# HG changeset patch
# User q2d2
# Date 1717457569 0
# Node ID f9e68fa06585ec63abe56765f39800ac578e045d
# Parent  9dbdf05beaa9bb4f082bd6333dfc6123a7894234
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit c7e80dcda727ce63b42aa8a946e9330310929797

diff -r 9dbdf05beaa9 -r f9e68fa06585 qiime2_core__tools__import.xml
--- a/qiime2_core__tools__import.xml	Thu Apr 25 21:28:32 2024 +0000
+++ b/qiime2_core__tools__import.xml	Mon Jun 03 23:32:49 2024 +0000
@@ -6,14 +6,14 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2024.2.1+dist.he188c3c2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2024.5.0+dist.he540b0b0" profile="22.05" license="BSD-3-Clause">
     <description>Import data into a QIIME 2 artifact</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <command>q2galaxy run tools import '$inputs'</command>
     <configfiles>
@@ -62,6 +62,7 @@
                 <option value="None">Select a QIIME 2 type to import.</option>
                 <option value="BLASTDB">BLASTDB</option>
                 <option value="Bowtie2Index">Bowtie2Index</option>
+                <option value="BrackenDB">BrackenDB</option>
                 <option value="DeblurStats">DeblurStats</option>
                 <option value="DistanceMatrix">DistanceMatrix</option>
                 <option value="EMPPairedEndSequences">EMPPairedEndSequences</option>
@@ -70,18 +71,28 @@
                 <option value="FeatureData__ob__AlignedProteinSequence__cb__">FeatureData[AlignedProteinSequence]</option>
                 <option value="FeatureData__ob__AlignedRNASequence__cb__">FeatureData[AlignedRNASequence]</option>
                 <option value="FeatureData__ob__AlignedSequence__cb__">FeatureData[AlignedSequence]</option>
+                <option value="FeatureData__ob__AlignmentMap__cb__">FeatureData[AlignmentMap]</option>
                 <option value="FeatureData__ob__BLAST6__cb__">FeatureData[BLAST6]</option>
+                <option value="FeatureData__ob__Contig__cb__">FeatureData[Contig]</option>
                 <option value="FeatureData__ob__DecontamScore__cb__">FeatureData[DecontamScore]</option>
                 <option value="FeatureData__ob__DifferentialAbundance__cb__">FeatureData[DifferentialAbundance]</option>
                 <option value="FeatureData__ob__Differential__cb__">FeatureData[Differential]</option>
                 <option value="FeatureData__ob__Importance__cb__">FeatureData[Importance]</option>
+                <option value="FeatureData__ob__KEGG__cb__">FeatureData[KEGG]</option>
+                <option value="FeatureData__ob__Kraken2Output__cb__">FeatureData[Kraken2Output]</option>
+                <option value="FeatureData__ob__Kraken2Report__cb__">FeatureData[Kraken2Report]</option>
+                <option value="FeatureData__ob__MAG__cb__">FeatureData[MAG]</option>
+                <option value="FeatureData__ob__NOG__cb__">FeatureData[NOG]</option>
+                <option value="FeatureData__ob__OG__cb__">FeatureData[OG]</option>
                 <option value="FeatureData__ob__PairedEndRNASequence__cb__">FeatureData[PairedEndRNASequence]</option>
                 <option value="FeatureData__ob__PairedEndSequence__cb__">FeatureData[PairedEndSequence]</option>
                 <option value="FeatureData__ob__ProteinSequence__cb__">FeatureData[ProteinSequence]</option>
                 <option value="FeatureData__ob__RNASequence__cb__">FeatureData[RNASequence]</option>
                 <option value="FeatureData__ob__SILVATaxidMap__cb__">FeatureData[SILVATaxidMap]</option>
                 <option value="FeatureData__ob__SILVATaxonomy__cb__">FeatureData[SILVATaxonomy]</option>
+                <option value="FeatureData__ob__SequenceCharacteristics__cb__">FeatureData[SequenceCharacteristics]</option>
                 <option value="FeatureData__ob__Sequence__cb__">FeatureData[Sequence]</option>
+                <option value="FeatureData__ob__SingleBowtie2Index__cb__">FeatureData[SingleBowtie2Index]</option>
                 <option value="FeatureData__ob__Taxonomy__cb__">FeatureData[Taxonomy]</option>
                 <option value="FeatureMap__ob__MAGtoContigs__cb__">FeatureMap[MAGtoContigs]</option>
                 <option value="FeatureTable__ob__Balance__cb__">FeatureTable[Balance]</option>
@@ -97,6 +108,9 @@
                 <option value="GenomeData__ob__Proteins__cb__">GenomeData[Proteins]</option>
                 <option value="Hierarchy">Hierarchy</option>
                 <option value="ImmutableMetadata">ImmutableMetadata</option>
+                <option value="KaijuDB">KaijuDB</option>
+                <option value="Kraken2DB">Kraken2DB</option>
+                <option value="Kraken2DBReport">Kraken2DBReport</option>
                 <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option>
                 <option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option>
                 <option value="PCoAResults">PCoAResults</option>
@@ -106,6 +120,10 @@
                 <option value="ProcrustesStatistics">ProcrustesStatistics</option>
                 <option value="QualityFilterStats">QualityFilterStats</option>
                 <option value="RawSequences">RawSequences</option>
+                <option value="ReferenceDB__ob__Diamond__cb__">ReferenceDB[Diamond]</option>
+                <option value="ReferenceDB__ob__EggnogProteinSequences__cb__">ReferenceDB[EggnogProteinSequences]</option>
+                <option value="ReferenceDB__ob__Eggnog__cb__">ReferenceDB[Eggnog]</option>
+                <option value="ReferenceDB__ob__NCBITaxonomy__cb__">ReferenceDB[NCBITaxonomy]</option>
                 <option value="SampleData__ob__AlignmentMap__cb__">SampleData[AlignmentMap]</option>
                 <option value="SampleData__ob__AlphaDiversity__cb__">SampleData[AlphaDiversity]</option>
                 <option value="SampleData__ob__ArtificialGrouping__cb__">SampleData[ArtificialGrouping]</option>
@@ -116,6 +134,8 @@
                 <option value="SampleData__ob__DADA2Stats__cb__">SampleData[DADA2Stats]</option>
                 <option value="SampleData__ob__FirstDifferences__cb__">SampleData[FirstDifferences]</option>
                 <option value="SampleData__ob__JoinedSequencesWithQuality__cb__">SampleData[JoinedSequencesWithQuality]</option>
