Mercurial > repos > q2d2 > qiime2_core__tools__export
changeset 5:37e37518cad1 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit c7e80dcda727ce63b42aa8a946e9330310929797
| author | q2d2 |
|---|---|
| date | Mon, 03 Jun 2024 23:32:51 +0000 |
| parents | e96704fc516d |
| children | 40bcc0e139fa |
| files | qiime2_core__tools__export.xml |
| diffstat | 1 files changed, 331 insertions(+), 78 deletions(-) [+] |
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--- a/qiime2_core__tools__export.xml Thu Apr 25 21:28:08 2024 +0000 +++ b/qiime2_core__tools__export.xml Mon Jun 03 23:32:51 2024 +0000 @@ -6,14 +6,14 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2024.2.1) + q2galaxy (version: 2024.5.0) for: - qiime2 (version: 2024.2.0) + qiime2 (version: 2024.5.0) --> -<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2024.2.1+dist.he188c3c2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2024.5.0+dist.he540b0b0" profile="22.05" license="BSD-3-Clause"> <description>Export data from a QIIME 2 artifact</description> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2024.2</container> + <container type="docker">quay.io/qiime2/amplicon:2024.5</container> </requirements> <command>q2galaxy run tools export '$inputs'</command> <configfiles> @@ -36,6 +36,7 @@ <option value="None" selected="true">export as is (no conversion)</option> <option value="BLASTDB">BLASTDB</option> <option value="Bowtie2Index">Bowtie2Index</option> + <option value="BrackenDB">BrackenDB</option> <option value="DeblurStats">DeblurStats</option> <option value="DistanceMatrix">DistanceMatrix</option> <option value="EMPPairedEndSequences">EMPPairedEndSequences</option> @@ -44,18 +45,28 @@ <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> + <option value="FeatureData__ob__AlignmentMap__cb__">FeatureData[AlignmentMap]</option> <option value="FeatureData__ob__BLAST6__cb__">FeatureData[BLAST6]</option> + <option value="FeatureData__ob__Contig__cb__">FeatureData[Contig]</option> <option value="FeatureData__ob__DecontamScore__cb__">FeatureData[DecontamScore]</option> <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> <option value="FeatureData__ob__RNASequence__cb__">FeatureData[RNASequence]</option> <option value="FeatureData__ob__SILVATaxidMap__cb__">FeatureData[SILVATaxidMap]</option> <option value="FeatureData__ob__SILVATaxonomy__cb__">FeatureData[SILVATaxonomy]</option> + <option value="FeatureData__ob__SequenceCharacteristics__cb__">FeatureData[SequenceCharacteristics]</option> <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__MAGtoContigs__cb__">FeatureMap[MAGtoContigs]</option> <option value="FeatureTable__ob__Balance__cb__">FeatureTable[Balance]</option> @@ -71,6 +82,9 @@ <option value="GenomeData__ob__Proteins__cb__">GenomeData[Proteins]</option> <option value="Hierarchy">Hierarchy</option> <option value="ImmutableMetadata">ImmutableMetadata</option> + <option value="KaijuDB">KaijuDB</option> + <option value="Kraken2DB">Kraken2DB</option> + <option value="Kraken2DBReport">Kraken2DBReport</option> <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option> <option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option> <option value="PCoAResults">PCoAResults</option> @@ -80,6 +94,10 @@ <option value="ProcrustesStatistics">ProcrustesStatistics</option> <option value="QualityFilterStats">QualityFilterStats</option> <option value="RawSequences">RawSequences</option> + <option value="ReferenceDB__ob__Diamond__cb__">ReferenceDB[Diamond]</option> + <option value="ReferenceDB__ob__EggnogProteinSequences__cb__">ReferenceDB[EggnogProteinSequences]</option> + <option value="ReferenceDB__ob__Eggnog__cb__">ReferenceDB[Eggnog]</option> + <option value="ReferenceDB__ob__NCBITaxonomy__cb__">ReferenceDB[NCBITaxonomy]</option> <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> @@ -90,6 +108,8 @@ <option