# HG changeset patch
# User q2d2
# Date 1714080512 0
# Node ID 9dbdf05beaa9bb4f082bd6333dfc6123a7894234
# Parent  10447a4b0cc3e639f21bb645691332be1cd7a614
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

diff -r 10447a4b0cc3 -r 9dbdf05beaa9 qiime2_core__tools__import.xml
--- a/qiime2_core__tools__import.xml	Thu Feb 01 21:22:08 2024 +0000
+++ b/qiime2_core__tools__import.xml	Thu Apr 25 21:28:32 2024 +0000
@@ -1,21 +1,21 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+Copyright (c) 2024, QIIME 2 development team.
 
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.3" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2024.2.1+dist.he188c3c2" profile="22.05" license="BSD-3-Clause">
     <description>Import data into a QIIME 2 artifact</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
     </requirements>
-    <command detect_errors="exit_code">q2galaxy run tools import '$inputs'</command>
+    <command>q2galaxy run tools import '$inputs'</command>
     <configfiles>
         <configfile name="inputs">&lt;%
 # This is an exercise in cheating the Cheetah
@@ -60,6 +60,7 @@
         <conditional name="import_root">
             <param name="type" type="select" label="Type of data to import:">
                 <option value="None">Select a QIIME 2 type to import.</option>
+                <option value="BLASTDB">BLASTDB</option>
                 <option value="Bowtie2Index">Bowtie2Index</option>
                 <option value="DeblurStats">DeblurStats</option>
                 <option value="DistanceMatrix">DistanceMatrix</option>
@@ -78,8 +79,11 @@
                 <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__Sequence__cb__">FeatureData[Sequence]</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>
                 <option value="FeatureTable__ob__Composition__cb__">FeatureTable[Composition]</option>
                 <option value="FeatureTable__ob__Design__cb__">FeatureTable[Design]</option>
@@ -87,6 +91,10 @@
                 <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__Genes__cb__">GenomeData[Genes]</option>
+                <option value="GenomeData__ob__Loci__cb__">GenomeData[Loci]</option>
+                <option value="GenomeData__ob__Proteins__cb__">GenomeData[Proteins]</option>
                 <option value="Hierarchy">Hierarchy</option>
                 <option value="ImmutableMetadata">ImmutableMetadata</option>
                 <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option>
@@ -98,18 +106,25 @@
                 <option value="ProcrustesStatistics">ProcrustesStatistics</option>
                 <option value="QualityFilterStats">QualityFilterStats</option>
                 <option value="RawSequences">RawSequences</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>
+                <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>
                 <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__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__PairedEndSequencesWithQuality__cb__">SampleData[PairedEndSequencesWithQuality]</option>
                 <option value="SampleData__ob__Probabilities__cb__">SampleData[Probabilities]</option>
                 <option value="SampleData__ob__RegressorPredictions__cb__">SampleData[RegressorPredictions]</option>
                 <option value="SampleData__ob__SequencesWithQuality__cb__">SampleData[SequencesWithQuality]</option>
                 <option value="SampleData__ob__Sequences__cb__">SampleData[Sequences]</option>
+                <option value="SampleData__ob__SingleBowtie2Index__cb__">SampleData[SingleBowtie2Index]</option>
                 <option value="SampleData__ob__TrueTargets__cb__">SampleData[TrueTargets]</option>
                 <option value="SampleEstimator__ob__Classifier__cb__">SampleEstimator[Classifier]</option>
                 <option value="SampleEstimator__ob__Regressor__cb__">SampleEstimator[Regressor]</option>
@@ -118,6 +133,63 @@
                 <option value="UchimeStats">UchimeStats</option>
             </param>
             <when value="None"/>
+            <when value="BLASTDB">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="BLASTDBDirFmtV5" selected="true">BLASTDB Directory Format V5</option>
+                    </param>
+                    <when value="BLASTDBDirFmtV5">
+                        <section name="import_idx1" expanded="true" title="Import idx1">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.ndb">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+\.ndb</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. 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: .+\.nhr">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+\.nhr</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_idx3" expanded="true" title="Import idx3">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.nin">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+\.nin</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_idx4" expanded="true" title="Import idx4">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.not">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+\.not</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_idx5" expanded="true" title="Import idx5">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.nsq">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+\.nsq</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_idx6" expanded="true" title="Import idx6">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.ntf">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+\.ntf</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_idx7" expanded="true" title="Import idx7">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.nto">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+\.nto</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_idx8" expanded="true" title="Import idx8">
+                            <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.njs">
+                                <validator type="regex" message="This filename doesn't match the regex.">.+\.njs</validator>
