# HG changeset patch
# User q2d2
# Date 1746471970 0
# Node ID f83fcc98462675dba5732739245f727ccab39ac4
# Parent  40bcc0e139fabc329ce604ae87d5ba9113d6d781
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit b1fccfb38b4873cd4699743033449014a2978e7d

diff -r 40bcc0e139fa -r f83fcc984626 qiime2_core__tools__export.xml
--- a/qiime2_core__tools__export.xml	Wed Oct 30 20:00:17 2024 +0000
+++ b/qiime2_core__tools__export.xml	Mon May 05 19:06:10 2025 +0000
@@ -1,22 +1,22 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2024, QIIME 2 development team.
+Copyright (c) 2025, QIIME 2 development team.
 
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.10.0)
+    q2galaxy (version: 2025.4.0)
 for:
-    qiime2 (version: 2024.10.1)
+    qiime2 (version: 2025.4.0)
 -->
-<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2024.10.0+dist.h3d8a7e27" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2025.4.0+dist.h1147124e" profile="22.05" license="BSD-3-Clause">
     <description>Export data from a QIIME 2 artifact</description>
     <xrefs>
         <xref type="bio.tools">qiime2</xref>
     </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
+        <container type="docker">quay.io/qiime2/amplicon:2025.4</container>
     </requirements>
     <command>q2galaxy run tools export '$inputs'</command>
     <configfiles>
@@ -55,6 +55,7 @@
                 <option value="EMPPairedEndSequences">EMPPairedEndSequences</option>
                 <option value="EMPSingleEndSequences">EMPSingleEndSequences</option>
                 <option value="ErrorCorrectionDetails">ErrorCorrectionDetails</option>
+                <option value="FeatureData__ob__ANCOMBC2Output__cb__">FeatureData[ANCOMBC2Output]</option>
                 <option value="FeatureData__ob__AlignedProteinSequence__cb__">FeatureData[AlignedProteinSequence]</option>
                 <option value="FeatureData__ob__AlignedRNASequence__cb__">FeatureData[AlignedRNASequence]</option>
                 <option value="FeatureData__ob__AlignedSequence__cb__">FeatureData[AlignedSequence]</option>
@@ -263,6 +264,12 @@
                     <option value="ErrorCorrectionDetailsFmt">Error Correction Details Format</option>
                 </param>
             </when>
+            <when value="FeatureData__ob__ANCOMBC2Output__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="ANCOMBC2OutputDirFmt">ANCOMBC2 Output Directory Format</option>
+                </param>
+            </when>
             <when value="FeatureData__ob__AlignedProteinSequence__cb__">
                 <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
                     <option value="None" selected="true">export as is (no conversion)</option>
@@ -855,9 +862,20 @@
     </inputs>
     <outputs>
         <collection name="exported" type="list" label="${tool.name} on ${on_string} as ${fmt_peek}">
