Mercurial > repos > q2d2 > qiime2_core__tools__export
changeset 9:6d6617a57925 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b
| author | q2d2 |
|---|---|
| date | Sat, 01 Nov 2025 17:33:56 +0000 (3 hours ago) |
| parents | 61fb1a11e004 |
| children | |
| files | qiime2_core__tools__export.xml |
| diffstat | 1 files changed, 229 insertions(+), 147 deletions(-) [+] |
line wrap: on
line diff
--- a/qiime2_core__tools__export.xml Tue Jul 15 22:07:57 2025 +0000 +++ b/qiime2_core__tools__export.xml Sat Nov 01 17:33:56 2025 +0000 @@ -6,17 +6,17 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2025.7.0) + q2galaxy (version: 2025.10.0) for: - qiime2 (version: 2025.7.0) + qiime2 (version: 2025.10.0) --> -<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2025.7.0+dist.h44bd78f6" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2025.10.0+dist.hbfe50fe0" profile="22.05" license="BSD-3-Clause"> <description>Export data from a QIIME 2 artifact</description> <xrefs> <xref type="bio.tools">qiime2</xref> </xrefs> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2025.7</container> + <container type="docker">quay.io/qiime2/amplicon:2025.10</container> </requirements> <command>q2galaxy run tools export '$inputs'</command> <configfiles> @@ -40,6 +40,7 @@ <option value="BLASTDB">BLASTDB</option> <option value="Bowtie2Index">Bowtie2Index</option> <option value="BrackenDB">BrackenDB</option> + <option value="DADA2BaseTransitionStats">DADA2BaseTransitionStats</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> @@ -101,6 +102,7 @@ <option value="Kraken2DBReport">Kraken2DBReport</option> <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option> <option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option> + <option value="NCBIAccessionIDs">NCBIAccessionIDs</option> <option value="PCoAResults">PCoAResults</option> <option value="Phylogeny__ob__Rooted__cb__">Phylogeny[Rooted]</option> <option value="Phylogeny__ob__Unrooted__cb__">Phylogeny[Unrooted]</option> @@ -121,6 +123,8 @@ <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="SRAFailedIDs">SRAFailedIDs</option> + <option value="SRAMetadata">SRAMetadata</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> @@ -174,6 +178,12 @@ <option value="BrackenDBDirectoryFormat">Bracken DB Directory Format</option> </param> </when> + <when value="DADA2BaseTransitionStats"> + <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="DADA2BaseTransitionStatsFormat">DADA2 Base Transition Stats 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> @@ -557,6 +567,12 @@ <option value="FastqGzFormat">Fastq Gz Format</option> </param> </when> + <when value="NCBIAccessionIDs"> + <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="NCBIAccessionIDsFormat">NCBI Accession I Ds Format</option> + </param> + </when> <when value="PCoAResults"> <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> @@ -677,6 +693,19 @@ <option value="NCBITaxonomyDirFmt">NCBI Taxonomy Directory Format</option> </param> </when> + <when value="SRAFailedIDs"> + <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="SRAFailedIDsFormat">SRA Failed I Ds Format</option> + </param> + </when> + <when value="SRAMetadata"> + <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="NCBIAccessionIDsFormat">NCBI Accession I Ds Format</option> + <option value="SRAMetadataFormat">SRA Metadata 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> @@ -862,7 +891,7 @@ </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 {'SingleLanePerSampleSingleEndFastqDirFmt', 'BooleanSeriesDirectoryFormat', 'ProteinSingleProfileHmmDirectoryFmt', 'DifferentialFormat', 'NewickDirectoryFormat', 'MultiBAMDirFmt', 'ProbabilitiesFormat', 'NCBITaxonomyDirFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'LSMatFormat', 'RNAFASTAFormat', 'NewickFormat', 'ProteinMultipleProfileHmmDirectoryFmt', 'TableJSONLFileFormat', 'ProcrustesStatisticsDirFmt', 'GenomeSequencesDirectoryFormat', 'SILVATaxidMapFormat', 'KaijuDBDirectoryFormat', 'GenesDirectoryFormat', 'ImmutableMetadataDirectoryFormat', 'DeblurStatsDirFmt', 'ANCOMBC2OutputDirFmt', 'BAMDirFmt', 'TrueTargetsDirectoryFormat', 'PlacementsFormat', 'Bowtie2IndexDirFmt', 'PairedRNASequencesDirectoryFormat', 'ImportanceFormat', 'BLAST6DirectoryFormat', 'DiamondDatabaseDirFmt', 'Kraken2ReportDirectoryFormat', 'SeppReferenceDirFmt', 'ProcrustesStatisticsFmt', 'AlignedDNAFASTAFormat', 'QualityFilterStatsDirFmt', 'ContigSequencesDirFmt', 'BIOMV210Format', 'EggnogRefDirFmt', 'FirstDifferencesDirectoryFormat', 'PlacementsDirFmt', 'ArtificialGroupingDirectoryFormat', 'DNAMultipleProfileHmmDirectoryFmt', 'OrdinationFormat', 'ImportanceDirectoryFormat', 'PressedProfileHmmsDirectoryFmt', 'MAGtoContigsDirFmt', 'OrthologAnnotationDirFmt', 'DeblurStatsFmt', 'Kraken2DBDirectoryFormat', 'QualityFilterStatsFmt', 'SILVATaxonomyDirectoryFormat', 'UchimeStatsDirFmt', 'UchimeStatsFmt', 'MultiBowtie2IndexDirFmt', 'DataLoafPackageDirFmt', 'EggnogProteinSequencesDirFmt', 'EMPSingleEndDirFmt', 'DNAFASTAFormat', 'QIIME1DemuxFormat', 'AlignedDNASequencesDirectoryFormat', 'DADA2StatsFormat', 'AlignedProteinFASTAFormat', 'DecontamScoreFormat', 'RNASequencesDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'RNAMultipleProfileHmmDirectoryFmt', 'EMPPairedEndDirFmt', 'ProteinFASTAFormat', 'BooleanSeriesFormat', 'MultiFASTADirectoryFormat', 'AlignedRNASequencesDirectoryFormat', 'DifferentialDirectoryFormat', 'FastqGzFormat', 'BrackenDBDirectoryFormat', 'ImmutableMetadataFormat', 'PairedDNASequencesDirectoryFormat', 'OrdinationDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'AlignedProteinSequencesDirectoryFormat', 'SILVATaxidMapDirectoryFormat', 'DADA2StatsDirFmt', 'MAGtoContigsFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'BIOMV210DirFmt', 'SequenceCharacteristicsFormat', 'ProteinSequencesDirectoryFormat', 'SequenceCharacteristicsDirectoryFormat', 'Kraken2DBReportFormat', 'DiamondDatabaseFileFmt', 'AlignedRNAFASTAFormat', 'PredictionsFormat', 'SILVATaxonomyFormat', 'AlphaDiversityFormat', 'ProbabilitiesDirectoryFormat', 'ErrorCorrectionDetailsFmt', 'ProteinsDirectoryFormat', 'DNASequencesDirectoryFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'LociDirectoryFormat', 'DecontamScoreDirFmt', 'ErrorCorrectionDetailsDirFmt', 'RNASingleProfileHmmDirectoryFmt', 'TSVTaxonomyFormat', 'PredictionsDirectoryFormat', 'FirstDifferencesFormat', 'MultiMAGSequencesDirFmt', 'SingleLanePerSamplePairedEndFastqDirFmt', 'MAGSequencesDirFmt', 'ArtificialGroupingFormat', 'BLAST6Format', 'BLASTDBDirFmtV5', 'AlphaDiversityDirectoryFormat', 'TableJSONLDirFmt', 'SampleEstimatorDirFmt', 'Kraken2DBReportDirectoryFormat', 'Kraken2OutputDirectoryFormat', 'SeedOrthologDirFmt', 'QIIME1DemuxDirFmt', 'DNASingleProfileHmmDirectoryFmt', 'TSVTaxonomyDirectoryFormat'}</filter> + <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'FastqGzFormat', 'BLAST6Format', 'TaxonomicClassiferTemporaryPickleDirFmt', 