# HG changeset patch
# User q2d2
# Date 1730318415 0
# Node ID 8a0db69428c7f816b759881dcd4e6bd289f65f91
# Parent  f9e68fa06585ec63abe56765f39800ac578e045d
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 5f71b597c9495eae67a447744fded834f56ca1f7

diff -r f9e68fa06585 -r 8a0db69428c7 qiime2_core__tools__import.xml
--- a/qiime2_core__tools__import.xml	Mon Jun 03 23:32:49 2024 +0000
+++ b/qiime2_core__tools__import.xml	Wed Oct 30 20:00:15 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 import" id="qiime2_core__tools__import" version="2024.5.0+dist.he540b0b0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2024.10.0+dist.h3d8a7e27" profile="22.05" license="BSD-3-Clause">
     <description>Import data into 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 import '$inputs'</command>
     <configfiles>
@@ -64,6 +67,16 @@
                 <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>
@@ -78,12 +91,9 @@
                 <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>
@@ -99,12 +109,15 @@
                 <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>
@@ -118,6 +131,15 @@
                 <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>
@@ -127,7 +149,6 @@
                 <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>
@@ -139,6 +160,8 @@
                 <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>
@@ -149,6 +172,7 @@
                 <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>
@@ -306,6 +330,136 @@
                     </when>
                 </conditional>
             </when>
+            <when value="Dist1D__ob__Multi__comma__ Independent__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option>
+                    </param>
+                    <when value="TableJSONLFileFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="Dist1D__ob__Multi__comma__ Matched__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option>
+                    </param>
+                    <when value="TableJSONLFileFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="Dist1D__ob__NestedOrdered__comma__ Independent__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option>
+                    </param>
+                    <when value="TableJSONLFileFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="Dist1D__ob__NestedOrdered__comma__ Matched__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option>
+                    </param>
+                    <when value="TableJSONLFileFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="Dist1D__ob__NestedUnordered__comma__ Independent__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option>
+                    </param>
+                    <when value="TableJSONLFileFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="Dist1D__ob__NestedUnordered__comma__ Matched__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option>
+                    </param>
+                    <when value="TableJSONLFileFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="Dist1D__ob__Ordered__comma__ Independent__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option>
+                    </param>
+                    <when value="TableJSONLFileFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="Dist1D__ob__Ordered__comma__ Matched__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option>
+                    </param>
+                    <when value="TableJSONLFileFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="Dist1D__ob__Unordered__comma__ Independent__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option>
+                    </param>
+                    <when value="TableJSONLFileFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="Dist1D__ob__Unordered__comma__ Matched__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option>
+                    </param>
+                    <when value="TableJSONLFileFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="DistanceMatrix">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -619,44 +773,6 @@
                     </when>
                 </conditional>
             </when>
-            <when value="FeatureData__ob__KEGG__cb__">
-                <conditional name="__q2galaxy__GUI__cond__format__">
-                    <param name="format" type="select" label="QIIME 2 file format to import from:">
-                        <option value="OrthologAnnotationDirFmt" selected="true">Ortholog Annotation Directory Format</option>
-                    </param>
-                    <when value="OrthologAnnotationDirFmt">
-                        <section name="import_annotations" expanded="true" title="Import annotations">
-                            <conditional name="__q2galaxy__GUI__cond__annotations__">
-                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
-                                    <option value="collection" selected="true">Use collection to import</option>
-                                    <option value="individual">Associate individual files</option>
-                                </param>
-                                <when value="collection">
-                                    <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .+\.annotations" collection_type="list"/>
-                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
-                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
-                                            <option value="no">No, use element identifiers as is</option>
-                                            <option value="yes">Yes, append an extension</option>
-                                        </param>
-                                        <when value="yes">
-                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
-                                        </when>
-                                        <when value="no"/>
-                                    </conditional>
-                                </when>
-                                <when value="individual">
-                                    <repeat name="elements" min="1" title="Add Elements">
-                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.annotations">
-                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.annotations</validator>
-                                        </param>
-                                        <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/>
-                                    </repeat>
-                                </when>
-                            </conditional>
-                        </section>
-                    </when>
-                </conditional>
-            </when>
             <when value="FeatureData__ob__Kraken2Output__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -771,82 +887,6 @@
                     </when>
                 </conditional>
