Mercurial > repos > q2d2 > qiime2_core__tools__export
changeset 6:40bcc0e139fa draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 5f71b597c9495eae67a447744fded834f56ca1f7
| author | q2d2 |
|---|---|
| date | Wed, 30 Oct 2024 20:00:17 +0000 |
| parents | 37e37518cad1 |
| children | |
| files | qiime2_core__tools__export.xml |
| diffstat | 1 files changed, 362 insertions(+), 142 deletions(-) [+] |
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--- a/qiime2_core__tools__export.xml Mon Jun 03 23:32:51 2024 +0000 +++ b/qiime2_core__tools__export.xml Wed Oct 30 20:00:17 2024 +0000 @@ -6,14 +6,17 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2024.5.0) + q2galaxy (version: 2024.10.0) for: - qiime2 (version: 2024.5.0) + qiime2 (version: 2024.10.1) --> -<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2024.5.0+dist.he540b0b0" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2024.10.0+dist.h3d8a7e27" 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:2024.5</container> + <container type="docker">quay.io/qiime2/amplicon:2024.10</container> </requirements> <command>q2galaxy run tools export '$inputs'</command> <configfiles> @@ -38,6 +41,16 @@ <option value="Bowtie2Index">Bowtie2Index</option> <option value="BrackenDB">BrackenDB</option> <option value="DeblurStats">DeblurStats</option> + <option value="Dist1D__ob__Multi__comma__ Independent__cb__">Dist1D[Multi, Independent]</option> + <option value="Dist1D__ob__Multi__comma__ Matched__cb__">Dist1D[Multi, Matched]</option> + <option value="Dist1D__ob__NestedOrdered__comma__ Independent__cb__">Dist1D[NestedOrdered, Independent]</option> + <option value="Dist1D__ob__NestedOrdered__comma__ Matched__cb__">Dist1D[NestedOrdered, Matched]</option> + <option value="Dist1D__ob__NestedUnordered__comma__ Independent__cb__">Dist1D[NestedUnordered, Independent]</option> + <option value="Dist1D__ob__NestedUnordered__comma__ Matched__cb__">Dist1D[NestedUnordered, Matched]</option> + <option value="Dist1D__ob__Ordered__comma__ Independent__cb__">Dist1D[Ordered, Independent]</option> + <option value="Dist1D__ob__Ordered__comma__ Matched__cb__">Dist1D[Ordered, Matched]</option> + <option value="Dist1D__ob__Unordered__comma__ Independent__cb__">Dist1D[Unordered, Independent]</option> + <option value="Dist1D__ob__Unordered__comma__ Matched__cb__">Dist1D[Unordered, Matched]</option> <option value="DistanceMatrix">DistanceMatrix</option> <option value="EMPPairedEndSequences">EMPPairedEndSequences</option> <option value="EMPSingleEndSequences">EMPSingleEndSequences</option> @@ -52,12 +65,9 @@ <option value="FeatureData__ob__DifferentialAbundance__cb__">FeatureData[DifferentialAbundance]</option> <option value="FeatureData__ob__Differential__cb__">FeatureData[Differential]</option> <option value="FeatureData__ob__Importance__cb__">FeatureData[Importance]</option> - <option value="FeatureData__ob__KEGG__cb__">FeatureData[KEGG]</option> <option value="FeatureData__ob__Kraken2Output__cb__">FeatureData[Kraken2Output]</option> <option value="FeatureData__ob__Kraken2Report__cb__">FeatureData[Kraken2Report]</option> <option value="FeatureData__ob__MAG__cb__">FeatureData[MAG]</option> - <option value="FeatureData__ob__NOG__cb__">FeatureData[NOG]</option> - <option value="FeatureData__ob__OG__cb__">FeatureData[OG]</option> <option value="FeatureData__ob__PairedEndRNASequence__cb__">FeatureData[PairedEndRNASequence]</option> <option value="FeatureData__ob__PairedEndSequence__cb__">FeatureData[PairedEndSequence]</option> <option value="FeatureData__ob__ProteinSequence__cb__">FeatureData[ProteinSequence]</option> @@ -73,12 +83,15 @@ <option value="FeatureTable__ob__Composition__cb__">FeatureTable[Composition]</option> <option value="FeatureTable__ob__Design__cb__">FeatureTable[Design]</option> <option value="FeatureTable__ob__Frequency__cb__">FeatureTable[Frequency]</option> + <option value="FeatureTable__ob__Normalized__cb__">FeatureTable[Normalized]</option> <option value="FeatureTable__ob__PercentileNormalized__cb__">FeatureTable[PercentileNormalized]</option> <option value="FeatureTable__ob__PresenceAbsence__cb__">FeatureTable[PresenceAbsence]</option> <option value="FeatureTable__ob__RelativeFrequency__cb__">FeatureTable[RelativeFrequency]</option> - <option value="GenomeData__ob__BLAST6__cb__">GenomeData[BLAST6]</option> + <option