'ANCOMBC2OutputDirFmt', 'EggnogProteinSequencesDirFmt', 'PredictionsFormat', 'DataLoafPackageDirFmt', 'Kraken2DBReportDirectoryFormat', 'DeblurStatsDirFmt', 'OrthologAnnotationDirFmt', 'ImmutableMetadataDirectoryFormat', 'PressedProfileHmmsDirectoryFmt', 'LociDirectoryFormat', 'ArtificialGroupingFormat', 'SRAMetadataFormat', 'PlacementsFormat', 'MAGtoContigsFormat', 'ImportanceFormat', 'DifferentialDirectoryFormat', 'EMPSingleEndDirFmt', 'SeppReferenceDirFmt', 'NewickFormat', 'BooleanSeriesFormat', 'ProteinsDirectoryFormat', 'ErrorCorrectionDetailsFmt', 'PredictionsDirectoryFormat', 'ProcrustesStatisticsFmt', 'MultiBAMDirFmt', 'ProteinSequencesDirectoryFormat', 'FirstDifferencesFormat', 'DNASequencesDirectoryFormat', 'DADA2StatsFormat', 'AlphaDiversityDirectoryFormat', 'ProteinFASTAFormat', 'DADA2BaseTransitionStatsFormat', 'RNAMultipleProfileHmmDirectoryFmt', 'ArtificialGroupingDirectoryFormat', 'KaijuDBDirectoryFormat', 'QualityFilterStatsFmt', 'BIOMV210DirFmt', 'UchimeStatsDirFmt', 'Kraken2DBReportFormat', 'SeedOrthologDirFmt', 'FirstDifferencesDirectoryFormat', 'DifferentialFormat', 'TrueTargetsDirectoryFormat', 'Kraken2DBDirectoryFormat', 'BLAST6DirectoryFormat', 'OrdinationDirectoryFormat', 'Kraken2OutputDirectoryFormat', 'BIOMV210Format', 'AlignedProteinSequencesDirectoryFormat', 'MAGtoContigsDirFmt', 'DecontamScoreDirFmt', 'RNAFASTAFormat', 'DistanceMatrixDirectoryFormat', 'SequenceCharacteristicsDirectoryFormat', 'QualityFilterStatsDirFmt', 'ProbabilitiesFormat', 'DADA2StatsDirFmt', 'Kraken2ReportDirectoryFormat', 'SingleLanePerSamplePairedEndFastqDirFmt', 'ErrorCorrectionDetailsDirFmt', 'SILVATaxidMapDirectoryFormat', 'SRAMetadataDirFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'AlignedRNAFASTAFormat', 'SequenceCharacteristicsFormat', 'MultiBowtie2IndexDirFmt', 'LSMatFormat', 'PlacementsDirFmt', 'BooleanSeriesDirectoryFormat', 'ProteinSingleProfileHmmDirectoryFmt', 'AlignedRNASequencesDirectoryFormat', 'GenomeSequencesDirectoryFormat', 'ContigSequencesDirFmt', 'SILVATaxidMapFormat', 'ImmutableMetadataFormat', 'DiamondDatabaseFileFmt', 'BLASTDBDirFmtV5', 'NCBITaxonomyDirFmt', 'SRAFailedIDsDirFmt', 'NCBIAccessionIDsFormat', 'QIIME1DemuxFormat', 'NCBIAccessionIDsDirFmt', 'RNASequencesDirectoryFormat', 'OrdinationFormat', 'DeblurStatsFmt', 'NewickDirectoryFormat', 'AlignedDNASequencesDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'DNAFASTAFormat', 'AlphaDiversityFormat', 'MultiFASTADirectoryFormat', 'PairedDNASequencesDirectoryFormat', 'SILVATaxonomyDirectoryFormat', 'EggnogRefDirFmt', 'GenesDirectoryFormat', 'SILVATaxonomyFormat', 'UchimeStatsFmt', 'TSVTaxonomyDirectoryFormat', 'DecontamScoreFormat', 'RNASingleProfileHmmDirectoryFmt', 'TableJSONLFileFormat', 'MAGSequencesDirFmt', 'AlignedDNAFASTAFormat', 'AlignedProteinFASTAFormat', 'TableJSONLDirFmt', 'SampleEstimatorDirFmt', 'DADA2BaseTransitionStatsDirFmt', 'ImportanceDirectoryFormat', 'BAMDirFmt', 'TSVTaxonomyFormat', 'PairedRNASequencesDirectoryFormat', 'SRAFailedIDsFormat', 'ProcrustesStatisticsDirFmt', 'ProbabilitiesDirectoryFormat', 'EMPPairedEndDirFmt', 'BrackenDBDirectoryFormat', 'ProteinMultipleProfileHmmDirectoryFmt', 'DiamondDatabaseDirFmt', 'MultiMAGSequencesDirFmt', 'DNAMultipleProfileHmmDirectoryFmt', 'DNASingleProfileHmmDirectoryFmt', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'Bowtie2IndexDirFmt', 'QIIME1DemuxDirFmt'}</filter> <discover_datasets pattern="__designation_and_ext__" visible="false"/> </collection> <data name="ANCOMBC2OutputDirFmt" label="${tool.name} on ${on_string} as ANCOMBC2OutputDirFmt"> @@ -976,6 +1005,14 @@ <filter>fmt_finder['output_format'] == 'ContigSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ContigSequencesDirFmt')</filter> <discover_datasets pattern="(?P<designation>[^)\.