on_string} as ${fmt_peek}"> - <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'QIIME1DemuxFormat', 'TSVTaxonomyFormat', 'ProcrustesStatisticsDirFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'UchimeStatsDirFmt', 'SILVATaxidMapFormat', 'NewickDirectoryFormat', 'AlignedDNAFASTAFormat', 'OrdinationDirectoryFormat', 'TableJSONLFileFormat', 'ProteinsDirectoryFormat', 'AlignedProteinSequencesDirectoryFormat', 'ArtificialGroupingDirectoryFormat', 'QualityFilterStatsFmt', 'ImmutableMetadataDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'UchimeStatsFmt', 'ProteinSingleProfileHmmDirectoryFmt', 'DADA2StatsFormat', 'BIOMV210DirFmt', 'MultiFASTADirectoryFormat', 'AlignedDNASequencesDirectoryFormat', 'TableJSONLDirFmt', 'SequenceCharacteristicsFormat', 'BooleanSeriesFormat', 'MultiBAMDirFmt', 'GenomeSequencesDirectoryFormat', 'AlignedRNASequencesDirectoryFormat', 'MultiBowtie2IndexDirFmt', 'ImportanceFormat', 'FirstDifferencesDirectoryFormat', 'ArtificialGroupingFormat', 'MAGtoContigsFormat', 'MAGSequencesDirFmt', 'KaijuDBDirectoryFormat', 'DiamondDatabaseFileFmt', 'DataLoafPackageDirFmt', 'QIIME1DemuxDirFmt', 'DNASingleProfileHmmDirectoryFmt', 'Kraken2ReportDirectoryFormat', 'ErrorCorrectionDetailsDirFmt', 'ProbabilitiesDirectoryFormat', 'DecontamScoreDirFmt', 'DeblurStatsDirFmt', 'SILVATaxidMapDirectoryFormat', 'SingleLanePerSampleSingleEndFastqDirFmt', 'BLASTDBDirFmtV5', 'ErrorCorrectionDetailsFmt', 'LociDirectoryFormat', 'FastqGzFormat', 'ImmutableMetadataFormat', 'RNAFASTAFormat', 'EggnogRefDirFmt', 'DNAFASTAFormat', 'PlacementsDirFmt', 'ProteinMultipleProfileHmmDirectoryFmt', 'EMPSingleEndDirFmt', 'SILVATaxonomyDirectoryFormat', 'BLAST6Format', 'DNAMultipleProfileHmmDirectoryFmt', 'DADA2StatsDirFmt', 'SILVATaxonomyFormat', 'DNASequencesDirectoryFormat', 'PairedRNASequencesDirectoryFormat', 'SeedOrthologDirFmt', 'SequenceCharacteristicsDirectoryFormat', 'ProbabilitiesFormat', 'Kraken2DBReportDirectoryFormat', 'QualityFilterStatsDirFmt', 'SingleLanePerSamplePairedEndFastqDirFmt', 'DifferentialFormat', 'BAMDirFmt', 'NCBITaxonomyDirFmt', 'NewickFormat', 'LSMatFormat', 'MultiMAGSequencesDirFmt', 'RNASingleProfileHmmDirectoryFmt', 'Kraken2DBDirectoryFormat', 'AlignedRNAFASTAFormat', 'ProteinSequencesDirectoryFormat', 'Kraken2OutputDirectoryFormat', 'SampleEstimatorDirFmt', 'RNAMultipleProfileHmmDirectoryFmt', 'ProcrustesStatisticsFmt', 'BooleanSeriesDirectoryFormat', 'FirstDifferencesFormat', 'Bowtie2IndexDirFmt', 'PredictionsFormat', 'BLAST6DirectoryFormat', 'ImportanceDirectoryFormat', 'DifferentialDirectoryFormat', 'EMPPairedEndDirFmt', 'SeppReferenceDirFmt', 'TrueTargetsDirectoryFormat', 'OrdinationFormat', 'EggnogProteinSequencesDirFmt', 'OrthologAnnotationDirFmt', 'DecontamScoreFormat', 'DeblurStatsFmt', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'MAGtoContigsDirFmt', 'Kraken2DBReportFormat', 'GenesDirectoryFormat', 'PredictionsDirectoryFormat', 'DiamondDatabaseDirFmt', 'TSVTaxonomyDirectoryFormat', 'ProteinFASTAFormat', 'BIOMV210Format', 'PairedDNASequencesDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'AlphaDiversityDirectoryFormat', 'RNASequencesDirectoryFormat', 'AlignedProteinFASTAFormat', 'PlacementsFormat', 'AlphaDiversityFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'ContigSequencesDirFmt', 'PressedProfileHmmsDirectoryFmt', 'BrackenDBDirectoryFormat'}</filter> + <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'DiamondDatabaseFileFmt', 'UchimeStatsDirFmt', 'PredictionsDirectoryFormat', 'SILVATaxidMapFormat', 'SequenceCharacteristicsFormat', 'DecontamScoreFormat', 