# HG changeset patch
# User q2d2
# Date 1730318417 0
# Node ID 40bcc0e139fabc329ce604ae87d5ba9113d6d781
# Parent  37e37518cad1bd18a34c363830fefbf47865d938
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 5f71b597c9495eae67a447744fded834f56ca1f7

diff -r 37e37518cad1 -r 40bcc0e139fa qiime2_core__tools__export.xml
--- a/qiime2_core__tools__export.xml	Mon Jun 03 23:32:51 2024 +0000
+++ b/qiime2_core__tools__export.xml	Wed Oct 30 20:00:17 2024 +0000
@@ -6,14 +6,17 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2024.5.0+dist.he540b0b0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2024.10.0+dist.h3d8a7e27" 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:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <command>q2galaxy run tools export '$inputs'</command>
     <configfiles>
@@ -38,6 +41,16 @@
                 <option value="Bowtie2Index">Bowtie2Index</option>
                 <option value="BrackenDB">BrackenDB</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>
+                <option value="Dist1D__ob__NestedOrdered__comma__ Independent__cb__">Dist1D[NestedOrdered, Independent]</option>
+                <option value="Dist1D__ob__NestedOrdered__comma__ Matched__cb__">Dist1D[NestedOrdered, Matched]</option>
+                <option value="Dist1D__ob__NestedUnordered__comma__ Independent__cb__">Dist1D[NestedUnordered, Independent]</option>
+                <option value="Dist1D__ob__NestedUnordered__comma__ Matched__cb__">Dist1D[NestedUnordered, Matched]</option>
+                <option value="Dist1D__ob__Ordered__comma__ Independent__cb__">Dist1D[Ordered, Independent]</option>
+                <option value="Dist1D__ob__Ordered__comma__ Matched__cb__">Dist1D[Ordered, Matched]</option>
+                <option value="Dist1D__ob__Unordered__comma__ Independent__cb__">Dist1D[Unordered, Independent]</option>
+                <option value="Dist1D__ob__Unordered__comma__ Matched__cb__">Dist1D[Unordered, Matched]</option>
                 <option value="DistanceMatrix">DistanceMatrix</option>
                 <option value="EMPPairedEndSequences">EMPPairedEndSequences</option>
                 <option value="EMPSingleEndSequences">EMPSingleEndSequences</option>
@@ -52,12 +65,9 @@
                 <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>
@@ -73,12 +83,15 @@
                 <option value="FeatureTable__ob__Composition__cb__">FeatureTable[Composition]</option>
                 <option value="FeatureTable__ob__Design__cb__">FeatureTable[Design]</option>
                 <option value="FeatureTable__ob__Frequency__cb__">FeatureTable[Frequency]</option>
+                <option value="FeatureTable__ob__Normalized__cb__">FeatureTable[Normalized]</option>
                 <option value="FeatureTable__ob__PercentileNormalized__cb__">FeatureTable[PercentileNormalized]</option>
                 <option value="FeatureTable__ob__PresenceAbsence__cb__">FeatureTable[PresenceAbsence]</option>
                 <option value="FeatureTable__ob__RelativeFrequency__cb__">FeatureTable[RelativeFrequency]</option>
-                <option value="GenomeData__ob__BLAST6__cb__">GenomeData[BLAST6]</option>
+                <option value="GenomeData__ob__DNASequence__cb__">GenomeData[DNASequence]</option>
                 <option value="GenomeData__ob__Genes__cb__">GenomeData[Genes]</option>
                 <option value="GenomeData__ob__Loci__cb__">GenomeData[Loci]</option>
+                <option value="GenomeData__ob__NOG__cb__">GenomeData[NOG]</option>
+                <option value="GenomeData__ob__Orthologs__cb__">GenomeData[Orthologs]</option>
                 <option value="GenomeData__ob__Proteins__cb__">GenomeData[Proteins]</option>
                 <option value="Hierarchy">Hierarchy</option>
                 <option value="ImmutableMetadata">ImmutableMetadata</option>
@@ -92,6 +105,15 @@
                 <option value="Phylogeny__ob__Unrooted__cb__">Phylogeny[Unrooted]</option>
                 <option value="Placements">Placements</option>
                 <option value="ProcrustesStatistics">ProcrustesStatistics</option>
+                <option value="ProfileHMM__ob__MultipleDNA__cb__">ProfileHMM[MultipleDNA]</option>
+                <option value="ProfileHMM__ob__MultipleProtein__cb__">ProfileHMM[MultipleProtein]</option>
+                <option value="ProfileHMM__ob__MultipleRNA__cb__">ProfileHMM[MultipleRNA]</option>
+                <option value="ProfileHMM__ob__PressedDNA__cb__">ProfileHMM[PressedDNA]</option>