             </when>
-            <when value="FeatureData__ob__NOG__cb__">
-                <conditional name="__q2galaxy__GUI__cond__format__">
-                    <param name="format" type="select" label="QIIME 2 file format to import from:">
-                        <option value="OrthologAnnotationDirFmt" selected="true">Ortholog Annotation Directory Format</option>
-                    </param>
-                    <when value="OrthologAnnotationDirFmt">
-                        <section name="import_annotations" expanded="true" title="Import annotations">
-                            <conditional name="__q2galaxy__GUI__cond__annotations__">
-                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
-                                    <option value="collection" selected="true">Use collection to import</option>
-                                    <option value="individual">Associate individual files</option>
-                                </param>
-                                <when value="collection">
-                                    <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .+\.annotations" collection_type="list"/>
-                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
-                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
-                                            <option value="no">No, use element identifiers as is</option>
-                                            <option value="yes">Yes, append an extension</option>
-                                        </param>
-                                        <when value="yes">
-                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
-                                        </when>
-                                        <when value="no"/>
-                                    </conditional>
-                                </when>
-                                <when value="individual">
-                                    <repeat name="elements" min="1" title="Add Elements">
-                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.annotations">
-                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.annotations</validator>
-                                        </param>
-                                        <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/>
-                                    </repeat>
-                                </when>
-                            </conditional>
-                        </section>
-                    </when>
-                </conditional>
-            </when>
-            <when value="FeatureData__ob__OG__cb__">
-                <conditional name="__q2galaxy__GUI__cond__format__">
-                    <param name="format" type="select" label="QIIME 2 file format to import from:">
-                        <option value="OrthologAnnotationDirFmt" selected="true">Ortholog Annotation Directory Format</option>
-                    </param>
-                    <when value="OrthologAnnotationDirFmt">
-                        <section name="import_annotations" expanded="true" title="Import annotations">
-                            <conditional name="__q2galaxy__GUI__cond__annotations__">
-                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
-                                    <option value="collection" selected="true">Use collection to import</option>
-                                    <option value="individual">Associate individual files</option>
-                                </param>
-                                <when value="collection">
-                                    <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .+\.annotations" collection_type="list"/>
-                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
-                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
-                                            <option value="no">No, use element identifiers as is</option>
-                                            <option value="yes">Yes, append an extension</option>
-                                        </param>
-                                        <when value="yes">
-                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
-                                        </when>
-                                        <when value="no"/>
-                                    </conditional>
-                                </when>
-                                <when value="individual">
-                                    <repeat name="elements" min="1" title="Add Elements">
-                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.annotations">
-                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.annotations</validator>
-                                        </param>
-                                        <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/>
-                                    </repeat>
-                                </when>
-                            </conditional>
-                        </section>
-                    </when>
-                </conditional>
-            </when>
             <when value="FeatureData__ob__PairedEndRNASequence__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -1152,6 +1192,26 @@
                     </when>
                 </conditional>
             </when>
+            <when value="FeatureTable__ob__Normalized__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="BIOMV100Format" selected="false">BIOMV100 Format</option>
+                        <option value="BIOMV210Format" selected="true">BIOMV210 Format</option>
+                    </param>
+                    <when value="BIOMV100Format">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a BIOMV100Format. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                    <when value="BIOMV210Format">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a BIOMV210Format. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="FeatureTable__ob__PercentileNormalized__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -1212,20 +1272,20 @@
                     </when>
                 </conditional>
             </when>
-            <when value="GenomeData__ob__BLAST6__cb__">
+            <when value="GenomeData__ob__DNASequence__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
-                        <option value="SeedOrthologDirFmt" selected="true">Seed Ortholog Directory Format</option>
+                        <option value="GenomeSequencesDirectoryFormat" selected="true">Genome Sequences Directory Format</option>
                     </param>
-                    <when value="SeedOrthologDirFmt">
-                        <section name="import_seed_orthologs" expanded="true" title="Import seed_orthologs">