'NCBITaxonomyDirFmt', 'ProteinMultipleProfileHmmDirectoryFmt', 'FastqGzFormat', 'ContigSequencesDirFmt', 'Bowtie2IndexDirFmt', 'MultiBowtie2IndexDirFmt', 'BooleanSeriesFormat', 'EMPPairedEndDirFmt', 'Kraken2DBReportDirectoryFormat', 'ProteinsDirectoryFormat', 'PlacementsDirFmt', 'DecontamScoreDirFmt', 'RNAFASTAFormat', 'OrdinationFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'Kraken2DBDirectoryFormat', 'AlignedDNAFASTAFormat', 'ImportanceDirectoryFormat', 'EggnogProteinSequencesDirFmt', 'DataLoafPackageDirFmt', 'DifferentialFormat', 'CasavaOneEightSingleLanePerSampleDirFmt', 'AlignedDNASequencesDirectoryFormat', 'FirstDifferencesFormat', 'ErrorCorrectionDetailsFmt', 'MAGSequencesDirFmt', 'LSMatFormat', 'BrackenDBDirectoryFormat', 'UchimeStatsFmt', 'PredictionsFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'PlacementsFormat', 'ANCOMBC2OutputDirFmt', 'TableJSONLDirFmt', 'MultiBAMDirFmt', 'QIIME1DemuxDirFmt', 'ProteinSequencesDirectoryFormat', 'BLAST6DirectoryFormat', 'BLAST6Format', 'SingleLanePerSamplePairedEndFastqDirFmt', 'Kraken2ReportDirectoryFormat', 'ArtificialGroupingFormat', 'DADA2StatsFormat', 'ProcrustesStatisticsDirFmt', 'ProbabilitiesFormat', 'AlphaDiversityFormat', 'PairedRNASequencesDirectoryFormat', 'AlignedRNASequencesDirectoryFormat', 'SeedOrthologDirFmt', 'AlignedProteinSequencesDirectoryFormat', 'TSVTaxonomyDirectoryFormat', 'SequenceCharacteristicsDirectoryFormat', 'PressedProfileHmmsDirectoryFmt', 'RNASequencesDirectoryFormat', 'GenesDirectoryFormat', 'SILVATaxonomyFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'MAGtoContigsFormat', 'RNAMultipleProfileHmmDirectoryFmt', 'ProteinFASTAFormat', 'DiamondDatabaseDirFmt', 'LociDirectoryFormat', 'ProcrustesStatisticsFmt', 'DNASingleProfileHmmDirectoryFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'QualityFilterStatsDirFmt', 'RNASingleProfileHmmDirectoryFmt', 'ImmutableMetadataFormat', 'DADA2StatsDirFmt', 'KaijuDBDirectoryFormat', 'QIIME1DemuxFormat', 'SILVATaxidMapDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'DifferentialDirectoryFormat', 'BIOMV210Format', 'FirstDifferencesDirectoryFormat', 'OrdinationDirectoryFormat', 'SILVATaxonomyDirectoryFormat', 'TSVTaxonomyFormat', 'ProbabilitiesDirectoryFormat', 'BLASTDBDirFmtV5', 'ArtificialGroupingDirectoryFormat', 'TableJSONLFileFormat', 'Kraken2OutputDirectoryFormat', 'GenomeSequencesDirectoryFormat', 'AlignedRNAFASTAFormat', 'Kraken2DBReportFormat', 'ErrorCorrectionDetailsDirFmt', 'QualityFilterStatsFmt', 'SampleEstimatorDirFmt', 'BAMDirFmt', 'DNASequencesDirectoryFormat', 'DNAMultipleProfileHmmDirectoryFmt', 'TrueTargetsDirectoryFormat', 'DNAFASTAFormat', 'BooleanSeriesDirectoryFormat', 'OrthologAnnotationDirFmt', 'ImportanceFormat', 'MAGtoContigsDirFmt', 'ProteinSingleProfileHmmDirectoryFmt', 'DeblurStatsFmt', 'NewickDirectoryFormat', 'AlphaDiversityDirectoryFormat', 'NewickFormat', 'EggnogRefDirFmt', 'PairedDNASequencesDirectoryFormat', 'DeblurStatsDirFmt', 'MultiFASTADirectoryFormat', 'EMPSingleEndDirFmt', 'MultiMAGSequencesDirFmt', 'ImmutableMetadataDirectoryFormat', 'AlignedProteinFASTAFormat', 'SeppReferenceDirFmt', 'BIOMV210DirFmt'}</filter> <discover_datasets pattern="__designation_and_ext__" visible="false"/> </collection> + <data name="ANCOMBC2OutputDirFmt" label="${tool.name} on ${on_string} as ANCOMBC2OutputDirFmt"> + <filter>fmt_finder['output_format'] == 'ANCOMBC2OutputDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ANCOMBC2OutputDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>lfc)\.(?P<ext>jsonl)" visible="true"/> + <discover_datasets pattern="(?P<designation>se)\.