value="GenomeData__ob__DNASequence__cb__">GenomeData[DNASequence]</option> <option value="GenomeData__ob__Genes__cb__">GenomeData[Genes]</option> <option value="GenomeData__ob__Loci__cb__">GenomeData[Loci]</option> + <option value="GenomeData__ob__NOG__cb__">GenomeData[NOG]</option> + <option value="GenomeData__ob__Orthologs__cb__">GenomeData[Orthologs]</option> <option value="GenomeData__ob__Proteins__cb__">GenomeData[Proteins]</option> <option value="Hierarchy">Hierarchy</option> <option value="ImmutableMetadata">ImmutableMetadata</option> @@ -92,6 +105,15 @@ <option value="Phylogeny__ob__Unrooted__cb__">Phylogeny[Unrooted]</option> <option value="Placements">Placements</option> <option value="ProcrustesStatistics">ProcrustesStatistics</option> + <option value="ProfileHMM__ob__MultipleDNA__cb__">ProfileHMM[MultipleDNA]</option> + <option value="ProfileHMM__ob__MultipleProtein__cb__">ProfileHMM[MultipleProtein]</option> + <option value="ProfileHMM__ob__MultipleRNA__cb__">ProfileHMM[MultipleRNA]</option> + <option value="ProfileHMM__ob__PressedDNA__cb__">ProfileHMM[PressedDNA]</option> + <option value="ProfileHMM__ob__PressedProtein__cb__">ProfileHMM[PressedProtein]</option> + <option value="ProfileHMM__ob__PressedRNA__cb__">ProfileHMM[PressedRNA]</option> + <option value="ProfileHMM__ob__SingleDNA__cb__">ProfileHMM[SingleDNA]</option> + <option value="ProfileHMM__ob__SingleProtein__cb__">ProfileHMM[SingleProtein]</option> + <option value="ProfileHMM__ob__SingleRNA__cb__">ProfileHMM[SingleRNA]</option> <option value="QualityFilterStats">QualityFilterStats</option> <option value="RawSequences">RawSequences</option> <option value="ReferenceDB__ob__Diamond__cb__">ReferenceDB[Diamond]</option> @@ -101,7 +123,6 @@ <option value="SampleData__ob__AlignmentMap__cb__">SampleData[AlignmentMap]</option> <option value="SampleData__ob__AlphaDiversity__cb__">SampleData[AlphaDiversity]</option> <option value="SampleData__ob__ArtificialGrouping__cb__">SampleData[ArtificialGrouping]</option> - <option value="SampleData__ob__BLAST6__cb__">SampleData[BLAST6]</option> <option value="SampleData__ob__BooleanSeries__cb__">SampleData[BooleanSeries]</option> <option value="SampleData__ob__ClassifierPredictions__cb__">SampleData[ClassifierPredictions]</option> <option value="SampleData__ob__Contigs__cb__">SampleData[Contigs]</option> @@ -113,6 +134,8 @@ <option value="SampleData__ob__MAGs__cb__">SampleData[MAGs]</option> <option value="SampleData__ob__MultiAlignmentMap__cb__">SampleData[MultiAlignmentMap]</option> <option value="SampleData__ob__MultiBowtie2Index__cb__">SampleData[MultiBowtie2Index]</option> + <option value="SampleData__ob__NOG__cb__">SampleData[NOG]</option> + <option value="SampleData__ob__Orthologs__cb__">SampleData[Orthologs]</option> <option value="SampleData__ob__PairedEndSequencesWithQuality__cb__">SampleData[PairedEndSequencesWithQuality]</option> <option value="SampleData__ob__Probabilities__cb__">SampleData[Probabilities]</option> <option value="SampleData__ob__RegressorPredictions__cb__">SampleData[RegressorPredictions]</option> @@ -123,6 +146,7 @@ <option value="SampleEstimator__ob__Classifier__cb__">SampleEstimator[Classifier]</option> <option value="SampleEstimator__ob__Regressor__cb__">SampleEstimator[Regressor]</option> <option value="SeppReferenceDatabase">SeppReferenceDatabase</option> + <option value="StatsTable__ob__Pairwise__cb__">StatsTable[Pairwise]</option> <option value="TaxonomicClassifier">TaxonomicClassifier</option> <option value="UchimeStats">UchimeStats</option> </param> @@ -155,6 +179,66 @@ <option value="DeblurStatsFmt">Deblur Stats Format</option> </param> </when> + <when value="Dist1D__ob__Multi__comma__ Independent__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="TableJSONLFileFormat">Table JSONL File Format</option> + </param> + </when> + <when value="Dist1D__ob__Multi__comma__ Matched__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="TableJSONLFileFormat">Table JSONL File Format</option> + </param> + </when> + <when value="Dist1D__ob__NestedOrdered__comma__ Independent__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="TableJSONLFileFormat">Table JSONL File Format</option> + </param> + </when> + <when value="Dist1D__ob__NestedOrdered__comma__ Matched__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="TableJSONLFileFormat">Table JSONL File Format</option> + </param> + </when> + <when value="Dist1D__ob__NestedUnordered__comma__ Independent__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="TableJSONLFileFormat">Table JSONL File Format</option> + </param> + </when> + <when value="Dist1D__ob__NestedUnordered__comma__ Matched__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="TableJSONLFileFormat">Table JSONL File Format</option> + </param> + </when> + <when value="Dist1D__ob__Ordered__comma__ Independent__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="TableJSONLFileFormat">Table JSONL File Format</option> + </param> + </when> + <when value="Dist1D__ob__Ordered__comma__ Matched__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="TableJSONLFileFormat">Table JSONL File Format</option> + </param> + </when> + <when value="Dist1D__ob__Unordered__comma__ Independent__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="TableJSONLFileFormat">Table JSONL File Format</option> + </param> + </when> + <when value="Dist1D__ob__Unordered__comma__ Matched__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="TableJSONLFileFormat">Table JSONL File Format</option> + </param> + </when> <when value="DistanceMatrix"> <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> @@ -239,12 +323,6 @@ <option value="ImportanceFormat">Importance Format</option> </param> </when> - <when value="FeatureData__ob__KEGG__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="OrthologAnnotationDirFmt">Ortholog Annotation Directory Format</option> - </param> - </when> <when value="FeatureData__ob__Kraken2Output__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> @@ -263,18 +341,6 @@ <option value="MAGSequencesDirFmt">MAG Sequences Directory Format</option> </param> </when> - <when value="FeatureData__ob__NOG__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="OrthologAnnotationDirFmt">Ortholog Annotation Directory Format</option> - </param> - </when> - <when value="FeatureData__ob__OG__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="OrthologAnnotationDirFmt">Ortholog Annotation Directory Format</option> - </param> - </when> <when value="FeatureData__ob__PairedEndRNASequence__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> @@ -374,6 +440,14 @@ <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> </param> </when> + <when value="FeatureTable__ob__Normalized__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="BIOMV210Format">BIOMV210 Format</option> + <option value="DNAFASTAFormat">DNAFASTA Format</option> + <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> + </param> + </when> <when value="FeatureTable__ob__PercentileNormalized__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> @@ -398,10 +472,10 @@ <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> </param> </when> - <when value="GenomeData__ob__BLAST6__cb__"> + <when value="GenomeData__ob__DNASequence__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="SeedOrthologDirFmt">Seed Ortholog Directory Format</option> + <option value="GenomeSequencesDirectoryFormat">Genome Sequences Directory Format</option> </param> </when> <when value="GenomeData__ob__Genes__cb__"> @@ -416,6 +490,18 @@ <option value="LociDirectoryFormat">Loci Directory Format</option> </param> </when> + <when value="GenomeData__ob__NOG__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="OrthologAnnotationDirFmt">Ortholog Annotation Directory Format</option> + </param> + </when> + <when value="GenomeData__ob__Orthologs__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="SeedOrthologDirFmt">Seed Ortholog Directory Format</option> + </param> + </when> <when value="GenomeData__ob__Proteins__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> @@ -449,6 +535,7 @@ <when value="Kraken2DBReport"> <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="Kraken2DBReportFormat">Kraken2DB Report Format</option> </param> </when> <when value="MultiplexedPairedEndBarcodeInSequence"> @@ -493,6 +580,60 @@ <option value="ProcrustesStatisticsFmt">Procrustes Statistics Format</option> </param> </when> + <when value="ProfileHMM__ob__MultipleDNA__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="DNAMultipleProfileHmmDirectoryFmt">DNA Multiple Profile Hmm Directory