-                            <conditional name="__q2galaxy__GUI__cond__seed_orthologs__">
+                    <when value="GenomeSequencesDirectoryFormat">
+                        <section name="import_genomes" expanded="true" title="Import genomes">
+                            <conditional name="__q2galaxy__GUI__cond__genomes__">
                                 <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
                                     <option value="collection" selected="true">Use collection to import</option>
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .*\..*\.seed_orthologs" collection_type="list"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information. Elements must match regex: .+\.(fasta|fa)$" collection_type="list"/>
                                     <conditional name="__q2galaxy__GUI__cond__add_ext__">
                                         <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
                                             <option value="no">No, use element identifiers as is</option>
@@ -1239,10 +1299,10 @@
                                 </when>
                                 <when value="individual">
                                     <repeat name="elements" min="1" title="Add Elements">
-                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\..*\.seed_orthologs">
-                                            <validator type="regex" message="This filename doesn't match the regex.">.*\..*\.seed_orthologs</validator>
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.(fasta|fa)$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.(fasta|fa)$</validator>
                                         </param>
-                                        <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/>
                                     </repeat>
                                 </when>
                             </conditional>
@@ -1326,6 +1386,82 @@
                     </when>
                 </conditional>
             </when>
+            <when value="GenomeData__ob__NOG__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="OrthologAnnotationDirFmt" selected="true">Ortholog Annotation Directory Format</option>
+                    </param>
+                    <when value="OrthologAnnotationDirFmt">
+                        <section name="import_annotations" expanded="true" title="Import annotations">
+                            <conditional name="__q2galaxy__GUI__cond__annotations__">
+                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
+                                    <option value="collection" selected="true">Use collection to import</option>
+                                    <option value="individual">Associate individual files</option>
+                                </param>
+                                <when value="collection">
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .+\.annotations" collection_type="list"/>
+                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
+                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
+                                            <option value="no">No, use element identifiers as is</option>
+                                            <option value="yes">Yes, append an extension</option>
+                                        </param>
+                                        <when value="yes">
+                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
+                                        </when>
+                                        <when value="no"/>
+                                    </conditional>
+                                </when>
+                                <when value="individual">
+                                    <repeat name="elements" min="1" title="Add Elements">
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.annotations">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.annotations</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="GenomeData__ob__Orthologs__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="SeedOrthologDirFmt" selected="true">Seed Ortholog Directory Format</option>
+                    </param>
+                    <when value="SeedOrthologDirFmt">
+                        <section name="import_seed_orthologs" expanded="true" title="Import seed_orthologs">
+                            <conditional name="__q2galaxy__GUI__cond__seed_orthologs__">
+                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
+                                    <option value="collection" selected="true">Use collection to import</option>
+                                    <option value="individual">Associate individual files</option>
+                                </param>
+                                <when value="collection">
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .*\..*\.seed_orthologs" collection_type="list"/>
+                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
+                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
+                                            <option value="no">No, use element identifiers as is</option>
+                                            <option value="yes">Yes, append an extension</option>
+                                        </param>
+                                        <when value="yes">
+                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
+                                        </when>
+                                        <when value="no"/>
+                                    </conditional>
+                                </when>
+                                <when value="individual">
+                                    <repeat name="elements" min="1" title="Add Elements">
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\..*\.seed_orthologs">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.*\..*\.seed_orthologs</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="GenomeData__ob__Proteins__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -1553,6 +1689,195 @@
                     </when>
                 </conditional>
             </when>
+            <when value="ProfileHMM__ob__MultipleDNA__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="DNAMultipleProfileHmmDirectoryFmt" selected="true">DNA Multiple Profile Hmm Directory Format</option>
+                    </param>
+                    <when value="DNAMultipleProfileHmmDirectoryFmt">
+                        <section name="import_profiles" expanded="true" title="Import profiles">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a DNAMultipleProfileHmmFileFmt. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="ProfileHMM__ob__MultipleProtein__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="ProteinMultipleProfileHmmDirectoryFmt" selected="true">Protein Multiple Profile Hmm Directory Format</option>