(?P<ext>jsonl)" visible="true"/> + <discover_datasets pattern="(?P<designation>W)\.(?P<ext>jsonl)" visible="true"/> + <discover_datasets pattern="(?P<designation>p)\.(?P<ext>jsonl)" visible="true"/> + <discover_datasets pattern="(?P<designation>q)\.(?P<ext>jsonl)" visible="true"/> + <discover_datasets pattern="(?P<designation>diff)\.(?P<ext>jsonl)" visible="true"/> + <discover_datasets pattern="(?P<designation>passed_ss)\.(?P<ext>jsonl)" visible="true"/> + <discover_datasets pattern="(?P<designation>structural-zeros)\.(?P<ext>jsonl)" visible="true"/> + </data> <data name="AlignedDNAFASTAFormat" label="${tool.name} on ${on_string} as AlignedDNAFASTAFormat"> <filter>fmt_finder['output_format'] == 'AlignedDNAFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'AlignedDNAFASTAFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> @@ -1110,13 +1128,13 @@ <filter>fmt_finder['output_format'] == 'Kraken2DBReportFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBReportFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> - <collection name="Kraken2OutputDirectoryFormat_reports" type="list" label="${tool.name} on ${on_string} as Kraken2OutputDirectoryFormat (reports)"> + <collection name="Kraken2OutputDirectoryFormat_outputs" type="list" label="${tool.name} on ${on_string} as Kraken2OutputDirectoryFormat (outputs)"> <filter>fmt_finder['output_format'] == 'Kraken2OutputDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2OutputDirectoryFormat')</filter> - <discover_datasets pattern="(?P<designation>.+output)\.(?P<ext>(txt|tsv)$)" visible="false"/> + <discover_datasets pattern="(?P<designation>.+\.output)\.(?P<ext>(txt|tsv)$)" visible="false"/> </collection> <collection name="Kraken2ReportDirectoryFormat_reports" type="list" label="${tool.name} on ${on_string} as Kraken2ReportDirectoryFormat (reports)"> <filter>fmt_finder['output_format'] == 'Kraken2ReportDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2ReportDirectoryFormat')</filter> - <discover_datasets pattern="(?P<designation>.+report)\.(?P<ext>(txt|tsv)$)" visible="false"/> + <discover_datasets pattern="(?P<designation>.+\.report)\.(?P<ext>(txt|tsv)$)" visible="false"/> </collection> <data name="LSMatFormat" label="${tool.name} on ${on_string} as LSMatFormat"> <filter>fmt_finder['output_format'] == 'LSMatFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'LSMatFormat')</filter> @@ -1414,16 +1432,6 @@ -------- These formats have documentation available. -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. - TSVTaxonomyFormat ***************** Format for a 2+ column TSV file with an expected minimal header. @@ -1439,6 +1447,30 @@ of data. +SequenceCharacteristicsFormat +***************************** + +Format for a TSV file with information about sequences like length of a +feature. The first column contains feature identifiers and is followed by +other optional columns. + +The file cannot be empty and must have at least two columns. + +Validation for additional columns can be added with a semantic validator +tied to a property. For example the "validate_seq_char_len" validator for +"FeatureData[SequenceCharacteristics % Properties("length")]" +adds validation for a numerical column called "length". + +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. @@ -1473,142 +1505,143 @@ - Each sequence must be DNA and cannot be empty. -SequenceCharacteristicsFormat -***************************** - -Format for a TSV file with information about sequences like length of a -feature. The first column contains feature identifiers and