-            <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'QIIME1DemuxFormat', 'TSVTaxonomyFormat', 'ProcrustesStatisticsDirFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'UchimeStatsDirFmt', 'SILVATaxidMapFormat', 'NewickDirectoryFormat', 'AlignedDNAFASTAFormat', 'OrdinationDirectoryFormat', 'TableJSONLFileFormat', 'ProteinsDirectoryFormat', 'AlignedProteinSequencesDirectoryFormat', 'ArtificialGroupingDirectoryFormat', 'QualityFilterStatsFmt', 'ImmutableMetadataDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'UchimeStatsFmt', 'ProteinSingleProfileHmmDirectoryFmt', 'DADA2StatsFormat', 'BIOMV210DirFmt', 'MultiFASTADirectoryFormat', 'AlignedDNASequencesDirectoryFormat', 'TableJSONLDirFmt', 'SequenceCharacteristicsFormat', 'BooleanSeriesFormat', 'MultiBAMDirFmt', 'GenomeSequencesDirectoryFormat', 'AlignedRNASequencesDirectoryFormat', 'MultiBowtie2IndexDirFmt', 'ImportanceFormat', 'FirstDifferencesDirectoryFormat', 'ArtificialGroupingFormat', 'MAGtoContigsFormat', 'MAGSequencesDirFmt', 'KaijuDBDirectoryFormat', 'DiamondDatabaseFileFmt', 'DataLoafPackageDirFmt', 'QIIME1DemuxDirFmt', 'DNASingleProfileHmmDirectoryFmt', 'Kraken2ReportDirectoryFormat', 'ErrorCorrectionDetailsDirFmt', 'ProbabilitiesDirectoryFormat', 'DecontamScoreDirFmt', 'DeblurStatsDirFmt', 'SILVATaxidMapDirectoryFormat', 'SingleLanePerSampleSingleEndFastqDirFmt', 'BLASTDBDirFmtV5', 'ErrorCorrectionDetailsFmt', 'LociDirectoryFormat', 'FastqGzFormat', 'ImmutableMetadataFormat', 'RNAFASTAFormat', 'EggnogRefDirFmt', 'DNAFASTAFormat', 'PlacementsDirFmt', 'ProteinMultipleProfileHmmDirectoryFmt', 'EMPSingleEndDirFmt', 'SILVATaxonomyDirectoryFormat', 'BLAST6Format', 'DNAMultipleProfileHmmDirectoryFmt', 'DADA2StatsDirFmt', 'SILVATaxonomyFormat', 'DNASequencesDirectoryFormat', 'PairedRNASequencesDirectoryFormat', 'SeedOrthologDirFmt', 'SequenceCharacteristicsDirectoryFormat', 'ProbabilitiesFormat', 'Kraken2DBReportDirectoryFormat', 'QualityFilterStatsDirFmt', 'SingleLanePerSamplePairedEndFastqDirFmt', 'DifferentialFormat', 'BAMDirFmt', 'NCBITaxonomyDirFmt', 'NewickFormat', 'LSMatFormat', 'MultiMAGSequencesDirFmt', 'RNASingleProfileHmmDirectoryFmt', 'Kraken2DBDirectoryFormat', 'AlignedRNAFASTAFormat', 'ProteinSequencesDirectoryFormat', 'Kraken2OutputDirectoryFormat', 'SampleEstimatorDirFmt', 'RNAMultipleProfileHmmDirectoryFmt', 'ProcrustesStatisticsFmt', 'BooleanSeriesDirectoryFormat', 'FirstDifferencesFormat', 'Bowtie2IndexDirFmt', 'PredictionsFormat', 'BLAST6DirectoryFormat', 'ImportanceDirectoryFormat', 'DifferentialDirectoryFormat', 'EMPPairedEndDirFmt', 'SeppReferenceDirFmt', 'TrueTargetsDirectoryFormat', 'OrdinationFormat', 'EggnogProteinSequencesDirFmt', 'OrthologAnnotationDirFmt', 'DecontamScoreFormat', 'DeblurStatsFmt', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'MAGtoContigsDirFmt', 'Kraken2DBReportFormat', 'GenesDirectoryFormat', 'PredictionsDirectoryFormat', 'DiamondDatabaseDirFmt', 'TSVTaxonomyDirectoryFormat', 'ProteinFASTAFormat', 'BIOMV210Format', 'PairedDNASequencesDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'AlphaDiversityDirectoryFormat', 'RNASequencesDirectoryFormat', 'AlignedProteinFASTAFormat', 'PlacementsFormat', 'AlphaDiversityFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'ContigSequencesDirFmt', 'PressedProfileHmmsDirectoryFmt', 'BrackenDBDirectoryFormat'}</filter>