(?P<ext>].+_contigs.(fasta|fa)$)" visible="false"/> </collection> + <data name="DADA2BaseTransitionStatsDirFmt" label="${tool.name} on ${on_string} as DADA2BaseTransitionStatsDirFmt"> + <filter>fmt_finder['output_format'] == 'DADA2BaseTransitionStatsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DADA2BaseTransitionStatsDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>Errorstats)\.(?P<ext>tsv)" visible="true"/> + </data> + <data name="DADA2BaseTransitionStatsFormat" label="${tool.name} on ${on_string} as DADA2BaseTransitionStatsFormat"> + <filter>fmt_finder['output_format'] == 'DADA2BaseTransitionStatsFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DADA2BaseTransitionStatsFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> <data name="DADA2StatsDirFmt" label="${tool.name} on ${on_string} as DADA2StatsDirFmt"> <filter>fmt_finder['output_format'] == 'DADA2StatsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DADA2StatsDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>stats)\.(?P<ext>tsv)" visible="true"/> @@ -1190,6 +1227,14 @@ <filter>fmt_finder['output_format'] == 'MultiplexedSingleEndBarcodeInSequenceDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiplexedSingleEndBarcodeInSequenceDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>forward)\.(?P<ext>fastq.gz)" visible="true"/> </data> + <data name="NCBIAccessionIDsDirFmt" label="${tool.name} on ${on_string} as NCBIAccessionIDsDirFmt"> + <filter>fmt_finder['output_format'] == 'NCBIAccessionIDsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'NCBIAccessionIDsDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>ncbi-accession-ids)\.(?P<ext>tsv)" visible="true"/> + </data> + <data name="NCBIAccessionIDsFormat" label="${tool.name} on ${on_string} as NCBIAccessionIDsFormat"> + <filter>fmt_finder['output_format'] == 'NCBIAccessionIDsFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'NCBIAccessionIDsFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> <data name="NCBITaxonomyDirFmt" label="${tool.name} on ${on_string} as NCBITaxonomyDirFmt"> <filter>fmt_finder['output_format'] == 'NCBITaxonomyDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'NCBITaxonomyDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>nodes)\.(?P<ext>dmp)" visible="true"/> @@ -1333,6 +1378,22 @@ <filter>fmt_finder['output_format'] == 'SILVATaxonomyFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SILVATaxonomyFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <data name="SRAFailedIDsDirFmt" label="${tool.name} on ${on_string} as SRAFailedIDsDirFmt"> + <filter>fmt_finder['output_format'] == 'SRAFailedIDsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SRAFailedIDsDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>sra-failed-ids)\.(?P<ext>tsv)" visible="true"/> + </data> + <data name="SRAFailedIDsFormat" label="${tool.name} on ${on_string} as SRAFailedIDsFormat"> + <filter>fmt_finder['output_format'] == 'SRAFailedIDsFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SRAFailedIDsFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <data name="SRAMetadataDirFmt" label="${tool.name} on ${on_string} as SRAMetadataDirFmt"> + <filter>fmt_finder['output_format'] == 'SRAMetadataDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SRAMetadataDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>sra-metadata)\.