+                <option value="ProfileHMM__ob__PressedProtein__cb__">ProfileHMM[PressedProtein]</option>
+                <option value="ProfileHMM__ob__PressedRNA__cb__">ProfileHMM[PressedRNA]</option>
+                <option value="ProfileHMM__ob__SingleDNA__cb__">ProfileHMM[SingleDNA]</option>
+                <option value="ProfileHMM__ob__SingleProtein__cb__">ProfileHMM[SingleProtein]</option>
+                <option value="ProfileHMM__ob__SingleRNA__cb__">ProfileHMM[SingleRNA]</option>
                 <option value="QualityFilterStats">QualityFilterStats</option>
                 <option value="RawSequences">RawSequences</option>
                 <option value="ReferenceDB__ob__Diamond__cb__">ReferenceDB[Diamond]</option>
@@ -101,7 +123,6 @@
                 <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>
-                <option value="SampleData__ob__BLAST6__cb__">SampleData[BLAST6]</option>
                 <option value="SampleData__ob__BooleanSeries__cb__">SampleData[BooleanSeries]</option>
                 <option value="SampleData__ob__ClassifierPredictions__cb__">SampleData[ClassifierPredictions]</option>
                 <option value="SampleData__ob__Contigs__cb__">SampleData[Contigs]</option>
@@ -113,6 +134,8 @@
                 <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>
+                <option value="SampleData__ob__NOG__cb__">SampleData[NOG]</option>
+                <option value="SampleData__ob__Orthologs__cb__">SampleData[Orthologs]</option>
                 <option value="SampleData__ob__PairedEndSequencesWithQuality__cb__">SampleData[PairedEndSequencesWithQuality]</option>
                 <option value="SampleData__ob__Probabilities__cb__">SampleData[Probabilities]</option>
                 <option value="SampleData__ob__RegressorPredictions__cb__">SampleData[RegressorPredictions]</option>
@@ -123,6 +146,7 @@
                 <option value="SampleEstimator__ob__Classifier__cb__">SampleEstimator[Classifier]</option>
                 <option value="SampleEstimator__ob__Regressor__cb__">SampleEstimator[Regressor]</option>
                 <option value="SeppReferenceDatabase">SeppReferenceDatabase</option>
+                <option value="StatsTable__ob__Pairwise__cb__">StatsTable[Pairwise]</option>
                 <option value="TaxonomicClassifier">TaxonomicClassifier</option>
                 <option value="UchimeStats">UchimeStats</option>
             </param>
@@ -155,6 +179,66 @@
                     <option value="DeblurStatsFmt">Deblur Stats Format</option>
                 </param>
             </when>
+            <when value="Dist1D__ob__Multi__comma__ Independent__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="TableJSONLFileFormat">Table JSONL File Format</option>
+                </param>
+            </when>
+            <when value="Dist1D__ob__Multi__comma__ Matched__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="TableJSONLFileFormat">Table JSONL File Format</option>
+                </param>
+            </when>
+            <when value="Dist1D__ob__NestedOrdered__comma__ Independent__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="TableJSONLFileFormat">Table JSONL File Format</option>
+                </param>
+            </when>
+            <when value="Dist1D__ob__NestedOrdered__comma__ Matched__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="TableJSONLFileFormat">Table JSONL File Format</option>
+                </param>
+            </when>
+            <when value="Dist1D__ob__NestedUnordered__comma__ Independent__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="TableJSONLFileFormat">Table JSONL File Format</option>
+                </param>
+            </when>
+            <when value="Dist1D__ob__NestedUnordered__comma__ Matched__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="TableJSONLFileFormat">Table JSONL File Format</option>
+                </param>
+            </when>
+            <when value="Dist1D__ob__Ordered__comma__ Independent__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="TableJSONLFileFormat">Table JSONL File Format</option>
+                </param>
+            </when>
+            <when value="Dist1D__ob__Ordered__comma__ Matched__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="TableJSONLFileFormat">Table JSONL File Format</option>
+                </param>
+            </when>