Format</option> + </param> + </when> + <when value="ProfileHMM__ob__MultipleProtein__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="ProteinMultipleProfileHmmDirectoryFmt">Protein Multiple Profile Hmm Directory Format</option> + </param> + </when> + <when value="ProfileHMM__ob__MultipleRNA__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="RNAMultipleProfileHmmDirectoryFmt">RNA Multiple Profile Hmm Directory Format</option> + </param> + </when> + <when value="ProfileHMM__ob__PressedDNA__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="PressedProfileHmmsDirectoryFmt">Pressed Profile Hmms Directory Format</option> + </param> + </when> + <when value="ProfileHMM__ob__PressedProtein__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="PressedProfileHmmsDirectoryFmt">Pressed Profile Hmms Directory Format</option> + </param> + </when> + <when value="ProfileHMM__ob__PressedRNA__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="PressedProfileHmmsDirectoryFmt">Pressed Profile Hmms Directory Format</option> + </param> + </when> + <when value="ProfileHMM__ob__SingleDNA__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="DNASingleProfileHmmDirectoryFmt">DNA Single Profile Hmm Directory Format</option> + </param> + </when> + <when value="ProfileHMM__ob__SingleProtein__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="ProteinSingleProfileHmmDirectoryFmt">Protein Single Profile Hmm Directory Format</option> + </param> + </when> + <when value="ProfileHMM__ob__SingleRNA__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="RNASingleProfileHmmDirectoryFmt">RNA Single Profile Hmm Directory Format</option> + </param> + </when> <when value="QualityFilterStats"> <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> @@ -547,12 +688,6 @@ <option value="ArtificialGroupingFormat">Artificial Grouping Format</option> </param> </when> - <when value="SampleData__ob__BLAST6__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="SeedOrthologDirFmt">Seed Ortholog Directory Format</option> - </param> - </when> <when value="SampleData__ob__BooleanSeries__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> @@ -622,6 +757,18 @@ <option value="MultiBowtie2IndexDirFmt">Multi Bowtie2 Index Directory Format</option> </param> </when> + <when value="SampleData__ob__NOG__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="OrthologAnnotationDirFmt">Ortholog Annotation Directory Format</option> + </param> + </when> + <when value="SampleData__ob__Orthologs__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="SeedOrthologDirFmt">Seed Ortholog Directory Format</option> + </param> + </when> <when value="SampleData__ob__PairedEndSequencesWithQuality__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> @@ -686,6 +833,12 @@ <option value="SeppReferenceDirFmt">Sepp Reference Directory Format</option> </param> </when> + <when value="StatsTable__ob__Pairwise__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="TableJSONLFileFormat">Table JSONL File Format</option> + </param> + </when> <when value="TaxonomicClassifier"> <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> @@ -702,7 +855,7 @@ </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 {'PredictionsDirectoryFormat', 'QualityFilterStatsDirFmt', 'ProteinSequencesDirectoryFormat', 'OrthologAnnotationDirFmt', 'FirstDifferencesDirectoryFormat', 'DecontamScoreDirFmt', 'BooleanSeriesFormat', 'Bowtie2IndexDirFmt', 'GenesDirectoryFormat', 'AlphaDiversityFormat', 'SILVATaxidMapFormat', 'RNASequencesDirectoryFormat', 'MultiBAMDirFmt', 'AlignedDNAFASTAFormat', 'SILVATaxonomyDirectoryFormat', 'SeedOrthologDirFmt', 'QIIME1DemuxDirFmt', 'ImportanceDirectoryFormat', 'BooleanSeriesDirectoryFormat', 'BLAST6DirectoryFormat', 'BAMDirFmt', 'ImmutableMetadataFormat', 'QualityFilterStatsFmt', 'Kraken2DBReportDirectoryFormat', 'SingleLanePerSamplePairedEndFastqDirFmt', 'MAGtoContigsDirFmt', 'AlignedRNASequencesDirectoryFormat', 'NewickFormat', 'NewickDirectoryFormat', 'ProcrustesStatisticsFmt', 'EMPSingleEndDirFmt', 'PlacementsFormat', 'LSMatFormat', 'OrdinationFormat', 'AlignedProteinFASTAFormat', 'DifferentialFormat', 'SILVATaxidMapDirectoryFormat', 'CasavaOneEightSingleLanePerSampleDirFmt', 'ProbabilitiesFormat', 'DADA2StatsFormat', 'DNASequencesDirectoryFormat', 'EMPPairedEndDirFmt', 'SequenceCharacteristicsFormat', 