+            <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'DiamondDatabaseFileFmt', 'UchimeStatsDirFmt', 'PredictionsDirectoryFormat', 'SILVATaxidMapFormat', 'SequenceCharacteristicsFormat', 'DecontamScoreFormat', 'NCBITaxonomyDirFmt', 'ProteinMultipleProfileHmmDirectoryFmt', 'FastqGzFormat', 'ContigSequencesDirFmt', 'Bowtie2IndexDirFmt', 'MultiBowtie2IndexDirFmt', 'BooleanSeriesFormat', 'EMPPairedEndDirFmt', 'Kraken2DBReportDirectoryFormat', 'ProteinsDirectoryFormat', 'PlacementsDirFmt', 'DecontamScoreDirFmt', 'RNAFASTAFormat', 'OrdinationFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'Kraken2DBDirectoryFormat', 'AlignedDNAFASTAFormat', 'ImportanceDirectoryFormat', 'EggnogProteinSequencesDirFmt', 'DataLoafPackageDirFmt', 'DifferentialFormat', 'CasavaOneEightSingleLanePerSampleDirFmt', 'AlignedDNASequencesDirectoryFormat', 'FirstDifferencesFormat', 'ErrorCorrectionDetailsFmt', 'MAGSequencesDirFmt', 'LSMatFormat', 'BrackenDBDirectoryFormat', 'UchimeStatsFmt', 'PredictionsFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'PlacementsFormat', 'ANCOMBC2OutputDirFmt', 'TableJSONLDirFmt', 'MultiBAMDirFmt', 'QIIME1DemuxDirFmt', 'ProteinSequencesDirectoryFormat', 'BLAST6DirectoryFormat', 'BLAST6Format', 'SingleLanePerSamplePairedEndFastqDirFmt', 'Kraken2ReportDirectoryFormat', 'ArtificialGroupingFormat', 'DADA2StatsFormat', 'ProcrustesStatisticsDirFmt', 'ProbabilitiesFormat', 'AlphaDiversityFormat', 'PairedRNASequencesDirectoryFormat', 'AlignedRNASequencesDirectoryFormat', 'SeedOrthologDirFmt', 'AlignedProteinSequencesDirectoryFormat', 'TSVTaxonomyDirectoryFormat', 'SequenceCharacteristicsDirectoryFormat', 'PressedProfileHmmsDirectoryFmt', 'RNASequencesDirectoryFormat', 'GenesDirectoryFormat', 'SILVATaxonomyFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'MAGtoContigsFormat', 'RNAMultipleProfileHmmDirectoryFmt', 'ProteinFASTAFormat', 'DiamondDatabaseDirFmt', 'LociDirectoryFormat', 'ProcrustesStatisticsFmt', 'DNASingleProfileHmmDirectoryFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'QualityFilterStatsDirFmt', 'RNASingleProfileHmmDirectoryFmt', 'ImmutableMetadataFormat', 'DADA2StatsDirFmt', 'KaijuDBDirectoryFormat', 'QIIME1DemuxFormat', 'SILVATaxidMapDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'DifferentialDirectoryFormat', 'BIOMV210Format', 'FirstDifferencesDirectoryFormat', 'OrdinationDirectoryFormat', 'SILVATaxonomyDirectoryFormat', 'TSVTaxonomyFormat', 'ProbabilitiesDirectoryFormat', 'BLASTDBDirFmtV5', 'ArtificialGroupingDirectoryFormat', 'TableJSONLFileFormat', 'Kraken2OutputDirectoryFormat', 'GenomeSequencesDirectoryFormat', 'AlignedRNAFASTAFormat', 'Kraken2DBReportFormat', 'ErrorCorrectionDetailsDirFmt', 'QualityFilterStatsFmt', 'SampleEstimatorDirFmt', 'BAMDirFmt', 'DNASequencesDirectoryFormat', 'DNAMultipleProfileHmmDirectoryFmt', 'TrueTargetsDirectoryFormat', 'DNAFASTAFormat', 'BooleanSeriesDirectoryFormat', 'OrthologAnnotationDirFmt', 'ImportanceFormat', 'MAGtoContigsDirFmt', 'ProteinSingleProfileHmmDirectoryFmt', 'DeblurStatsFmt', 'NewickDirectoryFormat', 'AlphaDiversityDirectoryFormat', 'NewickFormat', 'EggnogRefDirFmt', 'PairedDNASequencesDirectoryFormat', 'DeblurStatsDirFmt', 'MultiFASTADirectoryFormat', 'EMPSingleEndDirFmt', 'MultiMAGSequencesDirFmt', 'ImmutableMetadataDirectoryFormat', 'AlignedProteinFASTAFormat', 'SeppReferenceDirFmt', 'BIOMV210DirFmt'}</filter>
             <discover_datasets pattern="__designation_and_ext__" visible="false"/>
         </collection>
+        <data name="ANCOMBC2OutputDirFmt" label="${tool.name} on ${on_string} as ANCOMBC2OutputDirFmt">