+            <when value="Dist1D__ob__Unordered__comma__ Independent__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="TableJSONLFileFormat">Table JSONL File Format</option>
+                </param>
+            </when>
+            <when value="Dist1D__ob__Unordered__comma__ Matched__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="TableJSONLFileFormat">Table JSONL File Format</option>
+                </param>
+            </when>
             <when value="DistanceMatrix">
                 <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>
@@ -239,12 +323,6 @@
                     <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>
@@ -263,18 +341,6 @@
                     <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>
@@ -374,6 +440,14 @@
                     <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option>
                 </param>
             </when>
+            <when value="FeatureTable__ob__Normalized__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="BIOMV210Format">BIOMV210 Format</option>
+                    <option value="DNAFASTAFormat">DNAFASTA Format</option>
+                    <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option>
+                </param>
+            </when>
             <when value="FeatureTable__ob__PercentileNormalized__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>
@@ -398,10 +472,10 @@
                     <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option>
                 </param>
             </when>
-            <when value="GenomeData__ob__BLAST6__cb__">
+            <when value="GenomeData__ob__DNASequence__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="SeedOrthologDirFmt">Seed Ortholog Directory Format</option>
+                    <option value="GenomeSequencesDirectoryFormat">Genome Sequences Directory Format</option>
                 </param>
             </when>
             <when value="GenomeData__ob__Genes__cb__">
@@ -416,6 +490,18 @@
                     <option value="LociDirectoryFormat">Loci Directory Format</option>
                 </param>
             </when>
+            <when value="GenomeData__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="GenomeData__ob__Orthologs__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="SeedOrthologDirFmt">Seed Ortholog Directory Format</option>
+                </param>
+            </when>
             <when value="GenomeData__ob__Proteins__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>
@@ -449,6 +535,7 @@
             <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>
+                    <option value="Kraken2DBReportFormat">Kraken2DB Report Format</option>
                 </param>
             </when>
             <when value="MultiplexedPairedEndBarcodeInSequence">
@@ -493,6 +580,60 @@
                     <option value="ProcrustesStatisticsFmt">Procrustes Statistics Format</option>
                 </param>
             </when>
+            <when value="ProfileHMM__ob__MultipleDNA__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="DNAMultipleProfileHmmDirectoryFmt">DNA Multiple Profile Hmm Directory Format</option>
+                </param>
+            </when>
+            <when value="ProfileHMM__ob__MultipleProtein__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="ProteinMultipleProfileHmmDirectoryFmt">Protein Multiple Profile Hmm Directory Format</option>
+                </param>
+            </when>
+            <when value="ProfileHMM__ob__MultipleRNA__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="RNAMultipleProfileHmmDirectoryFmt">RNA Multiple Profile Hmm Directory Format</option>
+                </param>
+            </when>
+            <when value="ProfileHMM__ob__PressedDNA__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="PressedProfileHmmsDirectoryFmt">Pressed Profile Hmms Directory Format</option>
+                </param>
+            </when>
+            <when value="ProfileHMM__ob__PressedProtein__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="PressedProfileHmmsDirectoryFmt">Pressed Profile Hmms Directory Format</option>
+                </param>
+            </when>
+            <when value="ProfileHMM__ob__PressedRNA__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="PressedProfileHmmsDirectoryFmt">Pressed Profile Hmms Directory Format</option>
+                </param>
+            </when>