value="SampleData__ob__DADA2Stats__cb__">SampleData[DADA2Stats]</option> <option value="SampleData__ob__FirstDifferences__cb__">SampleData[FirstDifferences]</option> <option value="SampleData__ob__JoinedSequencesWithQuality__cb__">SampleData[JoinedSequencesWithQuality]</option> + <option value="SampleData__ob__Kraken2Output__cb__">SampleData[Kraken2Output]</option> + <option value="SampleData__ob__Kraken2Report__cb__">SampleData[Kraken2Report]</option> <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> @@ -123,6 +143,12 @@ <option value="Bowtie2IndexDirFmt">Bowtie2 Index Directory Format</option> </param> </when> + <when value="BrackenDB"> + <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="BrackenDBDirectoryFormat">Bracken DB Directory Format</option> + </param> + </when> <when value="DeblurStats"> <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> @@ -150,6 +176,7 @@ <when value="ErrorCorrectionDetails"> <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="ErrorCorrectionDetailsFmt">Error Correction Details Format</option> </param> </when> <when value="FeatureData__ob__AlignedProteinSequence__cb__"> @@ -170,12 +197,24 @@ <option value="AlignedDNAFASTAFormat">Aligned DNAFASTA Format</option> </param> </when> + <when value="FeatureData__ob__AlignmentMap__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="BAMDirFmt">BAM Directory Format</option> + </param> + </when> <when value="FeatureData__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="BLAST6Format">BLAST6 Format</option> </param> </when> + <when value="FeatureData__ob__Contig__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="ContigSequencesDirFmt">Contig Sequences Directory Format</option> + </param> + </when> <when value="FeatureData__ob__DecontamScore__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> @@ -200,6 +239,42 @@ <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> + <option value="Kraken2OutputDirectoryFormat">Kraken2 Output Directory Format</option> + </param> + </when> + <when value="FeatureData__ob__Kraken2Report__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="Kraken2ReportDirectoryFormat">Kraken2 Report Directory Format</option> + </param> + </when> + <when value="FeatureData__ob__MAG__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="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> @@ -237,12 +312,24 @@ <option value="SILVATaxonomyFormat">SILVA Taxonomy Format</option> </param> </when> + <when value="FeatureData__ob__SequenceCharacteristics__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="SequenceCharacteristicsFormat">Sequence Characteristics Format</option> + </param> + </when> <when value="FeatureData__ob__Sequence__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="DNAFASTAFormat">DNAFASTA Format</option> </param> </when> + <when value="FeatureData__ob__SingleBowtie2Index__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="Bowtie2IndexDirFmt">Bowtie2 Index Directory Format</option> + </param> + </when> <when value="FeatureData__ob__Taxonomy__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> @@ -259,6 +346,7 @@ <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> @@ -266,6 +354,7 @@ <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> @@ -273,6 +362,7 @@ <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> @@ -280,6 +370,7 @@ <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> @@ -287,6 +378,7 @@ <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> @@ -294,6 +386,7 @@ <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> @@ -301,6 +394,7 @@ <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> @@ -340,6 +434,23 @@ <option value="ImmutableMetadataFormat">Immutable Metadata Format</option> </param> </when> + <when value="KaijuDB"> + <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="KaijuDBDirectoryFormat">Kaiju DB