+                <option value="SampleData__ob__Kraken2Output__cb__">SampleData[Kraken2Output]</option>
+                <option value="SampleData__ob__Kraken2Report__cb__">SampleData[Kraken2Report]</option>
                 <option value="SampleData__ob__MAGs__cb__">SampleData[MAGs]</option>
                 <option value="SampleData__ob__MultiAlignmentMap__cb__">SampleData[MultiAlignmentMap]</option>
                 <option value="SampleData__ob__MultiBowtie2Index__cb__">SampleData[MultiBowtie2Index]</option>
@@ -235,6 +255,44 @@
                     </when>
                 </conditional>
             </when>
+            <when value="BrackenDB">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="BrackenDBDirectoryFormat" selected="true">Bracken DB Directory Format</option>
+                    </param>
+                    <when value="BrackenDBDirectoryFormat">
+                        <section name="import_kmers" expanded="true" title="Import kmers">
+                            <conditional name="__q2galaxy__GUI__cond__kmers__">
+                                <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 BrackenDBFormat. See the documentation below for more information. Elements must match regex: database(\d{2,})mers\.kmer_distrib$" 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: database(\d{2,})mers\.kmer_distrib$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">database(\d{2,})mers\.kmer_distrib$</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a BrackenDBFormat. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="DeblurStats">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -391,6 +449,44 @@
                     </when>
                 </conditional>
             </when>
+            <when value="FeatureData__ob__AlignmentMap__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="BAMDirFmt" selected="true">BAM Directory Format</option>
+                    </param>
+                    <when value="BAMDirFmt">
+                        <section name="import_bams" expanded="true" title="Import bams">
+                            <conditional name="__q2galaxy__GUI__cond__bams__">
+                                <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 BAMFormat. See the documentation below for more information. Elements must match regex: .+\.bam" 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: .+\.bam">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.bam</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a BAMFormat. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="FeatureData__ob__BLAST6__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -404,6 +500,44 @@
                     </when>
                 </conditional>
             </when>
+            <when value="FeatureData__ob__Contig__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="ContigSequencesDirFmt" selected="true">Contig Sequences Directory Format</option>
+                    </param>
+                    <when value="ContigSequencesDirFmt">
+                        <section name="import_sequences" expanded="true" title="Import sequences">
+                            <conditional name="__q2galaxy__GUI__cond__sequences__">
+                                <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 DNAFASTAFormat. See the documentation below for more information. Elements must match regex: [^\.].+_contigs.(fasta|fa)$" collection_type="list"/>
+                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
+                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
+                                            <option value="no">No, use element identifiers as is</option>
+                                            <option value="yes">Yes, append an extension</option>
+                                        </param>
+                                        <when value="yes">
+                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
+                                        </when>
+                                        <when value="no"/>
+                                    </conditional>
+                                </when>
+                                <when value="individual">
+                                    <repeat name="elements" min="1" title="Add Elements">
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: [^\.].+_contigs.(fasta|fa)$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">[^\.].+_contigs.(fasta|fa)$</validator>
+                                        </param>
+                                        <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>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="FeatureData__ob__DecontamScore__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -485,6 +619,234 @@
                     </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:">
+                        <option value="Kraken2OutputDirectoryFormat" selected="true">Kraken2 Output Directory Format</option>
+                    </param>
+                    <when value="Kraken2OutputDirectoryFormat">
+                        <section name="import_reports" expanded="true" title="Import reports">
+                            <conditional name="__q2galaxy__GUI__cond__reports__">
+                                <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 Kraken2OutputFormat. See the documentation below for more information. Elements must match regex: .+output\.(txt|tsv)$" 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: .+output\.(txt|tsv)$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+output\.(txt|tsv)$</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2OutputFormat. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="FeatureData__ob__Kraken2Report__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="Kraken2ReportDirectoryFormat" selected="true">Kraken2 Report Directory Format</option>
+                    </param>
+                    <when value="Kraken2ReportDirectoryFormat">
+                        <section name="import_reports" expanded="true" title="Import reports">
+                            <conditional name="__q2galaxy__GUI__cond__reports__">
+                                <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 Kraken2ReportFormat. See the documentation below for more information. Elements must match regex: .+report\.(txt|tsv)$" collection_type="list"/>