+            <when value="ProfileHMM__ob__SingleDNA__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="DNASingleProfileHmmDirectoryFmt">DNA Single Profile Hmm Directory Format</option>
+                </param>
+            </when>
+            <when value="ProfileHMM__ob__SingleProtein__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="ProteinSingleProfileHmmDirectoryFmt">Protein Single Profile Hmm Directory Format</option>
+                </param>
+            </when>
+            <when value="ProfileHMM__ob__SingleRNA__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="RNASingleProfileHmmDirectoryFmt">RNA Single Profile Hmm Directory Format</option>
+                </param>
+            </when>
             <when value="QualityFilterStats">
                 <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>
@@ -547,12 +688,6 @@
                     <option value="ArtificialGroupingFormat">Artificial Grouping Format</option>
                 </param>
             </when>
-            <when value="SampleData__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="SeedOrthologDirFmt">Seed Ortholog Directory Format</option>
-                </param>
-            </when>
             <when value="SampleData__ob__BooleanSeries__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>
@@ -622,6 +757,18 @@
                     <option value="MultiBowtie2IndexDirFmt">Multi Bowtie2 Index Directory Format</option>
                 </param>
             </when>
+            <when value="SampleData__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="SampleData__ob__Orthologs__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="SeedOrthologDirFmt">Seed Ortholog Directory Format</option>
+                </param>
+            </when>
             <when value="SampleData__ob__PairedEndSequencesWithQuality__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>
@@ -686,6 +833,12 @@
                     <option value="SeppReferenceDirFmt">Sepp Reference Directory Format</option>
                 </param>
             </when>
+            <when value="StatsTable__ob__Pairwise__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="TableJSONLFileFormat">Table JSONL File Format</option>
+                </param>
+            </when>
             <when value="TaxonomicClassifier">
                 <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>
@@ -702,7 +855,7 @@
     </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 {'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>
+            <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>
             <discover_datasets pattern="__designation_and_ext__" visible="false"/>
         </collection>
         <data name="AlignedDNAFASTAFormat" label="${tool.name} on ${on_string} as AlignedDNAFASTAFormat">
@@ -817,10 +970,18 @@
             <filter>fmt_finder['output_format'] == 'DNAFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNAFASTAFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <data name="DNAMultipleProfileHmmDirectoryFmt" label="${tool.name} on ${on_string} as DNAMultipleProfileHmmDirectoryFmt">
+            <filter>fmt_finder['output_format'] == 'DNAMultipleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNAMultipleProfileHmmDirectoryFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;.*)\.(?P&lt;ext&gt;hmm)" visible="true"/>
+        </data>
         <data name="DNASequencesDirectoryFormat" label="${tool.name} on ${on_string} as DNASequencesDirectoryFormat">
             <filter>fmt_finder['output_format'] == 'DNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNASequencesDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;dna-sequences)\.(?P&lt;ext&gt;fasta)" visible="true"/>
         </data>
+        <data name="DNASingleProfileHmmDirectoryFmt" label="${tool.name} on ${on_string} as DNASingleProfileHmmDirectoryFmt">
+            <filter>fmt_finder['output_format'] == 'DNASingleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNASingleProfileHmmDirectoryFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;.*)\.(?P&lt;ext&gt;hmm)" visible="true"/>
+        </data>
         <collection name="DataLoafPackageDirFmt_data_slices" type="list" label="${tool.name} on ${on_string} as DataLoafPackageDirFmt (data_slices)">
             <filter>fmt_finder['output_format'] == 'DataLoafPackageDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DataLoafPackageDirFmt')</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;csv)" visible="false"/>
@@ -909,6 +1070,10 @@