Directory Format</option> + </param> + </when> + <when value="Kraken2DB"> + <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="Kraken2DBDirectoryFormat">Kraken2DB Directory Format</option> + </param> + </when> + <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> + </param> + </when> <when value="MultiplexedPairedEndBarcodeInSequence"> <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> @@ -394,6 +505,30 @@ <option value="EMPSingleEndDirFmt">EMP Single End Directory Format</option> </param> </when> + <when value="ReferenceDB__ob__Diamond__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="DiamondDatabaseFileFmt">Diamond Database File Format</option> + </param> + </when> + <when value="ReferenceDB__ob__EggnogProteinSequences__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="EggnogProteinSequencesDirFmt">Eggnog Protein Sequences Directory Format</option> + </param> + </when> + <when value="ReferenceDB__ob__Eggnog__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="EggnogRefDirFmt">Eggnog Ref Directory Format</option> + </param> + </when> + <when value="ReferenceDB__ob__NCBITaxonomy__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="NCBITaxonomyDirFmt">NCBI Taxonomy Directory Format</option> + </param> + </when> <when value="SampleData__ob__AlignmentMap__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> @@ -456,9 +591,22 @@ <option value="SingleLanePerSampleSingleEndFastqDirFmt">Single Lane Per Sample Single End Fastq Directory Format</option> </param> </when> + <when value="SampleData__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> + <option value="Kraken2OutputDirectoryFormat">Kraken2 Output Directory Format</option> + </param> + </when> + <when value="SampleData__ob__Kraken2Report__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="Kraken2ReportDirectoryFormat">Kraken2 Report Directory Format</option> + </param> + </when> <when value="SampleData__ob__MAGs__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="MultiFASTADirectoryFormat">Multi FASTA Directory Format</option> <option value="MultiMAGSequencesDirFmt">Multi MAG Sequences Directory Format</option> </param> </when> @@ -554,7 +702,7 @@ </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 {'PairedDNASequencesDirectoryFormat', 'DataLoafPackageDirFmt', 'BIOMV210Format', 'BLAST6DirectoryFormat', 'ProteinFASTAFormat', 'ProbabilitiesFormat', 'MultiBowtie2IndexDirFmt', 'MultiMAGSequencesDirFmt', 'ImmutableMetadataFormat', 'DecontamScoreFormat', 'SILVATaxidMapFormat', 'AlignedProteinFASTAFormat', 'NewickFormat', 'PredictionsFormat', 'AlignedProteinSequencesDirectoryFormat', 'SeppReferenceDirFmt', 'TaxonomicClassiferTemporaryPickleDirFmt', 'PlacementsDirFmt', 'ImmutableMetadataDirectoryFormat', 'CasavaOneEightSingleLanePerSampleDirFmt', 'EMPPairedEndDirFmt', 'RNAFASTAFormat', 'EMPSingleEndDirFmt', 'ProcrustesStatisticsDirFmt', 'DADA2StatsDirFmt', 'ErrorCorrectionDetailsDirFmt', 'ProbabilitiesDirectoryFormat', 'MultiBAMDirFmt', 'SeedOrthologDirFmt', 'AlignedRNASequencesDirectoryFormat', 'MAGtoContigsDirFmt', 'DifferentialDirectoryFormat', 'QualityFilterStatsDirFmt', 'SILVATaxonomyFormat', 'DADA2StatsFormat', 'UchimeStatsFmt', 'DecontamScoreDirFmt', 'SingleLanePerSamplePairedEndFastqDirFmt', 'RNASequencesDirectoryFormat', 'SingleLanePerSampleSingleEndFastqDirFmt', 'DNAFASTAFormat', 'BooleanSeriesDirectoryFormat', 'LociDirectoryFormat', 'NewickDirectoryFormat', 'ProteinSequencesDirectoryFormat', 'DeblurStatsFmt', 'BooleanSeriesFormat', 'OrdinationFormat', 'AlphaDiversityFormat', 'TSVTaxonomyFormat', 'SampleEstimatorDirFmt', 'MAGtoContigsFormat', 'SILVATaxonomyDirectoryFormat', 'QIIME1DemuxDirFmt', 'BLASTDBDirFmtV5', 'ProteinsDirectoryFormat', 'LSMatFormat', 'PredictionsDirectoryFormat', 'DifferentialFormat', 'BAMDirFmt', 'ArtificialGroupingFormat', 'ImportanceDirectoryFormat', 'DNASequencesDirectoryFormat', 'SILVATaxidMapDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'QIIME1DemuxFormat', 'OrdinationDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'QualityFilterStatsFmt', 'PairedRNASequencesDirectoryFormat', 'DeblurStatsDirFmt', 'ContigSequencesDirFmt', 'GenesDirectoryFormat', 'ImportanceFormat', 'ProcrustesStatisticsFmt', 'ArtificialGroupingDirectoryFormat', 'FirstDifferencesDirectoryFormat', 'BLAST6Format', 'TSVTaxonomyDirectoryFormat', 'AlphaDiversityDirectoryFormat', 'BIOMV210DirFmt', 'TrueTargetsDirectoryFormat', 'AlignedDNASequencesDirectoryFormat', 'FastqGzFormat', 'AlignedRNAFASTAFormat', 'AlignedDNAFASTAFormat', 'FirstDifferencesFormat', 'Bowtie2IndexDirFmt', 'UchimeStatsDirFmt', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'PlacementsFormat'}</filter> + <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> <discover_datasets pattern="__designation_and_ext__" visible="false"/> </collection> <data name="AlignedDNAFASTAFormat" label="${tool.name} on ${on_string} as AlignedDNAFASTAFormat"> @@ -645,6 +793,10 @@ <discover_datasets pattern="(?P<designation>.+\.rev\.1)\.(?P<ext>bt2l?)" visible="true"/> <discover_datasets pattern="(?P<designation>.+\.rev\.2)\.(?P<ext>bt2l?)" visible="true"/> </data> + <collection name="BrackenDBDirectoryFormat_kmers" type="list" label="${tool.name} on ${on_string} as BrackenDBDirectoryFormat (kmers)"> + <filter>fmt_finder['output_format'] == 'BrackenDBDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BrackenDBDirectoryFormat')</filter> + <discover_datasets pattern="(?P<designation>database(\d{2,})mers)\.(?P<ext>kmer_distrib$)" visible="false"/> + </collection> <collection name="CasavaOneEightSingleLanePerSampleDirFmt_sequences" type="list" label="${tool.name} on ${on_string} as CasavaOneEightSingleLanePerSampleDirFmt (sequences)"> <filter>fmt_finder['output_format'] == 'CasavaOneEightSingleLanePerSampleDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'CasavaOneEightSingleLanePerSampleDirFmt')</filter> <discover_datasets pattern="(?P<designation>.+_.+_L[0-9][0-9][0-9]_R[12]_001)\.(?P<ext>fastq\.gz)" visible="false"/> @@ -693,6 +845,14 @@ <filter>fmt_finder['output_format'] == 'DecontamScoreFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DecontamScoreFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <data name="DiamondDatabaseDirFmt" label="${tool.name} on ${on_string} as DiamondDatabaseDirFmt"> + <filter>fmt_finder['output_format'] == 'DiamondDatabaseDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DiamondDatabaseDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>ref_db)\.(?P<ext>dmnd)" visible="true"/> + </data> + <data name="DiamondDatabaseFileFmt" label="${tool.name} on ${on_string} as DiamondDatabaseFileFmt"> + <filter>fmt_finder['output_format'] == 'DiamondDatabaseFileFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DiamondDatabaseFileFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> <data name="DifferentialDirectoryFormat" label="${tool.name} on ${on_string} as DifferentialDirectoryFormat"> <filter>fmt_finder['output_format'] == 'DifferentialDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DifferentialDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>differentials)\.(?P<ext>tsv)" visible="true"/> @@ -716,10 +876,23 @@ <discover_datasets assign_primary_output="true" pattern="(?P<designation>sequences)\.(?P<ext>fastq.gz)" visible="true"/> <discover_datasets pattern="(?P<designation>barcodes)\.(?P<ext>fastq.gz)" visible="true"/> </data> + <data name="EggnogProteinSequencesDirFmt" label="${tool.name} on ${on_string} as EggnogProteinSequencesDirFmt"> + <filter>fmt_finder['output_format'] == 'EggnogProteinSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'EggnogProteinSequencesDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>e5.taxid_info)\.