+                            </param>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="Bowtie2Index">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -358,7 +430,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FrictionlessCSVFileFormat. See the documentation below for more information. Elements must match regex: .+\.csv"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FrictionlessCSVFileFormat. See the documentation below for more information. Elements must match regex: .+\.csv" 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>
@@ -480,11 +552,38 @@
                     </when>
                 </conditional>
             </when>
+            <when value="FeatureData__ob__SILVATaxidMap__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="SILVATaxidMapFormat" selected="true">SILVA Taxid Map Format</option>
+                    </param>
+                    <when value="SILVATaxidMapFormat">
+                        <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 SILVATaxidMapFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="FeatureData__ob__SILVATaxonomy__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="SILVATaxonomyFormat" selected="true">SILVA Taxonomy Format</option>
+                    </param>
+                    <when value="SILVATaxonomyFormat">
+                        <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 SILVATaxonomyFormat. 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="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="DNAFASTAFormat">
                         <section name="import" expanded="true" title="Import">
@@ -498,6 +597,12 @@
                             <param name="data" type="data" format="data" help="This data should be formatted as a MixedCaseDNAFASTAFormat. See the documentation below for more information."/>
                         </section>
                     </when>
+                    <when value="RNAFASTAFormat">
+                        <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 RNAFASTAFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
                 </conditional>
             </when>
             <when value="FeatureData__ob__Taxonomy__cb__">
@@ -527,6 +632,19 @@
                     </when>
                 </conditional>
             </when>
+            <when value="FeatureMap__ob__MAGtoContigs__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="MAGtoContigsFormat" selected="true">MA Gto Contigs Format</option>
+                    </param>
+                    <when value="MAGtoContigsFormat">
+                        <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 MAGtoContigsFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="FeatureTable__ob__Balance__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -667,6 +785,158 @@
                     </when>
                 </conditional>
             </when>
+            <when value="GenomeData__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="GenomeData__ob__Genes__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="GenesDirectoryFormat" selected="true">Genes Directory Format</option>
+                    </param>
+                    <when value="GenesDirectoryFormat">
+                        <section name="import_genes" expanded="true" title="Import genes">
+                            <conditional name="__q2galaxy__GUI__cond__genes__">
+                                <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: (.*\_)?genes[0-9]*\.(fa|fna|fasta)$" collection_type="list"/>
+                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
+                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
+                                            <option value="no">No, use element identifiers as is</option>
+                                            <option value="yes">Yes, append an extension</option>
+                                        </param>
+                                        <when value="yes">
+                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
+                                        </when>
+                                        <when value="no"/>
+                                    </conditional>
+                                </when>
+                                <when value="individual">
+                                    <repeat name="elements" min="1" title="Add Elements">
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: (.*\_)?genes[0-9]*\.(fa|fna|fasta)$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">(.*\_)?genes[0-9]*\.(fa|fna|fasta)$</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="GenomeData__ob__Loci__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="LociDirectoryFormat" selected="true">Loci Directory Format</option>
+                    </param>
+                    <when value="LociDirectoryFormat">
+                        <section name="import_loci" expanded="true" title="Import loci">
+                            <conditional name="__q2galaxy__GUI__cond__loci__">
+                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
+                                    <option value="collection" selected="true">Use collection to import</option>
+                                    <option value="individual">Associate individual files</option>
+                                </param>
+                                <when value="collection">
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a GFF3Format. See the documentation below for more information. Elements must match regex: (.*\_)?loci[0-9]*\.gff$" 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>
+                                            <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: (.*\_)?loci[0-9]*\.gff$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">(.*\_)?loci[0-9]*\.gff$</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>
+                                </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:">
+                        <option value="ProteinsDirectoryFormat" selected="true">Proteins Directory Format</option>
+                    </param>