+                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
+                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
+                                            <option value="no">No, use element identifiers as is</option>
+                                            <option value="yes">Yes, append an extension</option>
+                                        </param>
+                                        <when value="yes">
+                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
+                                        </when>
+                                        <when value="no"/>
+                                    </conditional>
+                                </when>
+                                <when value="individual">
+                                    <repeat name="elements" min="1" title="Add Elements">
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+report\.(txt|tsv)$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+report\.(txt|tsv)$</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2ReportFormat. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="FeatureData__ob__MAG__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="MAGSequencesDirFmt" selected="true">MAG Sequences Directory Format</option>
+                    </param>
+                    <when value="MAGSequencesDirFmt">
+                        <section name="import_sequences" expanded="true" title="Import sequences">
+                            <conditional name="__q2galaxy__GUI__cond__sequences__">
+                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
+                                    <option value="collection" selected="true">Use collection to import</option>
+                                    <option value="individual">Associate individual files</option>
+                                </param>
+                                <when value="collection">
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information. Elements must match regex: ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12}\.(fa|fasta)$" 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: ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12}\.(fa|fasta)$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12}\.(fa|fasta)$</validator>
+                                        </param>
+                                        <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>
+                        </section>
+                    </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:">
@@ -578,13 +940,33 @@
                     </when>
                 </conditional>
             </when>
+            <when value="FeatureData__ob__SequenceCharacteristics__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="SequenceCharacteristicsFormat" selected="true">Sequence Characteristics Format</option>
+                    </param>
+                    <when value="SequenceCharacteristicsFormat">
+                        <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 SequenceCharacteristicsFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="FeatureData__ob__Sequence__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="BIOMV210Format" selected="false">BIOMV210 Format</option>
                         <option value="DNAFASTAFormat" selected="true">DNAFASTA Format</option>
                         <option value="MixedCaseDNAFASTAFormat" selected="false">Mixed Case DNAFASTA Format</option>
                         <option value="RNAFASTAFormat" selected="false">RNAFASTA Format</option>
                     </param>
+                    <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>
                     <when value="DNAFASTAFormat">
                         <section name="import" expanded="true" title="Import">
                             <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
@@ -605,6 +987,51 @@
                     </when>
                 </conditional>
             </when>
+            <when value="FeatureData__ob__SingleBowtie2Index__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="Bowtie2IndexDirFmt" selected="true">Bowtie2 Index Directory Format</option>
+                    </param>
+                    <when value="Bowtie2IndexDirFmt">
+                        <section name="import_idx1" expanded="true" title="Import idx1">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .+(?‹!\.rev)\.1\.bt2l?">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+(?&lt;!\.rev)\.1\.bt2l?</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_idx2" expanded="true" title="Import idx2">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .+(?‹!\.rev)\.2\.bt2l?">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+(?&lt;!\.rev)\.2\.bt2l?</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_ref3" expanded="true" title="Import ref3">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.3\.bt2l?">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+\.3\.bt2l?</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_ref4" expanded="true" title="Import ref4">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.4\.bt2l?">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+\.4\.bt2l?</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_rev1" expanded="true" title="Import rev1">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.rev\.1\.bt2l?">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+\.rev\.1\.bt2l?</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_rev2" expanded="true" title="Import rev2">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.rev\.2\.bt2l?">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+\.rev\.2\.bt2l?</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="FeatureData__ob__Taxonomy__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -836,7 +1263,7 @@
                                     <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 DNAFASTAFormat. See the documentation below for more information. Elements must match regex: (.*\_)?genes[0-9]*\.(fa|fna|fasta)$" collection_type="list"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information. Elements must match regex: .+\.(fa|fna|fasta)$" 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>