(?P<ext>tsv)" visible="true"/> + <discover_datasets pattern="(?P<designation>e5.proteomes)\.(?P<ext>faa)" visible="true"/> + </data> + <collection name="EggnogRefDirFmt_eggnog" type="list" label="${tool.name} on ${on_string} as EggnogRefDirFmt (eggnog)"> + <filter>fmt_finder['output_format'] == 'EggnogRefDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'EggnogRefDirFmt')</filter> + <discover_datasets pattern="(?P<designation>eggnog.*db)\.(?P<ext>*)" visible="false"/> + </collection> <data name="ErrorCorrectionDetailsDirFmt" label="${tool.name} on ${on_string} as ErrorCorrectionDetailsDirFmt"> <filter>fmt_finder['output_format'] == 'ErrorCorrectionDetailsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ErrorCorrectionDetailsDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>details)\.(?P<ext>tsv)" visible="true"/> </data> + <data name="ErrorCorrectionDetailsFmt" label="${tool.name} on ${on_string} as ErrorCorrectionDetailsFmt"> + <filter>fmt_finder['output_format'] == 'ErrorCorrectionDetailsFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ErrorCorrectionDetailsFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> <data name="FastqGzFormat" label="${tool.name} on ${on_string} as FastqGzFormat"> <filter>fmt_finder['output_format'] == 'FastqGzFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'FastqGzFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> @@ -734,7 +907,7 @@ </data> <collection name="GenesDirectoryFormat_genes" type="list" label="${tool.name} on ${on_string} as GenesDirectoryFormat (genes)"> <filter>fmt_finder['output_format'] == 'GenesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'GenesDirectoryFormat')</filter> - <discover_datasets pattern="(?P<designation>(.*\_)?genes[0-9]*)\.(?P<ext>(fa|fna|fasta)$)" visible="false"/> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>(fa|fna|fasta)$)" visible="false"/> </collection> <data name="ImmutableMetadataDirectoryFormat" label="${tool.name} on ${on_string} as ImmutableMetadataDirectoryFormat"> <filter>fmt_finder['output_format'] == 'ImmutableMetadataDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ImmutableMetadataDirectoryFormat')</filter> @@ -752,13 +925,41 @@ <filter>fmt_finder['output_format'] == 'ImportanceFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ImportanceFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <data name="KaijuDBDirectoryFormat" label="${tool.name} on ${on_string} as KaijuDBDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'KaijuDBDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'KaijuDBDirectoryFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>nodes)\.(?P<ext>dmp)" visible="true"/> + <discover_datasets pattern="(?P<designation>names)\.(?P<ext>dmp)" visible="true"/> + <discover_datasets pattern="(?P<designation>kaiju_db.+)\.(?P<ext>fmi)" visible="true"/> + </data> + <data name="Kraken2DBDirectoryFormat" label="${tool.name} on ${on_string} as Kraken2DBDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'Kraken2DBDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBDirectoryFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>hash)\.(?P<ext>k2d)" visible="true"/> + <discover_datasets pattern="(?P<designation>opts)\.(?P<ext>k2d)" visible="true"/> + <discover_datasets pattern="(?P<designation>taxo)\.(?P<ext>k2d)" visible="true"/> + </data> + <data name="Kraken2DBReportDirectoryFormat" label="${tool.name} on ${on_string} as Kraken2DBReportDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'Kraken2DBReportDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBReportDirectoryFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>report)\.