'DiamondDatabaseFileFmt', 'ImmutableMetadataDirectoryFormat', 'OrdinationDirectoryFormat', 'MultiBowtie2IndexDirFmt', 'SILVATaxonomyFormat', 'DistanceMatrixDirectoryFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'DiamondDatabaseDirFmt', 'BIOMV210DirFmt', 'BIOMV210Format', 'LociDirectoryFormat', 'QIIME1DemuxFormat', 'Kraken2ReportDirectoryFormat', 'TSVTaxonomyFormat', 'KaijuDBDirectoryFormat', 'ErrorCorrectionDetailsFmt', 'NCBITaxonomyDirFmt', 'AlignedProteinSequencesDirectoryFormat', 'ProteinFASTAFormat', 'AlphaDiversityDirectoryFormat', 'FastqGzFormat', 'ImportanceFormat', 'ContigSequencesDirFmt', 'RNAFASTAFormat', 'ErrorCorrectionDetailsDirFmt', 'SequenceCharacteristicsDirectoryFormat', 'UchimeStatsDirFmt', 'MAGSequencesDirFmt', 'PairedRNASequencesDirectoryFormat', 'DNAFASTAFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'DataLoafPackageDirFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'MultiFASTADirectoryFormat', 'BLASTDBDirFmtV5', 'BrackenDBDirectoryFormat', 'FirstDifferencesFormat', 'TSVTaxonomyDirectoryFormat', 'DifferentialDirectoryFormat', 'MultiMAGSequencesDirFmt', 'PlacementsDirFmt', 'BLAST6Format', 'AlignedRNAFASTAFormat', 'TrueTargetsDirectoryFormat', 'ArtificialGroupingDirectoryFormat', 'ProcrustesStatisticsDirFmt', 'ProteinsDirectoryFormat', 'MAGtoContigsFormat', 'AlignedDNASequencesDirectoryFormat', 'ArtificialGroupingFormat', 'SeppReferenceDirFmt', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'EggnogProteinSequencesDirFmt', 'ProbabilitiesDirectoryFormat', 'DeblurStatsDirFmt', 'DADA2StatsDirFmt', 'DecontamScoreFormat', 'UchimeStatsFmt', 'SampleEstimatorDirFmt', 'EggnogRefDirFmt', 'DeblurStatsFmt', 'PairedDNASequencesDirectoryFormat', 'Kraken2OutputDirectoryFormat', 'PredictionsFormat', 'Kraken2DBDirectoryFormat'}</filter> + <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> <discover_datasets pattern="__designation_and_ext__" visible="false"/> </collection> <data name="AlignedDNAFASTAFormat" label="${tool.name} on ${on_string} as AlignedDNAFASTAFormat"> @@ -817,10 +970,18 @@ <filter>fmt_finder['output_format'] == 'DNAFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNAFASTAFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <data name="DNAMultipleProfileHmmDirectoryFmt" label="${tool.name} on ${on_string} as DNAMultipleProfileHmmDirectoryFmt"> + <filter>fmt_finder['output_format'] == 'DNAMultipleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNAMultipleProfileHmmDirectoryFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>.*)\.(?P<ext>hmm)" visible="true"/> + </data> <data name="DNASequencesDirectoryFormat" label="${tool.name} on ${on_string} as DNASequencesDirectoryFormat"> <filter>fmt_finder['output_format'] == 'DNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNASequencesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>dna-sequences)\.(?P<ext>fasta)" visible="true"/> </data> + <data name="DNASingleProfileHmmDirectoryFmt" label="${tool.name} on ${on_string} as DNASingleProfileHmmDirectoryFmt"> + <filter>fmt_finder['output_format'] == 'DNASingleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNASingleProfileHmmDirectoryFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>.*)\.(?P<ext>hmm)" visible="true"/> + </data> <collection name="DataLoafPackageDirFmt_data_slices" type="list" label="${tool.name} on ${on_string} as DataLoafPackageDirFmt (data_slices)"> <filter>fmt_finder['output_format'] == 'DataLoafPackageDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DataLoafPackageDirFmt')</filter> <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>csv)" visible="false"/> @@ -909,6 +1070,10 @@ <filter>fmt_finder['output_format'] == 'GenesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'GenesDirectoryFormat')</filter> <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>(fa|fna|fasta)$)" visible="false"/> </collection> + <collection name="GenomeSequencesDirectoryFormat_genomes" type="list" label="${tool.name} on ${on_string} as GenomeSequencesDirectoryFormat (genomes)"> + <filter>fmt_finder['output_format'] == 'GenomeSequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'GenomeSequencesDirectoryFormat')</filter> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>(fasta|fa)$)" visible="false"/> + </collection> <data name="ImmutableMetadataDirectoryFormat" label="${tool.name} on ${on_string} as ImmutableMetadataDirectoryFormat"> <filter>fmt_finder['output_format'] == 'ImmutableMetadataDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ImmutableMetadataDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>metadata)\.