+            <filter>fmt_finder['output_format'] == 'ANCOMBC2OutputDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ANCOMBC2OutputDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;lfc)\.(?P&lt;ext&gt;jsonl)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;se)\.(?P&lt;ext&gt;jsonl)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;W)\.(?P&lt;ext&gt;jsonl)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;p)\.(?P&lt;ext&gt;jsonl)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;q)\.(?P&lt;ext&gt;jsonl)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;diff)\.(?P&lt;ext&gt;jsonl)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;passed_ss)\.(?P&lt;ext&gt;jsonl)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;structural-zeros)\.(?P&lt;ext&gt;jsonl)" visible="true"/>
+        </data>
         <data name="AlignedDNAFASTAFormat" label="${tool.name} on ${on_string} as AlignedDNAFASTAFormat">
             <filter>fmt_finder['output_format'] == 'AlignedDNAFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'AlignedDNAFASTAFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
@@ -1110,13 +1128,13 @@
             <filter>fmt_finder['output_format'] == 'Kraken2DBReportFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBReportFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
-        <collection name="Kraken2OutputDirectoryFormat_reports" type="list" label="${tool.name} on ${on_string} as Kraken2OutputDirectoryFormat (reports)">
+        <collection name="Kraken2OutputDirectoryFormat_outputs" type="list" label="${tool.name} on ${on_string} as Kraken2OutputDirectoryFormat (outputs)">
             <filter>fmt_finder['output_format'] == 'Kraken2OutputDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2OutputDirectoryFormat')</filter>
-            <discover_datasets pattern="(?P&lt;designation&gt;.+output)\.(?P&lt;ext&gt;(txt|tsv)$)" visible="false"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+\.output)\.(?P&lt;ext&gt;(txt|tsv)$)" visible="false"/>
         </collection>
         <collection name="Kraken2ReportDirectoryFormat_reports" type="list" label="${tool.name} on ${on_string} as Kraken2ReportDirectoryFormat (reports)">
             <filter>fmt_finder['output_format'] == 'Kraken2ReportDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2ReportDirectoryFormat')</filter>
-            <discover_datasets pattern="(?P&lt;designation&gt;.+report)\.(?P&lt;ext&gt;(txt|tsv)$)" visible="false"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+\.report)\.(?P&lt;ext&gt;(txt|tsv)$)" visible="false"/>
         </collection>
         <data name="LSMatFormat" label="${tool.name} on ${on_string} as LSMatFormat">
             <filter>fmt_finder['output_format'] == 'LSMatFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'LSMatFormat')</filter>
@@ -1414,16 +1432,6 @@
 --------
 These formats have documentation available.
 
-PressedProfileHmmsDirectoryFmt
-******************************
-
-The  &lt;hmmfile&gt;.h3m file contains the profile HMMs
-and their annotation in a binary format. The &lt;hmmfile&gt;.h3i file is an
-SSI index for the &lt;hmmfile&gt;.h3m file.  The &lt;hmmfile&gt;.h3f file contains
-precomputed data structures for the fast heuristic filter
-(the MSV filter).  The &lt;hmmfile&gt;.h3p file contains precomputed data
-structures for the rest of each profile.
-
 TSVTaxonomyFormat
 *****************
 Format for a 2+ column TSV file with an expected minimal header.