(?P<ext>txt)" visible="true"/> + </data> + <collection name="Kraken2OutputDirectoryFormat_reports" type="list" label="${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"/> + </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"/> + </collection> <data name="LSMatFormat" label="${tool.name} on ${on_string} as LSMatFormat"> <filter>fmt_finder['output_format'] == 'LSMatFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'LSMatFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <collection name="LociDirectoryFormat_loci" type="list" label="${tool.name} on ${on_string} as LociDirectoryFormat (loci)"> <filter>fmt_finder['output_format'] == 'LociDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'LociDirectoryFormat')</filter> - <discover_datasets pattern="(?P<designation>(.*\_)?loci[0-9]*)\.(?P<ext>gff$)" visible="false"/> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>gff$)" visible="false"/> + </collection> + <collection name="MAGSequencesDirFmt_sequences" type="list" label="${tool.name} on ${on_string} as MAGSequencesDirFmt (sequences)"> + <filter>fmt_finder['output_format'] == 'MAGSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MAGSequencesDirFmt')</filter> + <discover_datasets pattern="(?P<designation>^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12})\.(?P<ext>(fa|fasta)$)" visible="false"/> </collection> <data name="MAGtoContigsDirFmt" label="${tool.name} on ${on_string} as MAGtoContigsDirFmt"> <filter>fmt_finder['output_format'] == 'MAGtoContigsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MAGtoContigsDirFmt')</filter> @@ -781,6 +982,10 @@ <discover_datasets pattern="(?P<designation>.+\.rev\.1)\.(?P<ext>bt2l?)" visible="true"/> <discover_datasets pattern="(?P<designation>.+\.rev\.2)\.(?P<ext>bt2l?)" visible="true"/> </data> + <collection name="MultiFASTADirectoryFormat_sequences" type="list" label="${tool.name} on ${on_string} as MultiFASTADirectoryFormat (sequences)"> + <filter>fmt_finder['output_format'] == 'MultiFASTADirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiFASTADirectoryFormat')</filter> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>(fa|fasta)$)" visible="false"/> + </collection> <collection name="MultiMAGSequencesDirFmt_sequences" type="list" label="${tool.name} on ${on_string} as MultiMAGSequencesDirFmt (sequences)"> <filter>fmt_finder['output_format'] == 'MultiMAGSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiMAGSequencesDirFmt')</filter> <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>(fa|fasta)$)" visible="false"/> @@ -798,6 +1003,12 @@ <filter>fmt_finder['output_format'] == 'MultiplexedSingleEndBarcodeInSequenceDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiplexedSingleEndBarcodeInSequenceDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>forward)\.(?P<ext>fastq.gz)" visible="true"/> </data> + <data name="NCBITaxonomyDirFmt" label="${tool.name} on ${on_string} as NCBITaxonomyDirFmt"> + <filter>fmt_finder['output_format'] == 'NCBITaxonomyDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'NCBITaxonomyDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>nodes)\.(?P<ext>dmp)" visible="true"/> + <discover_datasets pattern="(?P<designation>names)\.(?P<ext>dmp)" visible="true"/> + <discover_datasets pattern="(?P<designation>prot)\.(?P<ext>accession2taxid.gz)" visible="true"/> + </data> <data name="NewickDirectoryFormat" label="${tool.name} on ${on_string} as NewickDirectoryFormat"> <filter>fmt_finder['output_format'] == 'NewickDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'NewickDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>tree)\.(?P<ext>nwk)" visible="true"/> @@ -814,6 +1025,10 @@ <filter>fmt_finder['output_format'] == 'OrdinationFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'OrdinationFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <collection name="OrthologAnnotationDirFmt_annotations" type="list" label="${tool.name} on ${on_string} as OrthologAnnotationDirFmt (annotations)"> + <filter>fmt_finder['output_format'] == 'OrthologAnnotationDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'OrthologAnnotationDirFmt')</filter> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>annotations)" visible="false"/> + </collection> <data name="PairedDNASequencesDirectoryFormat" label="${tool.name} on ${on_string} as PairedDNASequencesDirectoryFormat"> <filter>fmt_finder['output_format'] == 'PairedDNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PairedDNASequencesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>left-dna-sequences)\.