(?P<ext>tsv)" visible="true"/> + </data> + <data name="SRAMetadataFormat" label="${tool.name} on ${on_string} as SRAMetadataFormat"> + <filter>fmt_finder['output_format'] == 'SRAMetadataFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SRAMetadataFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> <data name="SampleEstimatorDirFmt" label="${tool.name} on ${on_string} as SampleEstimatorDirFmt"> <filter>fmt_finder['output_format'] == 'SampleEstimatorDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SampleEstimatorDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>sklearn_version)\.(?P<ext>json)" visible="true"/> @@ -1432,6 +1493,66 @@ -------- These formats have documentation available. +SRAFailedIDsFormat +****************** + +This is a "fake" format only used to store a list of failed SRA IDs, +which can be converted to QIIME's metadata and input into any fondue +action. + +NCBIAccessionIDsFormat +********************** + +This is a format used to store a list of SRA accession IDs (run, +study, BioProject, sample and experiment IDs), which can be converted +to QIIME's metadata. Artifacts containing of run, study and BioProject +IDs can be input into any fondue action. + +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". + +ANCOMBC2OutputDirFmt +******************** + +Stores the model statistics and optionally the structural zeros table= +output by the ANCOMBC2 method. + +The slices are: + - lfc: log-fold change + - se: standard error + - W: lfc / se (the test statistic) + - p: p-value + - q: adjusted p-value + - diff: differentially abundant boolean (i.e. q < alpha) + - passed_ss: whether sensitivity analysis was passed + +FastqGzFormat +************* + +A gzipped fastq file. + + +PressedProfileHmmsDirectoryFmt +****************************** + +The <hmmfile>.h3m file contains the profile HMMs +and their annotation in a binary format. The <hmmfile>.h3i file is an +SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains +precomputed data structures for the fast heuristic filter +(the MSV filter). The <hmmfile>.h3p file contains precomputed data +structures for the rest of each profile. + QIIME1DemuxFormat ***************** QIIME 1 demultiplexed FASTA format. @@ -1466,12 +1587,6 @@ - Each sequence must be DNA and cannot be empty. -FastqGzFormat -************* - -A gzipped fastq file. - - TSVTaxonomyFormat ***************** Format for a 2+ column TSV file with an expected minimal header. @@ -1487,161 +1602,128 @@ of data. -ANCOMBC2OutputDirFmt -******************** - -Stores the model statistics and optionally the structural zeros table= -output by the ANCOMBC2 method. - -The slices are: - - lfc: log-fold change - - se: standard error - - W: lfc / se (the test statistic) - - p: p-value - - q: adjusted p-value - - diff: differentially abundant boolean (i.e. q < alpha) - - passed_ss: whether sensitivity analysis was passed - -SequenceCharacteristicsFormat -***************************** - -Format for a TSV file with information about sequences like length of a -feature. The first column contains feature identifiers and is followed by -other optional columns. - -The file cannot be empty and must have at least two columns. - -Validation