@@ -1439,6 +1447,30 @@
 of data.
 
 
+SequenceCharacteristicsFormat
+*****************************
+
+Format for a TSV file with information about sequences like length of a
+feature. The first column contains feature identifiers and is followed by
+other optional columns.
+
+The file cannot be empty and must have at least two columns.
+
+Validation for additional columns can be added with a semantic validator
+tied to a property. For example the "validate_seq_char_len" validator for
+"FeatureData[SequenceCharacteristics % Properties("length")]"
+adds validation for a numerical column called "length".
+
+PressedProfileHmmsDirectoryFmt
+******************************
+
+The  &lt;hmmfile&gt;.h3m file contains the profile HMMs
+and their annotation in a binary format. The &lt;hmmfile&gt;.h3i file is an
+SSI index for the &lt;hmmfile&gt;.h3m file.  The &lt;hmmfile&gt;.h3f file contains
+precomputed data structures for the fast heuristic filter
+(the MSV filter).  The &lt;hmmfile&gt;.h3p file contains precomputed data
+structures for the rest of each profile.
+
 QIIME1DemuxFormat
 *****************
 QIIME 1 demultiplexed FASTA format.
@@ -1473,142 +1505,143 @@
 - Each sequence must be DNA and cannot be empty.
 
 
-SequenceCharacteristicsFormat
-*****************************
-
-Format for a TSV file with information about sequences like length of a
-feature. The first column contains feature identifiers and is followed by
-other optional columns.
-
-The file cannot be empty and must have at least two columns.
-
-Validation for additional columns can be added with a semantic validator
-tied to a property. For example the "validate_seq_char_len" validator for
-"FeatureData[SequenceCharacteristics % Properties("length")]"
-adds validation for a numerical column called "length".
-
 FastqGzFormat
 *************
 
 A gzipped fastq file.
 
 
+ANCOMBC2OutputDirFmt
+********************
+
+Stores the model statistics and optionally the structural zeros table=
+output by the ANCOMBC2 method.
+
+The slices are:
+    - lfc: log-fold change
+    - se: standard error
+    - W: lfc / se (the test statistic)
+    - p: p-value
+    - q: adjusted p-value
+    - diff: differentially abundant boolean (i.e. q &lt; alpha)
+    - passed_ss: whether sensitivity analysis was passed
+
 Additional formats without documentation:
 *****************************************
+ - BooleanSeriesFormat
+ - ProcrustesStatisticsFmt
+ - DADA2StatsDirFmt
+ - BAMDirFmt
+ - ProbabilitiesDirectoryFormat
+ - BLAST6Format
+ - PlacementsFormat
+ - BIOMV210DirFmt
+ - SingleLanePerSampleSingleEndFastqDirFmt
+ - RNAFASTAFormat
+ - SILVATaxidMapFormat
+ - EMPPairedEndDirFmt
+ - EggnogProteinSequencesDirFmt
+ - SingleLanePerSamplePairedEndFastqDirFmt
+ - TSVTaxonomyDirectoryFormat
+ - SampleEstimatorDirFmt
+ - DeblurStatsFmt
+ - EggnogRefDirFmt
+ - MAGtoContigsFormat