@@ -850,8 +1277,8 @@
                                 </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: (.*\_)?genes[0-9]*\.(fa|fna|fasta)$">
-                                            <validator type="regex" message="This filename doesn't match the regex.">(.*\_)?genes[0-9]*\.(fa|fna|fasta)$</validator>
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.(fa|fna|fasta)$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.(fa|fna|fasta)$</validator>
                                         </param>
                                         <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/>
                                     </repeat>
@@ -874,7 +1301,7 @@
                                     <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 GFF3Format. See the documentation below for more information. Elements must match regex: (.*\_)?loci[0-9]*\.gff$" collection_type="list"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a GFF3Format. See the documentation below for more information. Elements must match regex: .+\.gff$" 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>
@@ -888,8 +1315,8 @@
                                 </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: (.*\_)?loci[0-9]*\.gff$">
-                                            <validator type="regex" message="This filename doesn't match the regex.">(.*\_)?loci[0-9]*\.gff$</validator>
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.gff$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.gff$</validator>
                                         </param>
                                         <param name="data" type="data" format="data" help="This data should be formatted as a GFF3Format. See the documentation below for more information."/>
                                     </repeat>
@@ -912,7 +1339,7 @@
                                     <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 ProteinFASTAFormat. See the documentation below for more information. Elements must match regex: (.*\_)?proteins[0-9]*\.(fa|faa|fasta)$" collection_type="list"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a ProteinFASTAFormat. See the documentation below for more information. Elements must match regex: .+\.(fa|faa|fasta)$" 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>
@@ -926,8 +1353,8 @@
                                 </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: (.*\_)?proteins[0-9]*\.(fa|faa|fasta)$">
-                                            <validator type="regex" message="This filename doesn't match the regex.">(.*\_)?proteins[0-9]*\.(fa|faa|fasta)$</validator>
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.(fa|faa|fasta)$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.(fa|faa|fasta)$</validator>
                                         </param>
                                         <param name="data" type="data" format="data" help="This data should be formatted as a ProteinFASTAFormat. See the documentation below for more information."/>
                                     </repeat>
@@ -963,6 +1390,63 @@
                     </when>
                 </conditional>
             </when>
+            <when value="KaijuDB">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="KaijuDBDirectoryFormat" selected="true">Kaiju DB Directory Format</option>
+                    </param>
+                    <when value="KaijuDBDirectoryFormat">
+                        <section name="import_nodes" expanded="true" title="Import nodes">
+                            <param name="name" type="text" value="nodes.dmp" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a NCBITaxonomyNodesFormat. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_names" expanded="true" title="Import names">
+                            <param name="name" type="text" value="names.dmp" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a NCBITaxonomyNamesFormat. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_index" expanded="true" title="Import index">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: kaiju_db.+\.fmi">
+                                <validator type="regex" message="This filename doesn't match the regex.">kaiju_db.+\.fmi</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a KaijuIndexFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="Kraken2DB">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="Kraken2DBDirectoryFormat" selected="true">Kraken2DB Directory Format</option>
+                    </param>
+                    <when value="Kraken2DBDirectoryFormat">
+                        <section name="import_hash" expanded="true" title="Import hash">
+                            <param name="name" type="text" value="hash.k2d" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2DBFormat. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_opts" expanded="true" title="Import opts">
+                            <param name="name" type="text" value="opts.k2d" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2DBFormat. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_taxo" expanded="true" title="Import taxo">
+                            <param name="name" type="text" value="taxo.k2d" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2DBFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="Kraken2DBReport">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="Kraken2DBReportFormat" selected="true">Kraken2DB Report Format</option>
+                    </param>
+                    <when value="Kraken2DBReportFormat">
+                        <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 Kraken2DBReportFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="MultiplexedPairedEndBarcodeInSequence">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -1110,6 +1594,95 @@
                     </when>
                 </conditional>
             </when>
+            <when value="ReferenceDB__ob__Diamond__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="DiamondDatabaseFileFmt" selected="true">Diamond Database File Format</option>
+                    </param>
+                    <when value="DiamondDatabaseFileFmt">