             <filter>fmt_finder['output_format'] == 'GenesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'GenesDirectoryFormat')</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;(fa|fna|fasta)$)" visible="false"/>
         </collection>
+        <collection name="GenomeSequencesDirectoryFormat_genomes" type="list" label="${tool.name} on ${on_string} as GenomeSequencesDirectoryFormat (genomes)">
+            <filter>fmt_finder['output_format'] == 'GenomeSequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'GenomeSequencesDirectoryFormat')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;(fasta|fa)$)" visible="false"/>
+        </collection>
         <data name="ImmutableMetadataDirectoryFormat" label="${tool.name} on ${on_string} as ImmutableMetadataDirectoryFormat">
             <filter>fmt_finder['output_format'] == 'ImmutableMetadataDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ImmutableMetadataDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;metadata)\.(?P&lt;ext&gt;tsv)" visible="true"/>
@@ -941,6 +1106,10 @@
             <filter>fmt_finder['output_format'] == 'Kraken2DBReportDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBReportDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;report)\.(?P&lt;ext&gt;txt)" visible="true"/>
         </data>
+        <data name="Kraken2DBReportFormat" label="${tool.name} on ${on_string} as Kraken2DBReportFormat">
+            <filter>fmt_finder['output_format'] == 'Kraken2DBReportFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBReportFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
+        </data>
         <collection name="Kraken2OutputDirectoryFormat_reports" type="list" label="${tool.name} on ${on_string} as Kraken2OutputDirectoryFormat (reports)">
             <filter>fmt_finder['output_format'] == 'Kraken2OutputDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2OutputDirectoryFormat')</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+output)\.(?P&lt;ext&gt;(txt|tsv)$)" visible="false"/>
@@ -1055,6 +1224,13 @@
             <filter>fmt_finder['output_format'] == 'PredictionsFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PredictionsFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <data name="PressedProfileHmmsDirectoryFmt" label="${tool.name} on ${on_string} as PressedProfileHmmsDirectoryFmt">
+            <filter>fmt_finder['output_format'] == 'PressedProfileHmmsDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PressedProfileHmmsDirectoryFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;.*\.hmm)\.(?P&lt;ext&gt;h3m)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*\.hmm)\.(?P&lt;ext&gt;h3i)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*\.hmm)\.(?P&lt;ext&gt;h3f)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*\.hmm)\.(?P&lt;ext&gt;h3p)" visible="true"/>
+        </data>
         <data name="ProbabilitiesDirectoryFormat" label="${tool.name} on ${on_string} as ProbabilitiesDirectoryFormat">
             <filter>fmt_finder['output_format'] == 'ProbabilitiesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProbabilitiesDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;class_probabilities)\.(?P&lt;ext&gt;tsv)" visible="true"/>
@@ -1075,10 +1251,18 @@
             <filter>fmt_finder['output_format'] == 'ProteinFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinFASTAFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <data name="ProteinMultipleProfileHmmDirectoryFmt" label="${tool.name} on ${on_string} as ProteinMultipleProfileHmmDirectoryFmt">
+            <filter>fmt_finder['output_format'] == 'ProteinMultipleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinMultipleProfileHmmDirectoryFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;.*)\.(?P&lt;ext&gt;hmm)" visible="true"/>
+        </data>
         <data name="ProteinSequencesDirectoryFormat" label="${tool.name} on ${on_string} as ProteinSequencesDirectoryFormat">
             <filter>fmt_finder['output_format'] == 'ProteinSequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinSequencesDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;protein-sequences)\.(?P&lt;ext&gt;fasta)" visible="true"/>
         </data>
+        <data name="ProteinSingleProfileHmmDirectoryFmt" label="${tool.name} on ${on_string} as ProteinSingleProfileHmmDirectoryFmt">
+            <filter>fmt_finder['output_format'] == 'ProteinSingleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinSingleProfileHmmDirectoryFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;.*)\.(?P&lt;ext&gt;hmm)" visible="true"/>