+ - MultiplexedSingleEndBarcodeInSequenceDirFmt
+ - MultiBAMDirFmt
+ - TrueTargetsDirectoryFormat
+ - BLAST6DirectoryFormat
+ - MAGtoContigsDirFmt
+ - QualityFilterStatsFmt
+ - RNASequencesDirectoryFormat
+ - NewickFormat
+ - ImportanceFormat
+ - ProteinSequencesDirectoryFormat
+ - ImportanceDirectoryFormat
+ - OrdinationFormat
+ - DecontamScoreDirFmt
+ - Kraken2ReportDirectoryFormat
+ - AlignedRNAFASTAFormat
+ - ArtificialGroupingDirectoryFormat
+ - DiamondDatabaseFileFmt
+ - FirstDifferencesFormat
+ - LSMatFormat
+ - ArtificialGroupingFormat
+ - TaxonomicClassiferTemporaryPickleDirFmt
+ - ProteinSingleProfileHmmDirectoryFmt
+ - MAGSequencesDirFmt
+ - TableJSONLFileFormat
+ - ProteinFASTAFormat
+ - ProbabilitiesFormat
+ - AlignedRNASequencesDirectoryFormat
+ - SequenceCharacteristicsDirectoryFormat
+ - SILVATaxidMapDirectoryFormat
+ - LociDirectoryFormat
+ - DistanceMatrixDirectoryFormat
+ - ProteinMultipleProfileHmmDirectoryFmt
+ - MultiFASTADirectoryFormat
+ - BLASTDBDirFmtV5
+ - DecontamScoreFormat
+ - DNAFASTAFormat
+ - MultiplexedPairedEndBarcodeInSequenceDirFmt
+ - Kraken2OutputDirectoryFormat
+ - ProteinsDirectoryFormat
+ - Kraken2DBReportFormat
+ - PlacementsDirFmt
+ - GenomeSequencesDirectoryFormat
+ - PairedDNASequencesDirectoryFormat
+ - BIOMV210Format
+ - AlphaDiversityFormat
+ - DNASingleProfileHmmDirectoryFmt
+ - SILVATaxonomyDirectoryFormat
+ - MultiMAGSequencesDirFmt
+ - AlignedProteinFASTAFormat
+ - ImmutableMetadataDirectoryFormat
+ - GenesDirectoryFormat
+ - UchimeStatsDirFmt
+ - FirstDifferencesDirectoryFormat
+ - NewickDirectoryFormat
+ - PairedRNASequencesDirectoryFormat
+ - AlphaDiversityDirectoryFormat
+ - MultiBowtie2IndexDirFmt
+ - AlignedProteinSequencesDirectoryFormat
+ - SILVATaxonomyFormat
+ - BrackenDBDirectoryFormat
+ - TableJSONLDirFmt
  - DifferentialFormat
  - DNASequencesDirectoryFormat
- - Kraken2OutputDirectoryFormat
- - MultiBAMDirFmt
- - FirstDifferencesFormat
+ - DeblurStatsDirFmt
+ - DADA2StatsFormat
+ - Kraken2DBDirectoryFormat
+ - Bowtie2IndexDirFmt
+ - Kraken2DBReportDirectoryFormat
+ - SeedOrthologDirFmt
+ - QualityFilterStatsDirFmt
  - AlignedDNAFASTAFormat
  - ProcrustesStatisticsDirFmt
- - EggnogProteinSequencesDirFmt
- - DifferentialDirectoryFormat
- - MAGSequencesDirFmt
- - ProteinSingleProfileHmmDirectoryFmt
- - ImportanceFormat
+ - RNASingleProfileHmmDirectoryFmt
+ - ContigSequencesDirFmt
  - ImmutableMetadataFormat
- - ErrorCorrectionDetailsFmt
- - ArtificialGroupingFormat
- - OrthologAnnotationDirFmt
- - DecontamScoreFormat
- - FirstDifferencesDirectoryFormat
- - TrueTargetsDirectoryFormat
- - AlignedDNASequencesDirectoryFormat
- - QualityFilterStatsFmt
- - DeblurStatsFmt
  - BooleanSeriesDirectoryFormat
- - BIOMV210DirFmt
- - OrdinationFormat
- - LSMatFormat
- - ProteinMultipleProfileHmmDirectoryFmt
- - ImportanceDirectoryFormat
- - ImmutableMetadataDirectoryFormat
- - ErrorCorrectionDetailsDirFmt