+                    </param>
+                    <when value="ProteinMultipleProfileHmmDirectoryFmt">
+                        <section name="import_profiles" expanded="true" title="Import profiles">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProteinMultipleProfileHmmFileFmt. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="ProfileHMM__ob__MultipleRNA__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="RNAMultipleProfileHmmDirectoryFmt" selected="true">RNA Multiple Profile Hmm Directory Format</option>
+                    </param>
+                    <when value="RNAMultipleProfileHmmDirectoryFmt">
+                        <section name="import_profiles" expanded="true" title="Import profiles">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a RNAMultipleProfileHmmFileFmt. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="ProfileHMM__ob__PressedDNA__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="PressedProfileHmmsDirectoryFmt" selected="true">Pressed Profile Hmms Directory Format</option>
+                    </param>
+                    <when value="PressedProfileHmmsDirectoryFmt">
+                        <section name="import_h3m" expanded="true" title="Import h3m">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3m">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3m</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_h3i" expanded="true" title="Import h3i">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3i">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3i</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_h3f" expanded="true" title="Import h3f">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3f">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3f</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_h3p" expanded="true" title="Import h3p">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3p">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3p</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="ProfileHMM__ob__PressedProtein__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="PressedProfileHmmsDirectoryFmt" selected="true">Pressed Profile Hmms Directory Format</option>
+                    </param>
+                    <when value="PressedProfileHmmsDirectoryFmt">
+                        <section name="import_h3m" expanded="true" title="Import h3m">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3m">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3m</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_h3i" expanded="true" title="Import h3i">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3i">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3i</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_h3f" expanded="true" title="Import h3f">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3f">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3f</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_h3p" expanded="true" title="Import h3p">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3p">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3p</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="ProfileHMM__ob__PressedRNA__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="PressedProfileHmmsDirectoryFmt" selected="true">Pressed Profile Hmms Directory Format</option>
+                    </param>
+                    <when value="PressedProfileHmmsDirectoryFmt">
+                        <section name="import_h3m" expanded="true" title="Import h3m">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3m">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3m</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_h3i" expanded="true" title="Import h3i">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3i">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3i</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_h3f" expanded="true" title="Import h3f">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3f">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3f</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_h3p" expanded="true" title="Import h3p">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3p">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3p</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="ProfileHMM__ob__SingleDNA__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="DNASingleProfileHmmDirectoryFmt" selected="true">DNA Single Profile Hmm Directory Format</option>
+                    </param>
+                    <when value="DNASingleProfileHmmDirectoryFmt">
+                        <section name="import_profile" expanded="true" title="Import profile">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a DNASingleProfileHmmFileFmt. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="ProfileHMM__ob__SingleProtein__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="ProteinSingleProfileHmmDirectoryFmt" selected="true">Protein Single Profile Hmm Directory Format</option>
+                    </param>
+                    <when value="ProteinSingleProfileHmmDirectoryFmt">
+                        <section name="import_profile" expanded="true" title="Import profile">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a ProteinSingleProfileHmmFileFmt. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="ProfileHMM__ob__SingleRNA__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="RNASingleProfileHmmDirectoryFmt" selected="true">RNA Single Profile Hmm Directory Format</option>
+                    </param>
+                    <when value="RNASingleProfileHmmDirectoryFmt">
+                        <section name="import_profile" expanded="true" title="Import profile">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm">
+                                <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a RNASingleProfileHmmFileFmt. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="QualityFilterStats">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -1747,44 +2072,6 @@
                     </when>
                 </conditional>
             </when>
-            <when value="SampleData__ob__BLAST6__cb__">
-                <conditional name="__q2galaxy__GUI__cond__format__">
-                    <param name="format" type="select" label="QIIME 2 file format to import from:">
-                        <option value="SeedOrthologDirFmt" selected="true">Seed Ortholog Directory Format</option>
-                    </param>
-                    <when value="SeedOrthologDirFmt">
-                        <section name="import_seed_orthologs" expanded="true" title="Import seed_orthologs">
-                            <conditional name="__q2galaxy__GUI__cond__seed_orthologs__">
-                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