+        </data>
         <collection name="ProteinsDirectoryFormat_proteins" type="list" label="${tool.name} on ${on_string} as ProteinsDirectoryFormat (proteins)">
             <filter>fmt_finder['output_format'] == 'ProteinsDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinsDirectoryFormat')</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;(fa|faa|fasta)$)" visible="false"/>
@@ -1103,10 +1287,18 @@
             <filter>fmt_finder['output_format'] == 'RNAFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNAFASTAFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <data name="RNAMultipleProfileHmmDirectoryFmt" label="${tool.name} on ${on_string} as RNAMultipleProfileHmmDirectoryFmt">
+            <filter>fmt_finder['output_format'] == 'RNAMultipleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNAMultipleProfileHmmDirectoryFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;.*)\.(?P&lt;ext&gt;hmm)" visible="true"/>
+        </data>
         <data name="RNASequencesDirectoryFormat" label="${tool.name} on ${on_string} as RNASequencesDirectoryFormat">
             <filter>fmt_finder['output_format'] == 'RNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNASequencesDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;rna-sequences)\.(?P&lt;ext&gt;fasta)" visible="true"/>
         </data>
+        <data name="RNASingleProfileHmmDirectoryFmt" label="${tool.name} on ${on_string} as RNASingleProfileHmmDirectoryFmt">
+            <filter>fmt_finder['output_format'] == 'RNASingleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNASingleProfileHmmDirectoryFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;.*)\.(?P&lt;ext&gt;hmm)" visible="true"/>
+        </data>
         <data name="SILVATaxidMapDirectoryFormat" label="${tool.name} on ${on_string} as SILVATaxidMapDirectoryFormat">
             <filter>fmt_finder['output_format'] == 'SILVATaxidMapDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SILVATaxidMapDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;silva_taxmap)\.(?P&lt;ext&gt;tsv)" visible="true"/>
@@ -1172,6 +1364,14 @@
             <filter>fmt_finder['output_format'] == 'TSVTaxonomyFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TSVTaxonomyFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <data name="TableJSONLDirFmt" label="${tool.name} on ${on_string} as TableJSONLDirFmt">
+            <filter>fmt_finder['output_format'] == 'TableJSONLDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TableJSONLDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;data.table)\.(?P&lt;ext&gt;jsonl)" visible="true"/>
+        </data>
+        <data name="TableJSONLFileFormat" label="${tool.name} on ${on_string} as TableJSONLFileFormat">
+            <filter>fmt_finder['output_format'] == 'TableJSONLFileFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TableJSONLFileFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
+        </data>
         <data name="TaxonomicClassiferTemporaryPickleDirFmt" label="${tool.name} on ${on_string} as TaxonomicClassiferTemporaryPickleDirFmt">
             <filter>fmt_finder['output_format'] == 'TaxonomicClassiferTemporaryPickleDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TaxonomicClassiferTemporaryPickleDirFmt')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;sklearn_version)\.(?P&lt;ext&gt;json)" visible="true"/>
@@ -1214,10 +1414,29 @@
 --------
 These formats have documentation available.
 
-FastqGzFormat
-*************
+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.
 
-A gzipped fastq file.
+TSVTaxonomyFormat
+*****************
+Format for a 2+ column TSV file with an expected minimal header.
+
+The only header recognized by this format is:
+
+    Feature ID&lt;tab&gt;Taxon
+
+Optionally followed by other arbitrary columns.
+
+This format supports blank lines. The expected header must be the first
+non-blank line. In addition to the header, there must be at least one line
+of data.
 
 
 QIIME1DemuxFormat
@@ -1268,127 +1487,128 @@
 "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.
-
-The only header recognized by this format is:
+FastqGzFormat
+*************
 
-    Feature ID&lt;tab&gt;Taxon
-
-Optionally followed by other arbitrary columns.
-
-This format supports blank lines. The expected header must be the first
-non-blank line. In addition to the header, there must be at least one line
-of data.