is followed by -other optional columns. - -The file cannot be empty and must have at least two columns. - -Validation for additional columns can be added with a semantic validator -tied to a property. For example the "validate_seq_char_len" validator for -"FeatureData[SequenceCharacteristics % Properties("length")]" -adds validation for a numerical column called "length". - FastqGzFormat ************* A gzipped fastq file. +ANCOMBC2OutputDirFmt +******************** + +Stores the model statistics and optionally the structural zeros table= +output by the ANCOMBC2 method. + +The slices are: + - lfc: log-fold change + - se: standard error + - W: lfc / se (the test statistic) + - p: p-value + - q: adjusted p-value + - diff: differentially abundant boolean (i.e. q < alpha) + - passed_ss: whether sensitivity analysis was passed + Additional formats without documentation: ***************************************** + - BooleanSeriesFormat + - ProcrustesStatisticsFmt + - DADA2StatsDirFmt + - BAMDirFmt + - ProbabilitiesDirectoryFormat + - BLAST6Format + - PlacementsFormat + - BIOMV210DirFmt + - SingleLanePerSampleSingleEndFastqDirFmt + - RNAFASTAFormat + - SILVATaxidMapFormat + - EMPPairedEndDirFmt + - EggnogProteinSequencesDirFmt + - SingleLanePerSamplePairedEndFastqDirFmt + - TSVTaxonomyDirectoryFormat + - SampleEstimatorDirFmt + - DeblurStatsFmt + - EggnogRefDirFmt + - MAGtoContigsFormat + - MultiplexedSingleEndBarcodeInSequenceDirFmt + - MultiBAMDirFmt + - TrueTargetsDirectoryFormat + - BLAST6DirectoryFormat + - MAGtoContigsDirFmt + - QualityFilterStatsFmt + - RNASequencesDirectoryFormat + - NewickFormat + - ImportanceFormat + - ProteinSequencesDirectoryFormat + - ImportanceDirectoryFormat + - OrdinationFormat + - DecontamScoreDirFmt + - Kraken2ReportDirectoryFormat + - AlignedRNAFASTAFormat + - ArtificialGroupingDirectoryFormat + - DiamondDatabaseFileFmt + - FirstDifferencesFormat + - LSMatFormat + - ArtificialGroupingFormat + - TaxonomicClassiferTemporaryPickleDirFmt + - ProteinSingleProfileHmmDirectoryFmt + - MAGSequencesDirFmt + - TableJSONLFileFormat + - ProteinFASTAFormat + - ProbabilitiesFormat + - AlignedRNASequencesDirectoryFormat + - SequenceCharacteristicsDirectoryFormat + - SILVATaxidMapDirectoryFormat + - LociDirectoryFormat + - DistanceMatrixDirectoryFormat + - ProteinMultipleProfileHmmDirectoryFmt + - MultiFASTADirectoryFormat + - BLASTDBDirFmtV5 + - DecontamScoreFormat + - DNAFASTAFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - Kraken2OutputDirectoryFormat + - ProteinsDirectoryFormat + - Kraken2DBReportFormat + - PlacementsDirFmt + - GenomeSequencesDirectoryFormat + - PairedDNASequencesDirectoryFormat + - BIOMV210Format + - AlphaDiversityFormat + - DNASingleProfileHmmDirectoryFmt + - SILVATaxonomyDirectoryFormat + - MultiMAGSequencesDirFmt + - AlignedProteinFASTAFormat + - ImmutableMetadataDirectoryFormat + - GenesDirectoryFormat + - UchimeStatsDirFmt + - FirstDifferencesDirectoryFormat + - NewickDirectoryFormat + - PairedRNASequencesDirectoryFormat + - AlphaDiversityDirectoryFormat + - MultiBowtie2IndexDirFmt + - AlignedProteinSequencesDirectoryFormat + - SILVATaxonomyFormat + - BrackenDBDirectoryFormat + - TableJSONLDirFmt - DifferentialFormat - DNASequencesDirectoryFormat - - Kraken2OutputDirectoryFormat - - MultiBAMDirFmt - - FirstDifferencesFormat + - DeblurStatsDirFmt + - DADA2StatsFormat + - Kraken2DBDirectoryFormat + - Bowtie2IndexDirFmt + - Kraken2DBReportDirectoryFormat + - SeedOrthologDirFmt + - QualityFilterStatsDirFmt - AlignedDNAFASTAFormat - ProcrustesStatisticsDirFmt - - EggnogProteinSequencesDirFmt - - DifferentialDirectoryFormat - - MAGSequencesDirFmt - - ProteinSingleProfileHmmDirectoryFmt - - ImportanceFormat + - RNASingleProfileHmmDirectoryFmt + - ContigSequencesDirFmt - ImmutableMetadataFormat - - ErrorCorrectionDetailsFmt - - ArtificialGroupingFormat - - OrthologAnnotationDirFmt - - DecontamScoreFormat - - FirstDifferencesDirectoryFormat - - TrueTargetsDirectoryFormat - - AlignedDNASequencesDirectoryFormat - - QualityFilterStatsFmt - - DeblurStatsFmt - BooleanSeriesDirectoryFormat - - BIOMV210DirFmt - - OrdinationFormat - - LSMatFormat - - ProteinMultipleProfileHmmDirectoryFmt - - ImportanceDirectoryFormat - - ImmutableMetadataDirectoryFormat - - ErrorCorrectionDetailsDirFmt - - SingleLanePerSamplePairedEndFastqDirFmt - - Kraken2DBDirectoryFormat - - OrdinationDirectoryFormat - - BooleanSeriesFormat - - BLASTDBDirFmtV5 - - DADA2StatsFormat - - BLAST6Format - - KaijuDBDirectoryFormat - - ArtificialGroupingDirectoryFormat - - MultiFASTADirectoryFormat - - MAGtoContigsFormat - - DNASingleProfileHmmDirectoryFmt - - RNAFASTAFormat - - ProbabilitiesFormat - - SampleEstimatorDirFmt - - MultiplexedPairedEndBarcodeInSequenceDirFmt - - TableJSONLFileFormat - - LociDirectoryFormat - - QualityFilterStatsDirFmt - - TSVTaxonomyDirectoryFormat - - UchimeStatsFmt - - ProcrustesStatisticsFmt - - SILVATaxonomyDirectoryFormat - - AlphaDiversityFormat - - BLAST6DirectoryFormat - - MultiMAGSequencesDirFmt + - DiamondDatabaseDirFmt - SeppReferenceDirFmt - - DNAMultipleProfileHmmDirectoryFmt - - RNASequencesDirectoryFormat - - ProbabilitiesDirectoryFormat + - DifferentialDirectoryFormat + - CasavaOneEightSingleLanePerSampleDirFmt + - NCBITaxonomyDirFmt + - ErrorCorrectionDetailsFmt + - DataLoafPackageDirFmt + - OrthologAnnotationDirFmt - PredictionsFormat - - PlacementsFormat - - NewickFormat - - TableJSONLDirFmt - - BrackenDBDirectoryFormat - - ProteinSequencesDirectoryFormat - - GenomeSequencesDirectoryFormat - - MultiplexedSingleEndBarcodeInSequenceDirFmt - - EggnogRefDirFmt - - UchimeStatsDirFmt - - AlignedRNAFASTAFormat - - EMPSingleEndDirFmt - - DADA2StatsDirFmt - - TaxonomicClassiferTemporaryPickleDirFmt - - AlphaDiversityDirectoryFormat - - Kraken2ReportDirectoryFormat - - MultiBowtie2IndexDirFmt - - SILVATaxidMapFormat - - CasavaOneEightSingleLanePerSampleDirFmt - - RNASingleProfileHmmDirectoryFmt + - OrdinationDirectoryFormat + - AlignedDNASequencesDirectoryFormat - PredictionsDirectoryFormat - - DeblurStatsDirFmt - - Bowtie2IndexDirFmt - - SeedOrthologDirFmt - - DiamondDatabaseFileFmt - - ProteinFASTAFormat - - AlignedRNASequencesDirectoryFormat - - EMPPairedEndDirFmt - - NewickDirectoryFormat - - SequenceCharacteristicsDirectoryFormat - - ContigSequencesDirFmt - - Kraken2DBReportFormat - RNAMultipleProfileHmmDirectoryFmt - - PlacementsDirFmt - - DecontamScoreDirFmt - - SILVATaxonomyFormat - - DataLoafPackageDirFmt - - SILVATaxidMapDirectoryFormat - - DNAFASTAFormat - - ProteinsDirectoryFormat - - MAGtoContigsDirFmt + - DNAMultipleProfileHmmDirectoryFmt + - UchimeStatsFmt + - ErrorCorrectionDetailsDirFmt + - EMPSingleEndDirFmt + - KaijuDBDirectoryFormat - QIIME1DemuxDirFmt - - DiamondDatabaseDirFmt - - Kraken2DBReportDirectoryFormat - - PairedDNASequencesDirectoryFormat - - NCBITaxonomyDirFmt - - DistanceMatrixDirectoryFormat - - BIOMV210Format - - AlignedProteinFASTAFormat - - SingleLanePerSampleSingleEndFastqDirFmt - - BAMDirFmt - - PairedRNASequencesDirectoryFormat - - AlignedProteinSequencesDirectoryFormat - - GenesDirectoryFormat </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>