-                                    <option value="collection" selected="true">Use collection to import</option>
-                                    <option value="individual">Associate individual files</option>
-                                </param>
-                                <when value="collection">
-                                    <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .*\..*\.seed_orthologs" collection_type="list"/>
-                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
-                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
-                                            <option value="no">No, use element identifiers as is</option>
-                                            <option value="yes">Yes, append an extension</option>
-                                        </param>
-                                        <when value="yes">
-                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
-                                        </when>
-                                        <when value="no"/>
-                                    </conditional>
-                                </when>
-                                <when value="individual">
-                                    <repeat name="elements" min="1" title="Add Elements">
-                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\..*\.seed_orthologs">
-                                            <validator type="regex" message="This filename doesn't match the regex.">.*\..*\.seed_orthologs</validator>
-                                        </param>
-                                        <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/>
-                                    </repeat>
-                                </when>
-                            </conditional>
-                        </section>
-                    </when>
-                </conditional>
-            </when>
             <when value="SampleData__ob__BooleanSeries__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -2318,6 +2605,82 @@
                     </when>
                 </conditional>
             </when>
+            <when value="SampleData__ob__NOG__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="OrthologAnnotationDirFmt" selected="true">Ortholog Annotation Directory Format</option>
+                    </param>
+                    <when value="OrthologAnnotationDirFmt">
+                        <section name="import_annotations" expanded="true" title="Import annotations">
+                            <conditional name="__q2galaxy__GUI__cond__annotations__">
+                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
+                                    <option value="collection" selected="true">Use collection to import</option>
+                                    <option value="individual">Associate individual files</option>
+                                </param>
+                                <when value="collection">
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .+\.annotations" collection_type="list"/>
+                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
+                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
+                                            <option value="no">No, use element identifiers as is</option>
+                                            <option value="yes">Yes, append an extension</option>
+                                        </param>
+                                        <when value="yes">
+                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
+                                        </when>
+                                        <when value="no"/>
+                                    </conditional>
+                                </when>
+                                <when value="individual">
+                                    <repeat name="elements" min="1" title="Add Elements">
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.annotations">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.annotations</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="SampleData__ob__Orthologs__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="SeedOrthologDirFmt" selected="true">Seed Ortholog Directory Format</option>
+                    </param>
+                    <when value="SeedOrthologDirFmt">
+                        <section name="import_seed_orthologs" expanded="true" title="Import seed_orthologs">
+                            <conditional name="__q2galaxy__GUI__cond__seed_orthologs__">
+                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
+                                    <option value="collection" selected="true">Use collection to import</option>
+                                    <option value="individual">Associate individual files</option>
+                                </param>
+                                <when value="collection">
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .*\..*\.seed_orthologs" collection_type="list"/>
+                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
+                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
+                                            <option value="no">No, use element identifiers as is</option>
+                                            <option value="yes">Yes, append an extension</option>
+                                        </param>
+                                        <when value="yes">
+                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
+                                        </when>
+                                        <when value="no"/>
+                                    </conditional>
+                                </when>
+                                <when value="individual">
+                                    <repeat name="elements" min="1" title="Add Elements">
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\..*\.seed_orthologs">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.*\..*\.seed_orthologs</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="SampleData__ob__PairedEndSequencesWithQuality__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -2858,6 +3221,19 @@
                     </when>
                 </conditional>
             </when>
+            <when value="StatsTable__ob__Pairwise__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option>
+                    </param>
+                    <when value="TableJSONLFileFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="TaxonomicClassifier">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -2924,10 +3300,36 @@
 --------
 These formats have documentation available.
 
-FastqGzFormat
-*************
+HeaderlessTSVTaxonomyFormat
+***************************
+Format for a 2+ column TSV file without a header.