- - SingleLanePerSamplePairedEndFastqDirFmt
- - Kraken2DBDirectoryFormat
- - OrdinationDirectoryFormat
- - BooleanSeriesFormat
- - BLASTDBDirFmtV5
- - DADA2StatsFormat
- - BLAST6Format
- - KaijuDBDirectoryFormat
- - ArtificialGroupingDirectoryFormat
- - MultiFASTADirectoryFormat
- - MAGtoContigsFormat
- - DNASingleProfileHmmDirectoryFmt
- - RNAFASTAFormat
- - ProbabilitiesFormat
- - SampleEstimatorDirFmt
- - MultiplexedPairedEndBarcodeInSequenceDirFmt
- - TableJSONLFileFormat
- - LociDirectoryFormat
- - QualityFilterStatsDirFmt
- - TSVTaxonomyDirectoryFormat
- - UchimeStatsFmt
- - ProcrustesStatisticsFmt
- - SILVATaxonomyDirectoryFormat
- - AlphaDiversityFormat
- - BLAST6DirectoryFormat
- - MultiMAGSequencesDirFmt
+ - DiamondDatabaseDirFmt
  - SeppReferenceDirFmt
- - DNAMultipleProfileHmmDirectoryFmt
- - RNASequencesDirectoryFormat
- - ProbabilitiesDirectoryFormat
+ - DifferentialDirectoryFormat
+ - CasavaOneEightSingleLanePerSampleDirFmt
+ - NCBITaxonomyDirFmt
+ - ErrorCorrectionDetailsFmt
+ - DataLoafPackageDirFmt
+ - OrthologAnnotationDirFmt
  - PredictionsFormat
- - PlacementsFormat
- - NewickFormat
- - TableJSONLDirFmt
- - BrackenDBDirectoryFormat
- - ProteinSequencesDirectoryFormat
- - GenomeSequencesDirectoryFormat
- - MultiplexedSingleEndBarcodeInSequenceDirFmt
- - EggnogRefDirFmt
- - UchimeStatsDirFmt
- - AlignedRNAFASTAFormat
- - EMPSingleEndDirFmt
- - DADA2StatsDirFmt
- - TaxonomicClassiferTemporaryPickleDirFmt
- - AlphaDiversityDirectoryFormat
- - Kraken2ReportDirectoryFormat
- - MultiBowtie2IndexDirFmt
- - SILVATaxidMapFormat
- - CasavaOneEightSingleLanePerSampleDirFmt
- - RNASingleProfileHmmDirectoryFmt
+ - OrdinationDirectoryFormat
+ - AlignedDNASequencesDirectoryFormat
  - PredictionsDirectoryFormat
- - DeblurStatsDirFmt
- - Bowtie2IndexDirFmt
- - SeedOrthologDirFmt
- - DiamondDatabaseFileFmt
- - ProteinFASTAFormat
- - AlignedRNASequencesDirectoryFormat
- - EMPPairedEndDirFmt
- - NewickDirectoryFormat
- - SequenceCharacteristicsDirectoryFormat
- - ContigSequencesDirFmt
- - Kraken2DBReportFormat
  - RNAMultipleProfileHmmDirectoryFmt
- - PlacementsDirFmt
- - DecontamScoreDirFmt
- - SILVATaxonomyFormat
- - DataLoafPackageDirFmt
- - SILVATaxidMapDirectoryFormat
- - DNAFASTAFormat
- - ProteinsDirectoryFormat
- - MAGtoContigsDirFmt
+ - DNAMultipleProfileHmmDirectoryFmt
+ - UchimeStatsFmt
+ - ErrorCorrectionDetailsDirFmt
+ - EMPSingleEndDirFmt
+ - KaijuDBDirectoryFormat
  - QIIME1DemuxDirFmt
- - DiamondDatabaseDirFmt
- - Kraken2DBReportDirectoryFormat
- - PairedDNASequencesDirectoryFormat
- - NCBITaxonomyDirFmt
- - DistanceMatrixDirectoryFormat
- - BIOMV210Format
- - AlignedProteinFASTAFormat
- - SingleLanePerSampleSingleEndFastqDirFmt
- - BAMDirFmt
- - PairedRNASequencesDirectoryFormat
- - AlignedProteinSequencesDirectoryFormat
- - GenesDirectoryFormat
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>