+                        <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 DiamondDatabaseFileFmt. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="ReferenceDB__ob__EggnogProteinSequences__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="EggnogProteinSequencesDirFmt" selected="true">Eggnog Protein Sequences Directory Format</option>
+                    </param>
+                    <when value="EggnogProteinSequencesDirFmt">
+                        <section name="import_taxid_info" expanded="true" title="Import taxid_info">
+                            <param name="name" type="text" value="e5.taxid_info.tsv" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a EggnogRefTextFileFmt. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_proteins" expanded="true" title="Import proteins">
+                            <param name="name" type="text" value="e5.proteomes.faa" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a MixedCaseProteinFASTAFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="ReferenceDB__ob__Eggnog__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="EggnogRefDirFmt" selected="true">Eggnog Ref Directory Format</option>
+                    </param>
+                    <when value="EggnogRefDirFmt">
+                        <section name="import_eggnog" expanded="true" title="Import eggnog">
+                            <conditional name="__q2galaxy__GUI__cond__eggnog__">
+                                <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 EggnogRefBinFileFmt. See the documentation below for more information. Elements must match regex: eggnog.*db.*" 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: eggnog.*db.*">
+                                            <validator type="regex" message="This filename doesn't match the regex.">eggnog.*db.*</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a EggnogRefBinFileFmt. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="ReferenceDB__ob__NCBITaxonomy__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="NCBITaxonomyDirFmt" selected="true">NCBI Taxonomy Directory Format</option>
+                    </param>
+                    <when value="NCBITaxonomyDirFmt">
+                        <section name="import_node" expanded="true" title="Import node">
+                            <param name="name" type="text" value="nodes.dmp" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a NCBITaxonomyNodesFormat. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_names" expanded="true" title="Import names">
+                            <param name="name" type="text" value="names.dmp" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a NCBITaxonomyNamesFormat. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_tax_map" expanded="true" title="Import tax_map">
+                            <param name="name" type="text" value="prot.accession2taxid.gz" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a NCBITaxonomyBinaryFileFmt. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="SampleData__ob__AlignmentMap__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -1512,6 +2085,82 @@
                     </when>
                 </conditional>
             </when>
+            <when value="SampleData__ob__Kraken2Output__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="Kraken2OutputDirectoryFormat" selected="true">Kraken2 Output Directory Format</option>
+                    </param>
+                    <when value="Kraken2OutputDirectoryFormat">
+                        <section name="import_reports" expanded="true" title="Import reports">
+                            <conditional name="__q2galaxy__GUI__cond__reports__">
+                                <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 Kraken2OutputFormat. See the documentation below for more information. Elements must match regex: .+output\.(txt|tsv)$" collection_type="list"/>
+                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
+                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
+                                            <option value="no">No, use element identifiers as is</option>
+                                            <option value="yes">Yes, append an extension</option>
+                                        </param>
+                                        <when value="yes">
+                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
+                                        </when>
+                                        <when value="no"/>
+                                    </conditional>
+                                </when>
+                                <when value="individual">
+                                    <repeat name="elements" min="1" title="Add Elements">
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+output\.(txt|tsv)$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+output\.(txt|tsv)$</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2OutputFormat. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="SampleData__ob__Kraken2Report__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="Kraken2ReportDirectoryFormat" selected="true">Kraken2 Report Directory Format</option>
+                    </param>
+                    <when value="Kraken2ReportDirectoryFormat">
+                        <section name="import_reports" expanded="true" title="Import reports">
+                            <conditional name="__q2galaxy__GUI__cond__reports__">
+                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
+                                    <option value="collection" selected="true">Use collection to import</option>
+                                    <option value="individual">Associate individual files</option>
+                                </param>
+                                <when value="collection">
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a Kraken2ReportFormat. See the documentation below for more information. Elements must match regex: .+report\.(txt|tsv)$" 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: .+report\.(txt|tsv)$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+report\.(txt|tsv)$</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2ReportFormat. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="SampleData__ob__MAGs__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -2275,11 +2924,10 @@
 --------
 These formats have documentation available.