+
+This format supports comment lines starting with #, and blank lines.
+
+
+PressedProfileHmmsDirectoryFmt
+******************************
 
-A gzipped fastq file.
+The  &lt;hmmfile&gt;.h3m file contains the profile HMMs
+and their annotation in a binary format. The &lt;hmmfile&gt;.h3i file is an
+SSI index for the &lt;hmmfile&gt;.h3m file.  The &lt;hmmfile&gt;.h3f file contains
+precomputed data structures for the fast heuristic filter
+(the MSV filter).  The &lt;hmmfile&gt;.h3p file contains precomputed data
+structures for the rest of each profile.
+
+TSVTaxonomyFormat
+*****************
+Format for a 2+ column TSV file with an expected minimal header.
+
+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.
 
 
 SampleIdIndexedSingleEndPerSampleDirFmt
@@ -2974,13 +3376,6 @@
 - Each sequence must be DNA and cannot be empty.
 
 
-HeaderlessTSVTaxonomyFormat
-***************************
-Format for a 2+ column TSV file without a header.
-
-This format supports comment lines starting with #, and blank lines.
-
-
 SequenceCharacteristicsFormat
 *****************************
 
@@ -2995,107 +3390,106 @@
 "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
- - SILVATaxonomyFormat
- - MixedCaseAlignedRNAFASTAFormat
- - MAGSequencesDirFmt
+ - DifferentialFormat
  - Kraken2OutputDirectoryFormat
- - BAMDirFmt
- - EggnogProteinSequencesDirFmt
- - ImmutableMetadataFormat
- - EMPPairedEndCasavaDirFmt
- - LSMatFormat
- - SingleLanePerSampleSingleEndFastqDirFmt
- - AlignedProteinFASTAFormat
- - PairedDNASequencesDirectoryFormat
- - BooleanSeriesFormat
- - MultiplexedPairedEndBarcodeInSequenceDirFmt
- - DecontamScoreFormat
- - OrthologAnnotationDirFmt
- - GenesDirectoryFormat
  - MultiBAMDirFmt
- - BIOMV210Format
- - ErrorCorrectionDetailsFmt
- - DiamondDatabaseFileFmt
- - PairedRNASequencesDirectoryFormat
- - DifferentialFormat
- - Kraken2DBDirectoryFormat
- - DADA2StatsFormat
+ - FirstDifferencesFormat
+ - SingleEndFastqManifestPhred33V2
  - AlignedDNAFASTAFormat
+ - EggnogProteinSequencesDirFmt
+ - SingleEndFastqManifestPhred64
+ - MAGSequencesDirFmt
+ - ProteinSingleProfileHmmDirectoryFmt
+ - MixedCaseDNAFASTAFormat
  - ImportanceFormat
- - SingleEndFastqManifestPhred33
- - NewickFormat
- - MultiplexedFastaQualDirFmt
- - SingleLanePerSamplePairedEndFastqDirFmt
+ - ImmutableMetadataFormat
+ - ErrorCorrectionDetailsFmt
+ - ArtificialGroupingFormat
+ - OrthologAnnotationDirFmt
+ - DecontamScoreFormat
+ - SingleEndFastqManifestPhred64V2
+ - QualityFilterStatsFmt
  - DeblurStatsFmt
- - MixedCaseDNAFASTAFormat
- - SingleEndFastqManifestPhred33V2
- - QualityFilterStatsFmt
- - SingleEndFastqManifestPhred64
- - MultiFASTADirectoryFormat
- - ProcrustesStatisticsFmt
+ - OrdinationFormat
+ - PairedEndFastqManifestPhred33
+ - LSMatFormat
+ - ProteinMultipleProfileHmmDirectoryFmt