(?P<ext>tsv)" visible="true"/> @@ -941,6 +1106,10 @@ <filter>fmt_finder['output_format'] == 'Kraken2DBReportDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBReportDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>report)\.(?P<ext>txt)" visible="true"/> </data> + <data name="Kraken2DBReportFormat" label="${tool.name} on ${on_string} as Kraken2DBReportFormat"> + <filter>fmt_finder['output_format'] == 'Kraken2DBReportFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBReportFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> <collection name="Kraken2OutputDirectoryFormat_reports" type="list" label="${tool.name} on ${on_string} as Kraken2OutputDirectoryFormat (reports)"> <filter>fmt_finder['output_format'] == 'Kraken2OutputDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2OutputDirectoryFormat')</filter> <discover_datasets pattern="(?P<designation>.+output)\.(?P<ext>(txt|tsv)$)" visible="false"/> @@ -1055,6 +1224,13 @@ <filter>fmt_finder['output_format'] == 'PredictionsFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PredictionsFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <data name="PressedProfileHmmsDirectoryFmt" label="${tool.name} on ${on_string} as PressedProfileHmmsDirectoryFmt"> + <filter>fmt_finder['output_format'] == 'PressedProfileHmmsDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PressedProfileHmmsDirectoryFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>.*\.hmm)\.(?P<ext>h3m)" visible="true"/> + <discover_datasets pattern="(?P<designation>.*\.hmm)\.(?P<ext>h3i)" visible="true"/> + <discover_datasets pattern="(?P<designation>.*\.hmm)\.(?P<ext>h3f)" visible="true"/> + <discover_datasets pattern="(?P<designation>.*\.hmm)\.(?P<ext>h3p)" visible="true"/> + </data> <data name="ProbabilitiesDirectoryFormat" label="${tool.name} on ${on_string} as ProbabilitiesDirectoryFormat"> <filter>fmt_finder['output_format'] == 'ProbabilitiesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProbabilitiesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>class_probabilities)\.(?P<ext>tsv)" visible="true"/> @@ -1075,10 +1251,18 @@ <filter>fmt_finder['output_format'] == 'ProteinFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinFASTAFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <data name="ProteinMultipleProfileHmmDirectoryFmt" label="${tool.name} on ${on_string} as ProteinMultipleProfileHmmDirectoryFmt"> + <filter>fmt_finder['output_format'] == 'ProteinMultipleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinMultipleProfileHmmDirectoryFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>.*)\.(?P<ext>hmm)" visible="true"/> + </data> <data name="ProteinSequencesDirectoryFormat" label="${tool.name} on ${on_string} as ProteinSequencesDirectoryFormat"> <filter>fmt_finder['output_format'] == 'ProteinSequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinSequencesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>protein-sequences)\.(?P<ext>fasta)" visible="true"/> </data> + <data name="ProteinSingleProfileHmmDirectoryFmt" label="${tool.name} on ${on_string} as ProteinSingleProfileHmmDirectoryFmt"> + <filter>fmt_finder['output_format'] == 'ProteinSingleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinSingleProfileHmmDirectoryFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>.*)\.(?P<ext>hmm)" visible="true"/> + </data> <collection name="ProteinsDirectoryFormat_proteins" type="list" label="${tool.name} on ${on_string} as ProteinsDirectoryFormat (proteins)"> <filter>fmt_finder['output_format'] == 'ProteinsDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinsDirectoryFormat')</filter> <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>(fa|faa|fasta)$)" visible="false"/> @@ -1103,10 +1287,18 @@ <filter>fmt_finder['output_format'] == 'RNAFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNAFASTAFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <data name="RNAMultipleProfileHmmDirectoryFmt" label="${tool.name} on ${on_string} as RNAMultipleProfileHmmDirectoryFmt"> + <filter>fmt_finder['output_format'] == 'RNAMultipleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNAMultipleProfileHmmDirectoryFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>.