 
-HeaderlessTSVTaxonomyFormat
-***************************
-Format for a 2+ column TSV file without a header.
+FastqGzFormat
+*************
 
-This format supports comment lines starting with #, and blank lines.
+A gzipped fastq file.
 
 
 SampleIdIndexedSingleEndPerSampleDirFmt
@@ -2292,12 +2940,6 @@
      * `xyz.fastq.gz` is `xyz`
      * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001`
 
-FastqGzFormat
-*************
-
-A gzipped fastq file.
-
-
 QIIME1DemuxFormat
 *****************
 QIIME 1 demultiplexed FASTA format.
@@ -2332,6 +2974,27 @@
 - 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
+*****************************
+
+Format for a TSV file with information about sequences like length of a
+feature. The first column contains feature identifiers and is followed by
+other optional columns.
+
+The file cannot be empty and must have at least two columns.
+
+Validation for additional columns can be added with a semantic validator
+tied to a property. For example the "validate_seq_char_len" validator for
+"FeatureData[SequenceCharacteristics % Properties("length")]"
+adds validation for a numerical column called "length".
+
 TSVTaxonomyFormat
 *****************
 Format for a 2+ column TSV file with an expected minimal header.
@@ -2349,78 +3012,90 @@
 
 Additional formats without documentation:
 *****************************************
+ - DataLoafPackageDirFmt
+ - EggnogRefDirFmt
+ - NCBITaxonomyDirFmt
+ - SILVATaxonomyFormat
+ - MixedCaseAlignedRNAFASTAFormat
+ - MAGSequencesDirFmt
+ - Kraken2OutputDirectoryFormat
  - BAMDirFmt
- - TaxonomicClassiferTemporaryPickleDirFmt
- - BooleanSeriesFormat
- - SingleEndFastqManifestPhred33
- - SampleEstimatorDirFmt
- - MultiBAMDirFmt
- - MAGtoContigsFormat
- - MixedCaseAlignedRNAFASTAFormat
- - PlacementsFormat
- - PredictionsFormat
- - SingleEndFastqManifestPhred64
- - MultiplexedPairedEndBarcodeInSequenceDirFmt
+ - EggnogProteinSequencesDirFmt
+ - ImmutableMetadataFormat
+ - EMPPairedEndCasavaDirFmt
+ - LSMatFormat
  - SingleLanePerSampleSingleEndFastqDirFmt
  - AlignedProteinFASTAFormat
  - PairedDNASequencesDirectoryFormat
- - DataLoafPackageDirFmt
- - ArtificialGroupingFormat
- - PairedEndFastqManifestPhred33
- - DNAFASTAFormat
- - EMPSingleEndDirFmt
- - SingleLanePerSamplePairedEndFastqDirFmt
+ - BooleanSeriesFormat
+ - MultiplexedPairedEndBarcodeInSequenceDirFmt
+ - DecontamScoreFormat
+ - OrthologAnnotationDirFmt
+ - GenesDirectoryFormat
+ - MultiBAMDirFmt
+ - BIOMV210Format
+ - ErrorCorrectionDetailsFmt
+ - DiamondDatabaseFileFmt
  - PairedRNASequencesDirectoryFormat
- - SeppReferenceDirFmt
  - DifferentialFormat