+ - SingleLanePerSamplePairedEndFastqDirFmt
  - CasavaOneEightLanelessPerSampleDirFmt
- - SILVATaxidMapFormat
- - SingleEndFastqManifestPhred64V2
- - Kraken2ReportDirectoryFormat
+ - Kraken2DBDirectoryFormat
  - MixedCaseAlignedDNAFASTAFormat
+ - MultiplexedFastaQualDirFmt
+ - BooleanSeriesFormat
+ - BLASTDBDirFmtV5
+ - DADA2StatsFormat
  - BLAST6Format
+ - KaijuDBDirectoryFormat
+ - MultiFASTADirectoryFormat
+ - PairedEndFastqManifestPhred64
+ - MAGtoContigsFormat
+ - DNASingleProfileHmmDirectoryFmt
+ - RNAFASTAFormat
  - ProbabilitiesFormat
- - PairedEndFastqManifestPhred33
+ - SampleEstimatorDirFmt
+ - MultiplexedPairedEndBarcodeInSequenceDirFmt
+ - TableJSONLFileFormat
+ - LociDirectoryFormat
+ - PairedEndFastqManifestPhred33V2
+ - UchimeStatsFmt
+ - ProcrustesStatisticsFmt
+ - AlphaDiversityFormat
  - MultiMAGSequencesDirFmt
+ - SeppReferenceDirFmt
+ - DNAMultipleProfileHmmDirectoryFmt
+ - PredictionsFormat
+ - PlacementsFormat
+ - NewickFormat
+ - BrackenDBDirectoryFormat
+ - GenomeSequencesDirectoryFormat
+ - EggnogRefDirFmt
+ - PairedEndFastqManifestPhred64V2
+ - AlignedRNAFASTAFormat
  - EMPSingleEndDirFmt
- - Bowtie2IndexDirFmt
  - TaxonomicClassiferTemporaryPickleDirFmt
- - LociDirectoryFormat
- - ArtificialGroupingFormat
- - MAGtoContigsFormat
- - BrackenDBDirectoryFormat
- - ProteinFASTAFormat
- - RNAFASTAFormat
- - BIOMV100Format
- - Kraken2DBReportFormat
- - PairedEndFastqManifestPhred64
+ - Kraken2ReportDirectoryFormat
  - MultiBowtie2IndexDirFmt
- - EMPPairedEndDirFmt
- - OrdinationFormat
+ - SILVATaxidMapFormat
+ - CasavaOneEightSingleLanePerSampleDirFmt
+ - RNASingleProfileHmmDirectoryFmt
+ - MixedCaseRNAFASTAFormat
+ - Bowtie2IndexDirFmt
  - SeedOrthologDirFmt
- - SampleEstimatorDirFmt
- - PlacementsFormat
- - DNAFASTAFormat
- - UchimeStatsFmt
- - PairedEndFastqManifestPhred33V2
- - AlignedRNAFASTAFormat
- - KaijuDBDirectoryFormat
+ - DiamondDatabaseFileFmt
+ - ProteinFASTAFormat
+ - EMPPairedEndDirFmt
  - ContigSequencesDirFmt
+ - Kraken2DBReportFormat
+ - RNAMultipleProfileHmmDirectoryFmt
+ - SILVATaxonomyFormat
+ - BIOMV100Format
+ - DataLoafPackageDirFmt
+ - MixedCaseAlignedRNAFASTAFormat
  - EMPSingleEndCasavaDirFmt
- - FirstDifferencesFormat
- - SeppReferenceDirFmt
- - PredictionsFormat
+ - DNAFASTAFormat
  - ProteinsDirectoryFormat
- - MixedCaseRNAFASTAFormat
- - PairedEndFastqManifestPhred64V2
- - BLASTDBDirFmtV5
- - AlphaDiversityFormat
- - CasavaOneEightSingleLanePerSampleDirFmt
+ - PairedDNASequencesDirectoryFormat
+ - NCBITaxonomyDirFmt
+ - BIOMV210Format
+ - AlignedProteinFASTAFormat
+ - SingleLanePerSampleSingleEndFastqDirFmt
+ - EMPPairedEndCasavaDirFmt
+ - BAMDirFmt
+ - PairedRNASequencesDirectoryFormat
+ - GenesDirectoryFormat
+ - SingleEndFastqManifestPhred33
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>