# HG changeset patch
# User q2d2
# Date 1762018436 0
# Node ID 6d6617a579257dfe30644d78de45e227c3a5929f
# Parent  61fb1a11e004ff8c3cbc946d1fe0442097b9cd0a
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

diff -r 61fb1a11e004 -r 6d6617a57925 qiime2_core__tools__export.xml
--- 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 ${on_string} as ANCOMBC2OutputDirFmt">
@@ -976,6 +1005,14 @@
             <filter>fmt_finder['output_format'] == 'ContigSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ContigSequencesDirFmt')</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;[^)\.(?P&lt;ext&gt;].+_contigs.(fasta|fa)$)" visible="false"/>
         </collection>
+        <data name="DADA2BaseTransitionStatsDirFmt" label="${tool.name} on ${on_string} as DADA2BaseTransitionStatsDirFmt">
+            <filter>fmt_finder['output_format'] == 'DADA2BaseTransitionStatsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DADA2BaseTransitionStatsDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;Errorstats)\.(?P&lt;ext&gt;tsv)" visible="true"/>
+        </data>
+        <data name="DADA2BaseTransitionStatsFormat" label="${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 ${on_string} as DADA2StatsDirFmt">
             <filter>fmt_finder['output_format'] == 'DADA2StatsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DADA2StatsDirFmt')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;stats)\.(?P&lt;ext&gt;tsv)" visible="true"/>
@@ -1190,6 +1227,14 @@
             <filter>fmt_finder['output_format'] == 'MultiplexedSingleEndBarcodeInSequenceDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiplexedSingleEndBarcodeInSequenceDirFmt')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;forward)\.(?P&lt;ext&gt;fastq.gz)" visible="true"/>
         </data>
+        <data name="NCBIAccessionIDsDirFmt" label="${tool.name} on ${on_string} as NCBIAccessionIDsDirFmt">
+            <filter>fmt_finder['output_format'] == 'NCBIAccessionIDsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'NCBIAccessionIDsDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;ncbi-accession-ids)\.(?P&lt;ext&gt;tsv)" visible="true"/>
+        </data>
+        <data name="NCBIAccessionIDsFormat" label="${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 ${on_string} as NCBITaxonomyDirFmt">
             <filter>fmt_finder['output_format'] == 'NCBITaxonomyDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'NCBITaxonomyDirFmt')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;nodes)\.(?P&lt;ext&gt;dmp)" visible="true"/>
@@ -1333,6 +1378,22 @@
             <filter>fmt_finder['output_format'] == 'SILVATaxonomyFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SILVATaxonomyFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <data name="SRAFailedIDsDirFmt" label="${tool.name} on ${on_string} as SRAFailedIDsDirFmt">
+            <filter>fmt_finder['output_format'] == 'SRAFailedIDsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SRAFailedIDsDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;sra-failed-ids)\.(?P&lt;ext&gt;tsv)" visible="true"/>
+        </data>
+        <data name="SRAFailedIDsFormat" label="${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 ${on_string} as SRAMetadataDirFmt">
+            <filter>fmt_finder['output_format'] == 'SRAMetadataDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SRAMetadataDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;sra-metadata)\.(?P&lt;ext&gt;tsv)" visible="true"/>
+        </data>
+        <data name="SRAMetadataFormat" label="${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&lt;designation&gt;sklearn_version)\.(?P&lt;ext&gt;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 &lt; alpha)
+    - passed_ss: whether sensitivity analysis was passed
+
+FastqGzFormat
+*************
+
+A gzipped fastq file.
+
+
+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.
@@ -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 &lt; 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  &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.
-
 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>