# HG changeset patch
# User q2d2
# Date 1717457571 0
# Node ID 37e37518cad1bd18a34c363830fefbf47865d938
# Parent  e96704fc516dfe733b261bcfe84a594643810a3c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit c7e80dcda727ce63b42aa8a946e9330310929797

diff -r e96704fc516d -r 37e37518cad1 qiime2_core__tools__export.xml
--- 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 ${on_string} as AlignedDNAFASTAFormat">
@@ -645,6 +793,10 @@
             <discover_datasets pattern="(?P&lt;designation&gt;.+\.rev\.1)\.(?P&lt;ext&gt;bt2l?)" visible="true"/>
             <discover_datasets pattern="(?P&lt;designation&gt;.+\.rev\.2)\.(?P&lt;ext&gt;bt2l?)" visible="true"/>
         </data>
+        <collection name="BrackenDBDirectoryFormat_kmers" type="list" label="${tool.name} on ${on_string} as BrackenDBDirectoryFormat (kmers)">
+            <filter>fmt_finder['output_format'] == 'BrackenDBDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BrackenDBDirectoryFormat')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;database(\d{2,})mers)\.(?P&lt;ext&gt;kmer_distrib$)" visible="false"/>
+        </collection>
         <collection name="CasavaOneEightSingleLanePerSampleDirFmt_sequences" type="list" label="${tool.name} on ${on_string} as CasavaOneEightSingleLanePerSampleDirFmt (sequences)">
             <filter>fmt_finder['output_format'] == 'CasavaOneEightSingleLanePerSampleDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'CasavaOneEightSingleLanePerSampleDirFmt')</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+_.+_L[0-9][0-9][0-9]_R[12]_001)\.(?P&lt;ext&gt;fastq\.gz)" visible="false"/>
@@ -693,6 +845,14 @@
             <filter>fmt_finder['output_format'] == 'DecontamScoreFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DecontamScoreFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <data name="DiamondDatabaseDirFmt" label="${tool.name} on ${on_string} as DiamondDatabaseDirFmt">
+            <filter>fmt_finder['output_format'] == 'DiamondDatabaseDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DiamondDatabaseDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;ref_db)\.(?P&lt;ext&gt;dmnd)" visible="true"/>
+        </data>
+        <data name="DiamondDatabaseFileFmt" label="${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 ${on_string} as DifferentialDirectoryFormat">
             <filter>fmt_finder['output_format'] == 'DifferentialDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DifferentialDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;differentials)\.(?P&lt;ext&gt;tsv)" visible="true"/>
@@ -716,10 +876,23 @@
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;sequences)\.(?P&lt;ext&gt;fastq.gz)" visible="true"/>
             <discover_datasets pattern="(?P&lt;designation&gt;barcodes)\.(?P&lt;ext&gt;fastq.gz)" visible="true"/>
         </data>
+        <data name="EggnogProteinSequencesDirFmt" label="${tool.name} on ${on_string} as EggnogProteinSequencesDirFmt">
+            <filter>fmt_finder['output_format'] == 'EggnogProteinSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'EggnogProteinSequencesDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;e5.taxid_info)\.(?P&lt;ext&gt;tsv)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;e5.proteomes)\.(?P&lt;ext&gt;faa)" visible="true"/>
+        </data>
+        <collection name="EggnogRefDirFmt_eggnog" type="list" label="${tool.name} on ${on_string} as EggnogRefDirFmt (eggnog)">
+            <filter>fmt_finder['output_format'] == 'EggnogRefDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'EggnogRefDirFmt')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;eggnog.*db)\.(?P&lt;ext&gt;*)" visible="false"/>
+        </collection>
         <data name="ErrorCorrectionDetailsDirFmt" label="${tool.name} on ${on_string} as ErrorCorrectionDetailsDirFmt">
             <filter>fmt_finder['output_format'] == 'ErrorCorrectionDetailsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ErrorCorrectionDetailsDirFmt')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;details)\.(?P&lt;ext&gt;tsv)" visible="true"/>
         </data>
+        <data name="ErrorCorrectionDetailsFmt" label="${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 ${on_string} as GenesDirectoryFormat (genes)">
             <filter>fmt_finder['output_format'] == 'GenesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'GenesDirectoryFormat')</filter>
-            <discover_datasets pattern="(?P&lt;designation&gt;(.*\_)?genes[0-9]*)\.(?P&lt;ext&gt;(fa|fna|fasta)$)" visible="false"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;(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 ${on_string} as KaijuDBDirectoryFormat">
+            <filter>fmt_finder['output_format'] == 'KaijuDBDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'KaijuDBDirectoryFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;nodes)\.(?P&lt;ext&gt;dmp)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;names)\.(?P&lt;ext&gt;dmp)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;kaiju_db.+)\.(?P&lt;ext&gt;fmi)" visible="true"/>
+        </data>
+        <data name="Kraken2DBDirectoryFormat" label="${tool.name} on ${on_string} as Kraken2DBDirectoryFormat">
+            <filter>fmt_finder['output_format'] == 'Kraken2DBDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBDirectoryFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;hash)\.(?P&lt;ext&gt;k2d)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;opts)\.(?P&lt;ext&gt;k2d)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;taxo)\.(?P&lt;ext&gt;k2d)" visible="true"/>
+        </data>
+        <data name="Kraken2DBReportDirectoryFormat" label="${tool.name} on ${on_string} as Kraken2DBReportDirectoryFormat">
+            <filter>fmt_finder['output_format'] == 'Kraken2DBReportDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBReportDirectoryFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;report)\.(?P&lt;ext&gt;txt)" visible="true"/>
+        </data>
+        <collection name="Kraken2OutputDirectoryFormat_reports" type="list" label="${tool.name} on ${on_string} as Kraken2OutputDirectoryFormat (reports)">