*)\.(?P<ext>hmm)" visible="true"/> + </data> <data name="RNASequencesDirectoryFormat" label="${tool.name} on ${on_string} as RNASequencesDirectoryFormat"> <filter>fmt_finder['output_format'] == 'RNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNASequencesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>rna-sequences)\.(?P<ext>fasta)" visible="true"/> </data> + <data name="RNASingleProfileHmmDirectoryFmt" label="${tool.name} on ${on_string} as RNASingleProfileHmmDirectoryFmt"> + <filter>fmt_finder['output_format'] == 'RNASingleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNASingleProfileHmmDirectoryFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>.*)\.(?P<ext>hmm)" visible="true"/> + </data> <data name="SILVATaxidMapDirectoryFormat" label="${tool.name} on ${on_string} as SILVATaxidMapDirectoryFormat"> <filter>fmt_finder['output_format'] == 'SILVATaxidMapDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SILVATaxidMapDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>silva_taxmap)\.(?P<ext>tsv)" visible="true"/> @@ -1172,6 +1364,14 @@ <filter>fmt_finder['output_format'] == 'TSVTaxonomyFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TSVTaxonomyFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <data name="TableJSONLDirFmt" label="${tool.name} on ${on_string} as TableJSONLDirFmt"> + <filter>fmt_finder['output_format'] == 'TableJSONLDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TableJSONLDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>data.table)\.(?P<ext>jsonl)" visible="true"/> + </data> + <data name="TableJSONLFileFormat" label="${tool.name} on ${on_string} as TableJSONLFileFormat"> + <filter>fmt_finder['output_format'] == 'TableJSONLFileFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TableJSONLFileFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> <data name="TaxonomicClassiferTemporaryPickleDirFmt" label="${tool.name} on ${on_string} as TaxonomicClassiferTemporaryPickleDirFmt"> <filter>fmt_finder['output_format'] == 'TaxonomicClassiferTemporaryPickleDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TaxonomicClassiferTemporaryPickleDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>sklearn_version)\.(?P<ext>json)" visible="true"/> @@ -1214,10 +1414,29 @@ -------- These formats have documentation available. -FastqGzFormat -************* +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. -A gzipped fastq file. +TSVTaxonomyFormat +***************** +Format for a 2+ column TSV file with an expected minimal header. + +The only header recognized by this format is: + + Feature ID<tab>Taxon + +Optionally followed by other arbitrary columns. + +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. QIIME1DemuxFormat @@ -1268,127 +1487,128 @@ "FeatureData[SequenceCharacteristics % Properties("length")]" adds validation for a numerical column called "length". -TSVTaxonomyFormat -***************** -Format for a 2+ column TSV file with an expected minimal header. - -The only header recognized by this format is: +FastqGzFormat +************* - Feature ID<tab>Taxon - -Optionally followed by other arbitrary columns. - -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. +A gzipped fastq file. Additional formats without documentation: ***************************************** - - DataLoafPackageDirFmt - - EggnogRefDirFmt - - NCBITaxonomyDirFmt - - BIOMV210DirFmt - - FirstDifferencesDirectoryFormat - - PredictionsDirectoryFormat - - QIIME1DemuxDirFmt - - SILVATaxonomyFormat - - MAGSequencesDirFmt - - AlphaDiversityDirectoryFormat + - DifferentialFormat + - DNASequencesDirectoryFormat - Kraken2OutputDirectoryFormat - - BAMDirFmt - - TSVTaxonomyDirectoryFormat - - EggnogProteinSequencesDirFmt - - ImmutableMetadataFormat - - LSMatFormat - - SingleLanePerSampleSingleEndFastqDirFmt - - AlignedProteinFASTAFormat - - PairedDNASequencesDirectoryFormat - - BooleanSeriesFormat - - MultiplexedPairedEndBarcodeInSequenceDirFmt - - DecontamScoreFormat - - OrthologAnnotationDirFmt - - GenesDirectoryFormat - MultiBAMDirFmt - - BIOMV210Format - - DecontamScoreDirFmt + - FirstDifferencesFormat + - AlignedDNAFASTAFormat + - ProcrustesStatisticsDirFmt + - EggnogProteinSequencesDirFmt + - DifferentialDirectoryFormat + - MAGSequencesDirFmt + - ProteinSingleProfileHmmDirectoryFmt + - ImportanceFormat + - ImmutableMetadataFormat - ErrorCorrectionDetailsFmt - - DiamondDatabaseFileFmt - - AlignedProteinSequencesDirectoryFormat - - PairedRNASequencesDirectoryFormat - - DifferentialFormat - - Kraken2DBDirectoryFormat - - DADA2StatsFormat - - DNASequencesDirectoryFormat - - ErrorCorrectionDetailsDirFmt - - DiamondDatabaseDirFmt + - ArtificialGroupingFormat + - OrthologAnnotationDirFmt + - DecontamScoreFormat + - FirstDifferencesDirectoryFormat + - TrueTargetsDirectoryFormat + - AlignedDNASequencesDirectoryFormat + - QualityFilterStatsFmt + - DeblurStatsFmt + - BooleanSeriesDirectoryFormat + - BIOMV210DirFmt + - OrdinationFormat + - LSMatFormat + - ProteinMultipleProfileHmmDirectoryFmt + - ImportanceDirectoryFormat - ImmutableMetadataDirectoryFormat - - BooleanSeriesDirectoryFormat - - AlignedDNAFASTAFormat - - ImportanceFormat - - NewickFormat - - DistanceMatrixDirectoryFormat + - ErrorCorrectionDetailsDirFmt - SingleLanePerSamplePairedEndFastqDirFmt - - PlacementsDirFmt - - DeblurStatsFmt - - SILVATaxidMapDirectoryFormat - - QualityFilterStatsFmt - - AlignedDNASequencesDirectoryFormat - - ImportanceDirectoryFormat - - NewickDirectoryFormat + - 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 + - SeppReferenceDirFmt + - DNAMultipleProfileHmmDirectoryFmt + - RNASequencesDirectoryFormat + - ProbabilitiesDirectoryFormat + - PredictionsFormat + - PlacementsFormat + - NewickFormat + - TableJSONLDirFmt + - BrackenDBDirectoryFormat + - ProteinSequencesDirectoryFormat + - GenomeSequencesDirectoryFormat - MultiplexedSingleEndBarcodeInSequenceDirFmt - - MultiFASTADirectoryFormat - - ProcrustesStatisticsFmt - - SILVATaxidMapFormat + - EggnogRefDirFmt - UchimeStatsDirFmt - - Kraken2ReportDirectoryFormat - - BLAST6Format - - QualityFilterStatsDirFmt - - ProbabilitiesFormat - - SILVATaxonomyDirectoryFormat - - MultiMAGSequencesDirFmt + - AlignedRNAFASTAFormat - EMPSingleEndDirFmt - - Bowtie2IndexDirFmt - - ProcrustesStatisticsDirFmt - - DeblurStatsDirFmt - - ArtificialGroupingDirectoryFormat + - DADA2StatsDirFmt - TaxonomicClassiferTemporaryPickleDirFmt - - LociDirectoryFormat - - ArtificialGroupingFormat - - MAGtoContigsFormat - - BrackenDBDirectoryFormat - - ProteinFASTAFormat - - RNAFASTAFormat - - DADA2StatsDirFmt - - BLAST6DirectoryFormat - - ProbabilitiesDirectoryFormat + - AlphaDiversityDirectoryFormat + - Kraken2ReportDirectoryFormat - MultiBowtie2IndexDirFmt + - SILVATaxidMapFormat + - CasavaOneEightSingleLanePerSampleDirFmt + - RNASingleProfileHmmDirectoryFmt + - PredictionsDirectoryFormat + - DeblurStatsDirFmt + - Bowtie2IndexDirFmt + - SeedOrthologDirFmt + - DiamondDatabaseFileFmt + - ProteinFASTAFormat + - AlignedRNASequencesDirectoryFormat - EMPPairedEndDirFmt - - OrdinationFormat - - SeedOrthologDirFmt + - NewickDirectoryFormat + - SequenceCharacteristicsDirectoryFormat + - ContigSequencesDirFmt + - Kraken2DBReportFormat + - RNAMultipleProfileHmmDirectoryFmt + - PlacementsDirFmt + - DecontamScoreDirFmt + - SILVATaxonomyFormat + - DataLoafPackageDirFmt + - SILVATaxidMapDirectoryFormat + - DNAFASTAFormat + - ProteinsDirectoryFormat - MAGtoContigsDirFmt - - SampleEstimatorDirFmt - - PlacementsFormat - - ProteinSequencesDirectoryFormat - - RNASequencesDirectoryFormat - - DNAFASTAFormat - - UchimeStatsFmt - - AlignedRNAFASTAFormat - - TrueTargetsDirectoryFormat + - QIIME1DemuxDirFmt + - DiamondDatabaseDirFmt - Kraken2DBReportDirectoryFormat - - KaijuDBDirectoryFormat - - ContigSequencesDirFmt - - FirstDifferencesFormat - - SeppReferenceDirFmt - - OrdinationDirectoryFormat - - PredictionsFormat - - ProteinsDirectoryFormat - - BLASTDBDirFmtV5 - - AlignedRNASequencesDirectoryFormat - - SequenceCharacteristicsDirectoryFormat - - AlphaDiversityFormat - - CasavaOneEightSingleLanePerSampleDirFmt - - DifferentialDirectoryFormat + - PairedDNASequencesDirectoryFormat + - NCBITaxonomyDirFmt + - DistanceMatrixDirectoryFormat + - BIOMV210Format + - AlignedProteinFASTAFormat + - SingleLanePerSampleSingleEndFastqDirFmt + - BAMDirFmt + - PairedRNASequencesDirectoryFormat + - AlignedProteinSequencesDirectoryFormat + - GenesDirectoryFormat </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>