(?P<ext>fasta)" visible="true"/> @@ -866,7 +1081,7 @@ </data> <collection name="ProteinsDirectoryFormat_proteins" type="list" label="${tool.name} on ${on_string} as ProteinsDirectoryFormat (proteins)"> <filter>fmt_finder['output_format'] == 'ProteinsDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinsDirectoryFormat')</filter> - <discover_datasets pattern="(?P<designation>(.*\_)?proteins[0-9]*)\.(?P<ext>(fa|faa|fasta)$)" visible="false"/> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>(fa|faa|fasta)$)" visible="false"/> </collection> <data name="QIIME1DemuxDirFmt" label="${tool.name} on ${on_string} as QIIME1DemuxDirFmt"> <filter>fmt_finder['output_format'] == 'QIIME1DemuxDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'QIIME1DemuxDirFmt')</filter> @@ -923,6 +1138,14 @@ <discover_datasets pattern="(?P<designation>tree)\.(?P<ext>nwk)" visible="true"/> <discover_datasets pattern="(?P<designation>raxml-info)\.(?P<ext>txt)" visible="true"/> </data> + <data name="SequenceCharacteristicsDirectoryFormat" label="${tool.name} on ${on_string} as SequenceCharacteristicsDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'SequenceCharacteristicsDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SequenceCharacteristicsDirectoryFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>sequence_characteristics)\.(?P<ext>tsv)" visible="true"/> + </data> + <data name="SequenceCharacteristicsFormat" label="${tool.name} on ${on_string} as SequenceCharacteristicsFormat"> + <filter>fmt_finder['output_format'] == 'SequenceCharacteristicsFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SequenceCharacteristicsFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> <collection name="SingleLanePerSamplePairedEndFastqDirFmt_sequences" type="list" label="${tool.name} on ${on_string} as SingleLanePerSamplePairedEndFastqDirFmt (sequences)"> <filter>fmt_finder['output_format'] == 'SingleLanePerSamplePairedEndFastqDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SingleLanePerSamplePairedEndFastqDirFmt')</filter> <discover_datasets pattern="(?P<designation>.+_.+_L[0-9][0-9][0-9]_R[12]_001)\.(?P<ext>fastq\.gz)" visible="false"/> @@ -1031,6 +1254,20 @@ - 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". + TSVTaxonomyFormat ***************** Format for a 2+ column TSV file with an expected minimal header. @@ -1048,94 +1285,110 @@ Additional formats without documentation: ***************************************** + - DataLoafPackageDirFmt + - EggnogRefDirFmt + - NCBITaxonomyDirFmt + - BIOMV210DirFmt + - FirstDifferencesDirectoryFormat + - PredictionsDirectoryFormat + - QIIME1DemuxDirFmt + - SILVATaxonomyFormat + - MAGSequencesDirFmt + - AlphaDiversityDirectoryFormat + - Kraken2OutputDirectoryFormat - BAMDirFmt - - TaxonomicClassiferTemporaryPickleDirFmt - - ProbabilitiesDirectoryFormat - - BooleanSeriesFormat - - ErrorCorrectionDetailsDirFmt - - AlignedRNASequencesDirectoryFormat - - ProcrustesStatisticsDirFmt - - DifferentialDirectoryFormat - - SampleEstimatorDirFmt - - PlacementsDirFmt - - SILVATaxidMapDirectoryFormat - - BIOMV210DirFmt - - MultiBAMDirFmt - - QualityFilterStatsDirFmt - - TrueTargetsDirectoryFormat - - MAGtoContigsFormat - - ArtificialGroupingDirectoryFormat - - BooleanSeriesDirectoryFormat - - PlacementsFormat - - PredictionsFormat - - MultiplexedPairedEndBarcodeInSequenceDirFmt - - DeblurStatsDirFmt + - TSVTaxonomyDirectoryFormat + - EggnogProteinSequencesDirFmt + - ImmutableMetadataFormat + - LSMatFormat - SingleLanePerSampleSingleEndFastqDirFmt - AlignedProteinFASTAFormat - PairedDNASequencesDirectoryFormat - - UchimeStatsDirFmt - - DataLoafPackageDirFmt - - ArtificialGroupingFormat - - PredictionsDirectoryFormat - - SILVATaxonomyDirectoryFormat - - DNAFASTAFormat - - EMPSingleEndDirFmt - - SingleLanePerSamplePairedEndFastqDirFmt + - BooleanSeriesFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - DecontamScoreFormat + - OrthologAnnotationDirFmt + - GenesDirectoryFormat + - MultiBAMDirFmt + - BIOMV210Format + - DecontamScoreDirFmt + - ErrorCorrectionDetailsFmt + - DiamondDatabaseFileFmt - AlignedProteinSequencesDirectoryFormat - PairedRNASequencesDirectoryFormat - - SeppReferenceDirFmt - - MAGtoContigsDirFmt - DifferentialFormat - - UchimeStatsFmt - - SILVATaxonomyFormat - - FirstDifferencesDirectoryFormat + - Kraken2DBDirectoryFormat + - DADA2StatsFormat - DNASequencesDirectoryFormat - - GenesDirectoryFormat - - EMPPairedEndDirFmt + - ErrorCorrectionDetailsDirFmt + - DiamondDatabaseDirFmt + - ImmutableMetadataDirectoryFormat + - BooleanSeriesDirectoryFormat - AlignedDNAFASTAFormat - - SILVATaxidMapFormat - - ProteinsDirectoryFormat - - MultiMAGSequencesDirFmt + - ImportanceFormat + - NewickFormat + - DistanceMatrixDirectoryFormat + - SingleLanePerSamplePairedEndFastqDirFmt + - PlacementsDirFmt + - DeblurStatsFmt + - SILVATaxidMapDirectoryFormat - QualityFilterStatsFmt - AlignedDNASequencesDirectoryFormat - - LSMatFormat - - ImmutableMetadataFormat - - DeblurStatsFmt - - AlphaDiversityFormat - - MultiBowtie2IndexDirFmt - - ImportanceFormat - - FirstDifferencesFormat - - DADA2StatsFormat - - DistanceMatrixDirectoryFormat - - ImmutableMetadataDirectoryFormat - - OrdinationFormat - - DecontamScoreDirFmt - - CasavaOneEightSingleLanePerSampleDirFmt + - ImportanceDirectoryFormat + - NewickDirectoryFormat - MultiplexedSingleEndBarcodeInSequenceDirFmt - - AlphaDiversityDirectoryFormat + - MultiFASTADirectoryFormat + - ProcrustesStatisticsFmt + - SILVATaxidMapFormat + - UchimeStatsDirFmt + - Kraken2ReportDirectoryFormat + - BLAST6Format + - QualityFilterStatsDirFmt + - ProbabilitiesFormat + - SILVATaxonomyDirectoryFormat + - MultiMAGSequencesDirFmt + - EMPSingleEndDirFmt + - Bowtie2IndexDirFmt + - ProcrustesStatisticsDirFmt + - DeblurStatsDirFmt + - ArtificialGroupingDirectoryFormat + - TaxonomicClassiferTemporaryPickleDirFmt + - LociDirectoryFormat + - ArtificialGroupingFormat + - MAGtoContigsFormat + - BrackenDBDirectoryFormat - ProteinFASTAFormat - RNAFASTAFormat - - ContigSequencesDirFmt - - ImportanceDirectoryFormat - DADA2StatsDirFmt - - NewickFormat - - OrdinationDirectoryFormat - - TSVTaxonomyDirectoryFormat - - BLAST6Format - - LociDirectoryFormat + - BLAST6DirectoryFormat + - ProbabilitiesDirectoryFormat + - MultiBowtie2IndexDirFmt + - EMPPairedEndDirFmt + - OrdinationFormat + - SeedOrthologDirFmt + - MAGtoContigsDirFmt + - SampleEstimatorDirFmt + - PlacementsFormat - ProteinSequencesDirectoryFormat - RNASequencesDirectoryFormat - - BIOMV210Format - - ProbabilitiesFormat - - BLASTDBDirFmtV5 - - DecontamScoreFormat + - DNAFASTAFormat + - UchimeStatsFmt - AlignedRNAFASTAFormat - - NewickDirectoryFormat - - ProcrustesStatisticsFmt - - BLAST6DirectoryFormat - - SeedOrthologDirFmt - - QIIME1DemuxDirFmt - - Bowtie2IndexDirFmt + - TrueTargetsDirectoryFormat + - Kraken2DBReportDirectoryFormat + - KaijuDBDirectoryFormat + - ContigSequencesDirFmt + - FirstDifferencesFormat + - SeppReferenceDirFmt + - OrdinationDirectoryFormat + - PredictionsFormat + - ProteinsDirectoryFormat + - BLASTDBDirFmtV5 + - AlignedRNASequencesDirectoryFormat + - SequenceCharacteristicsDirectoryFormat + - AlphaDiversityFormat + - CasavaOneEightSingleLanePerSampleDirFmt + - DifferentialDirectoryFormat </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>