- - UchimeStatsFmt
- - SILVATaxonomyFormat
- - PairedEndFastqManifestPhred64
- - GenesDirectoryFormat
- - MultiFASTADirectoryFormat
- - EMPPairedEndDirFmt
- - CasavaOneEightLanelessPerSampleDirFmt
+ - Kraken2DBDirectoryFormat
+ - DADA2StatsFormat
  - AlignedDNAFASTAFormat
- - SILVATaxidMapFormat
- - PairedEndFastqManifestPhred33V2
+ - ImportanceFormat
+ - SingleEndFastqManifestPhred33
+ - NewickFormat
+ - MultiplexedFastaQualDirFmt
+ - SingleLanePerSamplePairedEndFastqDirFmt
+ - DeblurStatsFmt
+ - MixedCaseDNAFASTAFormat
  - SingleEndFastqManifestPhred33V2
- - MixedCaseDNAFASTAFormat
- - ProteinsDirectoryFormat
- - MultiMAGSequencesDirFmt
- - EMPSingleEndCasavaDirFmt
  - QualityFilterStatsFmt
- - LSMatFormat
- - ImmutableMetadataFormat
- - DeblurStatsFmt
- - PairedEndFastqManifestPhred64V2
+ - SingleEndFastqManifestPhred64
+ - MultiFASTADirectoryFormat
+ - ProcrustesStatisticsFmt
+ - CasavaOneEightLanelessPerSampleDirFmt
+ - SILVATaxidMapFormat
  - SingleEndFastqManifestPhred64V2
- - AlphaDiversityFormat
- - MultiBowtie2IndexDirFmt
- - EMPPairedEndCasavaDirFmt
- - ImportanceFormat
- - FirstDifferencesFormat
+ - Kraken2ReportDirectoryFormat
  - MixedCaseAlignedDNAFASTAFormat
- - MultiplexedFastaQualDirFmt
- - DADA2StatsFormat
- - OrdinationFormat
- - CasavaOneEightSingleLanePerSampleDirFmt
+ - BLAST6Format
+ - ProbabilitiesFormat
+ - PairedEndFastqManifestPhred33
+ - MultiMAGSequencesDirFmt
+ - EMPSingleEndDirFmt
+ - Bowtie2IndexDirFmt
+ - TaxonomicClassiferTemporaryPickleDirFmt
+ - LociDirectoryFormat
+ - ArtificialGroupingFormat
+ - MAGtoContigsFormat
+ - BrackenDBDirectoryFormat
  - ProteinFASTAFormat
  - RNAFASTAFormat
  - BIOMV100Format
+ - Kraken2DBReportFormat
+ - PairedEndFastqManifestPhred64
+ - MultiBowtie2IndexDirFmt
+ - EMPPairedEndDirFmt
+ - OrdinationFormat
+ - SeedOrthologDirFmt
+ - SampleEstimatorDirFmt
+ - PlacementsFormat
+ - DNAFASTAFormat
+ - UchimeStatsFmt
+ - PairedEndFastqManifestPhred33V2
+ - AlignedRNAFASTAFormat
+ - KaijuDBDirectoryFormat
  - ContigSequencesDirFmt
- - NewickFormat
- - BLAST6Format
- - LociDirectoryFormat
- - BIOMV210Format
- - ProbabilitiesFormat
- - ErrorCorrectionDetailsFmt
+ - EMPSingleEndCasavaDirFmt
+ - FirstDifferencesFormat
+ - SeppReferenceDirFmt
+ - PredictionsFormat
+ - ProteinsDirectoryFormat
+ - MixedCaseRNAFASTAFormat
+ - PairedEndFastqManifestPhred64V2
  - BLASTDBDirFmtV5
- - DecontamScoreFormat
- - AlignedRNAFASTAFormat
- - ProcrustesStatisticsFmt
- - SeedOrthologDirFmt
- - Bowtie2IndexDirFmt
- - MixedCaseRNAFASTAFormat
+ - AlphaDiversityFormat
+ - CasavaOneEightSingleLanePerSampleDirFmt
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>