+A gzipped fastq file.
 
 
 Additional formats without documentation:
 *****************************************
- - DataLoafPackageDirFmt
- - EggnogRefDirFmt
- - NCBITaxonomyDirFmt
- - BIOMV210DirFmt
- - FirstDifferencesDirectoryFormat
- - PredictionsDirectoryFormat
- - QIIME1DemuxDirFmt
- - SILVATaxonomyFormat
- - MAGSequencesDirFmt
- - AlphaDiversityDirectoryFormat
+ - DifferentialFormat
+ - DNASequencesDirectoryFormat
  - Kraken2OutputDirectoryFormat
- - BAMDirFmt
- - TSVTaxonomyDirectoryFormat
- - EggnogProteinSequencesDirFmt
- - ImmutableMetadataFormat
- - LSMatFormat
- - SingleLanePerSampleSingleEndFastqDirFmt
- - AlignedProteinFASTAFormat
- - PairedDNASequencesDirectoryFormat
- - BooleanSeriesFormat
- - MultiplexedPairedEndBarcodeInSequenceDirFmt
- - DecontamScoreFormat
- - OrthologAnnotationDirFmt
- - GenesDirectoryFormat
  - MultiBAMDirFmt
- - BIOMV210Format
- - DecontamScoreDirFmt
+ - FirstDifferencesFormat
+ - AlignedDNAFASTAFormat
+ - ProcrustesStatisticsDirFmt
+ - EggnogProteinSequencesDirFmt
+ - DifferentialDirectoryFormat
+ - MAGSequencesDirFmt
+ - ProteinSingleProfileHmmDirectoryFmt
+ - ImportanceFormat
+ - ImmutableMetadataFormat
  - ErrorCorrectionDetailsFmt
- - DiamondDatabaseFileFmt
- - AlignedProteinSequencesDirectoryFormat
- - PairedRNASequencesDirectoryFormat
- - DifferentialFormat
- - Kraken2DBDirectoryFormat
- - DADA2StatsFormat
- - DNASequencesDirectoryFormat
- - ErrorCorrectionDetailsDirFmt
- - DiamondDatabaseDirFmt
+ - ArtificialGroupingFormat
+ - OrthologAnnotationDirFmt
+ - DecontamScoreFormat
+ - FirstDifferencesDirectoryFormat
+ - TrueTargetsDirectoryFormat
+ - AlignedDNASequencesDirectoryFormat
+ - QualityFilterStatsFmt
+ - DeblurStatsFmt
+ - BooleanSeriesDirectoryFormat
+ - BIOMV210DirFmt
+ - OrdinationFormat
+ - LSMatFormat
+ - ProteinMultipleProfileHmmDirectoryFmt
+ - ImportanceDirectoryFormat
  - ImmutableMetadataDirectoryFormat
- - BooleanSeriesDirectoryFormat
- - AlignedDNAFASTAFormat
- - ImportanceFormat
- - NewickFormat
- - DistanceMatrixDirectoryFormat
+ - ErrorCorrectionDetailsDirFmt
  - SingleLanePerSamplePairedEndFastqDirFmt
- - PlacementsDirFmt
- - DeblurStatsFmt
- - SILVATaxidMapDirectoryFormat
- - QualityFilterStatsFmt
- - AlignedDNASequencesDirectoryFormat
- - ImportanceDirectoryFormat
- - NewickDirectoryFormat
+ - 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
+ - SeppReferenceDirFmt
+ - DNAMultipleProfileHmmDirectoryFmt
+ - RNASequencesDirectoryFormat
+ - ProbabilitiesDirectoryFormat
+ - PredictionsFormat
+ - PlacementsFormat
+ - NewickFormat
+ - TableJSONLDirFmt
+ - BrackenDBDirectoryFormat
+ - ProteinSequencesDirectoryFormat
+ - GenomeSequencesDirectoryFormat