for additional columns can be added with a semantic validator -tied to a property. For example the "validate_seq_char_len" validator for -"FeatureData[SequenceCharacteristics % Properties("length")]" -adds validation for a numerical column called "length". - -PressedProfileHmmsDirectoryFmt -****************************** - -The <hmmfile>.h3m file contains the profile HMMs -and their annotation in a binary format. The <hmmfile>.h3i file is an -SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains -precomputed data structures for the fast heuristic filter -(the MSV filter). The <hmmfile>.h3p file contains precomputed data -structures for the rest of each profile. - Additional formats without documentation: ***************************************** - - DiamondDatabaseDirFmt - - PredictionsFormat + - ContigSequencesDirFmt + - BrackenDBDirectoryFormat + - SILVATaxidMapFormat + - ErrorCorrectionDetailsDirFmt + - EggnogRefDirFmt + - SRAFailedIDsDirFmt + - CasavaOneEightSingleLanePerSampleDirFmt + - RNAMultipleProfileHmmDirectoryFmt + - BLAST6Format + - LSMatFormat + - RNAFASTAFormat + - PlacementsDirFmt + - NewickFormat + - BooleanSeriesDirectoryFormat + - MAGSequencesDirFmt + - TSVTaxonomyDirectoryFormat - DiamondDatabaseFileFmt - - Kraken2DBReportFormat - - MultiFASTADirectoryFormat - - Kraken2OutputDirectoryFormat - - ProcrustesStatisticsDirFmt - - SeedOrthologDirFmt - - DNAFASTAFormat - - Kraken2DBDirectoryFormat + - MAGtoContigsDirFmt + - DADA2BaseTransitionStatsDirFmt + - BLAST6DirectoryFormat + - QIIME1DemuxDirFmt - Kraken2DBReportDirectoryFormat - - PlacementsFormat - - FirstDifferencesDirectoryFormat - - DeblurStatsFmt - - ErrorCorrectionDetailsDirFmt - - PairedDNASequencesDirectoryFormat - - PredictionsDirectoryFormat - - AlphaDiversityFormat - - OrdinationFormat - - PlacementsDirFmt - - MultiMAGSequencesDirFmt - - AlignedProteinFASTAFormat - - EMPPairedEndDirFmt + - RNASequencesDirectoryFormat + - NewickDirectoryFormat + - ProteinSequencesDirectoryFormat - OrthologAnnotationDirFmt - - UchimeStatsFmt - - LSMatFormat - - DeblurStatsDirFmt - - MAGtoContigsDirFmt - - PairedRNASequencesDirectoryFormat - - AlphaDiversityDirectoryFormat - - MultiBowtie2IndexDirFmt - - AlignedProteinSequencesDirectoryFormat - - ImmutableMetadataDirectoryFormat - - DifferentialFormat - - ImmutableMetadataFormat - - DNASequencesDirectoryFormat - - TableJSONLDirFmt - - DistanceMatrixDirectoryFormat - - Bowtie2IndexDirFmt - - ImportanceDirectoryFormat - - AlignedDNAFASTAFormat - - SILVATaxonomyDirectoryFormat - - ContigSequencesDirFmt - - EggnogProteinSequencesDirFmt - - DifferentialDirectoryFormat - - CasavaOneEightSingleLanePerSampleDirFmt - - BooleanSeriesFormat + - FirstDifferencesDirectoryFormat + - BAMDirFmt + - DeblurStatsFmt + - AlignedRNAFASTAFormat + - DiamondDatabaseDirFmt + - ProteinsDirectoryFormat + - MAGtoContigsFormat + - UchimeStatsDirFmt + - NCBIAccessionIDsDirFmt + - DecontamScoreFormat + - DADA2StatsDirFmt - EMPSingleEndDirFmt - ProteinSingleProfileHmmDirectoryFmt - ProbabilitiesFormat - - DADA2StatsFormat - - BIOMV210DirFmt - - AlignedDNASequencesDirectoryFormat + - ProteinFASTAFormat + - MultiBAMDirFmt + - BIOMV210Format + - AlignedRNASequencesDirectoryFormat + - Kraken2DBReportFormat - ImportanceFormat - - DADA2StatsDirFmt - - GenesDirectoryFormat - - SeppReferenceDirFmt - - SILVATaxonomyFormat - - SILVATaxidMapDirectoryFormat - - OrdinationDirectoryFormat - - BooleanSeriesDirectoryFormat - - BrackenDBDirectoryFormat - - BIOMV210Format + - SeedOrthologDirFmt + - SequenceCharacteristicsDirectoryFormat + - EMPPairedEndDirFmt + - MultiplexedSingleEndBarcodeInSequenceDirFmt + - ArtificialGroupingFormat - ProteinMultipleProfileHmmDirectoryFmt - ProbabilitiesDirectoryFormat - - QIIME1DemuxDirFmt - - QualityFilterStatsFmt - - NCBITaxonomyDirFmt - - Kraken2ReportDirectoryFormat - - BAMDirFmt - - BLAST6Format - - ProteinsDirectoryFormat - - NewickFormat - - SingleLanePerSampleSingleEndFastqDirFmt - - DataLoafPackageDirFmt - - RNAFASTAFormat - - UchimeStatsDirFmt - - ProcrustesStatisticsFmt + - SampleEstimatorDirFmt + - DistanceMatrixDirectoryFormat + - Kraken2OutputDirectoryFormat + - EggnogProteinSequencesDirFmt + - DecontamScoreDirFmt + - DNAFASTAFormat + - ImportanceDirectoryFormat + - OrdinationFormat - DNASingleProfileHmmDirectoryFmt - TrueTargetsDirectoryFormat - SingleLanePerSamplePairedEndFastqDirFmt - - TSVTaxonomyDirectoryFormat + - PairedDNASequencesDirectoryFormat + - DeblurStatsDirFmt + - ImmutableMetadataFormat + - AlphaDiversityFormat + - AlignedProteinFASTAFormat + - GenesDirectoryFormat + - DADA2BaseTransitionStatsFormat + - AlphaDiversityDirectoryFormat - TaxonomicClassiferTemporaryPickleDirFmt - - MAGtoContigsFormat - - ArtificialGroupingFormat - - MultiBAMDirFmt - - QualityFilterStatsDirFmt - - BLAST6DirectoryFormat - - FirstDifferencesFormat - - KaijuDBDirectoryFormat - - DecontamScoreFormat - - RNASequencesDirectoryFormat - - LociDirectoryFormat + - SILVATaxonomyFormat + - OrdinationDirectoryFormat - DNAMultipleProfileHmmDirectoryFmt - - ProteinSequencesDirectoryFormat - - TableJSONLFileFormat - - AlignedRNAFASTAFormat - BLASTDBDirFmtV5 - - MAGSequencesDirFmt + - PlacementsFormat + - MultiFASTADirectoryFormat + - PairedRNASequencesDirectoryFormat + - BooleanSeriesFormat + - SRAMetadataFormat + - AlignedProteinSequencesDirectoryFormat + - RNASingleProfileHmmDirectoryFmt + - DifferentialFormat + - DNASequencesDirectoryFormat - GenomeSequencesDirectoryFormat - - SampleEstimatorDirFmt - - RNASingleProfileHmmDirectoryFmt + - QualityFilterStatsDirFmt + - ProcrustesStatisticsFmt + - MultiMAGSequencesDirFmt + - AlignedDNAFASTAFormat + - SILVATaxonomyDirectoryFormat + - DADA2StatsFormat + - SILVATaxidMapDirectoryFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - TableJSONLFileFormat + - DifferentialDirectoryFormat + - BIOMV210DirFmt + - PredictionsFormat + - Kraken2ReportDirectoryFormat + - SeppReferenceDirFmt + - LociDirectoryFormat + - Bowtie2IndexDirFmt + - UchimeStatsFmt + - ProcrustesStatisticsDirFmt + - MultiBowtie2IndexDirFmt + - AlignedDNASequencesDirectoryFormat + - ErrorCorrectionDetailsFmt + - ImmutableMetadataDirectoryFormat + - NCBITaxonomyDirFmt + - SRAMetadataDirFmt + - TableJSONLDirFmt + - QualityFilterStatsFmt + - Kraken2DBDirectoryFormat + - DataLoafPackageDirFmt + - SingleLanePerSampleSingleEndFastqDirFmt + - PredictionsDirectoryFormat + - FirstDifferencesFormat - ArtificialGroupingDirectoryFormat - - NewickDirectoryFormat - - MultiplexedSingleEndBarcodeInSequenceDirFmt - - ProteinFASTAFormat - - ErrorCorrectionDetailsFmt - - AlignedRNASequencesDirectoryFormat - - DecontamScoreDirFmt - - EggnogRefDirFmt - - SequenceCharacteristicsDirectoryFormat - - SILVATaxidMapFormat - - MultiplexedPairedEndBarcodeInSequenceDirFmt - - RNAMultipleProfileHmmDirectoryFmt + - KaijuDBDirectoryFormat </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>