+            <filter>fmt_finder['output_format'] == 'Kraken2OutputDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2OutputDirectoryFormat')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+output)\.(?P&lt;ext&gt;(txt|tsv)$)" 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"/>
+        </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 ${on_string} as LociDirectoryFormat (loci)">
             <filter>fmt_finder['output_format'] == 'LociDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'LociDirectoryFormat')</filter>
-            <discover_datasets pattern="(?P&lt;designation&gt;(.*\_)?loci[0-9]*)\.(?P&lt;ext&gt;gff$)" visible="false"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;gff$)" visible="false"/>
+        </collection>
+        <collection name="MAGSequencesDirFmt_sequences" type="list" label="${tool.name} on ${on_string} as MAGSequencesDirFmt (sequences)">
+            <filter>fmt_finder['output_format'] == 'MAGSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MAGSequencesDirFmt')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12})\.(?P&lt;ext&gt;(fa|fasta)$)" visible="false"/>
         </collection>
         <data name="MAGtoContigsDirFmt" label="${tool.name} on ${on_string} as MAGtoContigsDirFmt">
             <filter>fmt_finder['output_format'] == 'MAGtoContigsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MAGtoContigsDirFmt')</filter>
@@ -781,6 +982,10 @@
             <discover_datasets pattern="(?P&lt;designation&gt;.+\.rev\.1)\.(?P&lt;ext&gt;bt2l?)" visible="true"/>
             <discover_datasets pattern="(?P&lt;designation&gt;.+\.rev\.2)\.(?P&lt;ext&gt;bt2l?)" visible="true"/>
         </data>
+        <collection name="MultiFASTADirectoryFormat_sequences" type="list" label="${tool.name} on ${on_string} as MultiFASTADirectoryFormat (sequences)">
+            <filter>fmt_finder['output_format'] == 'MultiFASTADirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiFASTADirectoryFormat')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;(fa|fasta)$)" visible="false"/>
+        </collection>
         <collection name="MultiMAGSequencesDirFmt_sequences" type="list" label="${tool.name} on ${on_string} as MultiMAGSequencesDirFmt (sequences)">
             <filter>fmt_finder['output_format'] == 'MultiMAGSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiMAGSequencesDirFmt')</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;(fa|fasta)$)" 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&lt;designation&gt;forward)\.(?P&lt;ext&gt;fastq.gz)" visible="true"/>
         </data>
+        <data name="NCBITaxonomyDirFmt" label="${tool.name} on ${on_string} as NCBITaxonomyDirFmt">
+            <filter>fmt_finder['output_format'] == 'NCBITaxonomyDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'NCBITaxonomyDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;nodes)\.(?P&lt;ext&gt;dmp)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;names)\.(?P&lt;ext&gt;dmp)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;prot)\.(?P&lt;ext&gt;accession2taxid.gz)" visible="true"/>
+        </data>
         <data name="NewickDirectoryFormat" label="${tool.name} on ${on_string} as NewickDirectoryFormat">
             <filter>fmt_finder['output_format'] == 'NewickDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'NewickDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;tree)\.(?P&lt;ext&gt;nwk)" visible="true"/>
@@ -814,6 +1025,10 @@
             <filter>fmt_finder['output_format'] == 'OrdinationFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'OrdinationFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <collection name="OrthologAnnotationDirFmt_annotations" type="list" label="${tool.name} on ${on_string} as OrthologAnnotationDirFmt (annotations)">
+            <filter>fmt_finder['output_format'] == 'OrthologAnnotationDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'OrthologAnnotationDirFmt')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;annotations)" visible="false"/>
+        </collection>
         <data name="PairedDNASequencesDirectoryFormat" label="${tool.name} on ${on_string} as PairedDNASequencesDirectoryFormat">
             <filter>fmt_finder['output_format'] == 'PairedDNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PairedDNASequencesDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;left-dna-sequences)\.(?P&lt;ext&gt;fasta)" visible="true"/>
@@ -866,7 +1081,7 @@
         </data>
         <collection name="ProteinsDirectoryFormat_proteins" type="list" label="${tool.name} on ${on_string} as ProteinsDirectoryFormat (proteins)">
             <filter>fmt_finder['output_format'] == 'ProteinsDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinsDirectoryFormat')</filter>
-            <discover_datasets pattern="(?P&lt;designation&gt;(.*\_)?proteins[0-9]*)\.(?P&lt;ext&gt;(fa|faa|fasta)$)" visible="false"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;(fa|faa|fasta)$)" visible="false"/>
         </collection>
         <data name="QIIME1DemuxDirFmt" label="${tool.name} on ${on_string} as QIIME1DemuxDirFmt">
             <filter>fmt_finder['output_format'] == 'QIIME1DemuxDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'QIIME1DemuxDirFmt')</filter>
@@ -923,6 +1138,14 @@
             <discover_datasets pattern="(?P&lt;designation&gt;tree)\.(?P&lt;ext&gt;nwk)" visible="true"/>
             <discover_datasets pattern="(?P&lt;designation&gt;raxml-info)\.(?P&lt;ext&gt;txt)" visible="true"/>
         </data>
+        <data name="SequenceCharacteristicsDirectoryFormat" label="${tool.name} on ${on_string} as SequenceCharacteristicsDirectoryFormat">
+            <filter>fmt_finder['output_format'] == 'SequenceCharacteristicsDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SequenceCharacteristicsDirectoryFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;sequence_characteristics)\.(?P&lt;ext&gt;tsv)" visible="true"/>
+        </data>
+        <data name="SequenceCharacteristicsFormat" label="${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&lt;designation&gt;.+_.+_L[0-9][0-9][0-9]_R[12]_001)\.(?P&lt;ext&gt;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>