  - MultiplexedSingleEndBarcodeInSequenceDirFmt
- - MultiFASTADirectoryFormat
- - ProcrustesStatisticsFmt
- - SILVATaxidMapFormat
+ - EggnogRefDirFmt
  - UchimeStatsDirFmt
- - Kraken2ReportDirectoryFormat
- - BLAST6Format
- - QualityFilterStatsDirFmt
- - ProbabilitiesFormat
- - SILVATaxonomyDirectoryFormat
- - MultiMAGSequencesDirFmt
+ - AlignedRNAFASTAFormat
  - EMPSingleEndDirFmt
- - Bowtie2IndexDirFmt
- - ProcrustesStatisticsDirFmt
- - DeblurStatsDirFmt
- - ArtificialGroupingDirectoryFormat
+ - DADA2StatsDirFmt
  - TaxonomicClassiferTemporaryPickleDirFmt
- - LociDirectoryFormat
- - ArtificialGroupingFormat
- - MAGtoContigsFormat
- - BrackenDBDirectoryFormat
- - ProteinFASTAFormat
- - RNAFASTAFormat
- - DADA2StatsDirFmt
- - BLAST6DirectoryFormat
- - ProbabilitiesDirectoryFormat
+ - AlphaDiversityDirectoryFormat
+ - Kraken2ReportDirectoryFormat
  - MultiBowtie2IndexDirFmt
+ - SILVATaxidMapFormat
+ - CasavaOneEightSingleLanePerSampleDirFmt
+ - RNASingleProfileHmmDirectoryFmt
+ - PredictionsDirectoryFormat
+ - DeblurStatsDirFmt
+ - Bowtie2IndexDirFmt
+ - SeedOrthologDirFmt
+ - DiamondDatabaseFileFmt
+ - ProteinFASTAFormat
+ - AlignedRNASequencesDirectoryFormat
  - EMPPairedEndDirFmt
- - OrdinationFormat
- - SeedOrthologDirFmt
+ - NewickDirectoryFormat
+ - SequenceCharacteristicsDirectoryFormat
+ - ContigSequencesDirFmt
+ - Kraken2DBReportFormat
+ - RNAMultipleProfileHmmDirectoryFmt
+ - PlacementsDirFmt
+ - DecontamScoreDirFmt
+ - SILVATaxonomyFormat
+ - DataLoafPackageDirFmt
+ - SILVATaxidMapDirectoryFormat
+ - DNAFASTAFormat
+ - ProteinsDirectoryFormat
  - MAGtoContigsDirFmt
- - SampleEstimatorDirFmt
- - PlacementsFormat
- - ProteinSequencesDirectoryFormat
- - RNASequencesDirectoryFormat
- - DNAFASTAFormat
- - UchimeStatsFmt
- - AlignedRNAFASTAFormat
- - TrueTargetsDirectoryFormat
+ - QIIME1DemuxDirFmt
+ - DiamondDatabaseDirFmt
  - Kraken2DBReportDirectoryFormat
- - KaijuDBDirectoryFormat
- - ContigSequencesDirFmt
- - FirstDifferencesFormat
- - SeppReferenceDirFmt
- - OrdinationDirectoryFormat
- - PredictionsFormat
- - ProteinsDirectoryFormat
- - BLASTDBDirFmtV5
- - AlignedRNASequencesDirectoryFormat
- - SequenceCharacteristicsDirectoryFormat
- - AlphaDiversityFormat
- - CasavaOneEightSingleLanePerSampleDirFmt
- - DifferentialDirectoryFormat
+ - PairedDNASequencesDirectoryFormat
+ - NCBITaxonomyDirFmt
+ - DistanceMatrixDirectoryFormat
+ - BIOMV210Format
+ - AlignedProteinFASTAFormat
+ - SingleLanePerSampleSingleEndFastqDirFmt
+ - BAMDirFmt
+ - PairedRNASequencesDirectoryFormat
+ - AlignedProteinSequencesDirectoryFormat
+ - GenesDirectoryFormat
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>