+                    <when value="ProteinsDirectoryFormat">
+                        <section name="import_proteins" expanded="true" title="Import proteins">
+                            <conditional name="__q2galaxy__GUI__cond__proteins__">
+                                <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 ProteinFASTAFormat. See the documentation below for more information. Elements must match regex: (.*\_)?proteins[0-9]*\.(fa|faa|fasta)$" collection_type="list"/>
+                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
+                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
+                                            <option value="no">No, use element identifiers as is</option>
+                                            <option value="yes">Yes, append an extension</option>
+                                        </param>
+                                        <when value="yes">
+                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
+                                        </when>
+                                        <when value="no"/>
+                                    </conditional>
+                                </when>
+                                <when value="individual">
+                                    <repeat name="elements" min="1" title="Add Elements">
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: (.*\_)?proteins[0-9]*\.(fa|faa|fasta)$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">(.*\_)?proteins[0-9]*\.(fa|faa|fasta)$</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a ProteinFASTAFormat. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="Hierarchy">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -840,6 +1110,44 @@
                     </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:">
+                        <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="SampleData__ob__AlphaDiversity__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -866,6 +1174,44 @@
                     </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:">
@@ -892,6 +1238,44 @@
                     </when>
                 </conditional>
             </when>
+            <when value="SampleData__ob__Contigs__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="SampleData__ob__DADA2Stats__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -939,7 +1323,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz" 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>
@@ -970,7 +1354,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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>
@@ -1001,7 +1385,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+\.fastq\.gz" 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>
@@ -1056,7 +1440,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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>
@@ -1095,7 +1479,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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>
@@ -1128,6 +1512,163 @@
                     </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:">
+                        <option value="MultiFASTADirectoryFormat" selected="false">Multi FASTA Directory Format</option>
+                        <option value="MultiMAGSequencesDirFmt" selected="true">Multi MAG Sequences Directory Format</option>
+                    </param>
+                    <when value="MultiFASTADirectoryFormat">
+                        <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: .+\.(fa|fasta)$" collection_type="list"/>
+                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
+                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
+                                            <option value="no">No, use element identifiers as is</option>
+                                            <option value="yes">Yes, append an extension</option>
+                                        </param>
+                                        <when value="yes">
+                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
+                                        </when>
+                                        <when value="no"/>
+                                    </conditional>
+                                </when>
+                                <when value="individual">
+                                    <repeat name="elements" min="1" title="Add Elements">
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.(fa|fasta)$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.(fa|fasta)$</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
+                    <when value="MultiMAGSequencesDirFmt">
+                        <section name="import_sequences" expanded="true" title="Import sequences">
+                            <conditional name="__q2galaxy__GUI__cond__sequences__">
+                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
+                                    <option value="collection" selected="true">Use collection to import</option>
+                                    <option value="individual">Associate individual files</option>
+                                </param>
+                                <when value="collection">
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information. Elements must match regex: .+\.(fa|fasta)$" 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: .+\.(fa|fasta)$">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.(fa|fasta)$</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>
+                        <section name="import_manifest" expanded="true" title="Import manifest">
+                            <param name="name" type="text" value="MANIFEST" 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 MultiMAGManifestFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="SampleData__ob__MultiAlignmentMap__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="MultiBAMDirFmt" selected="true">Multi BAM Directory Format</option>
+                    </param>
+                    <when value="MultiBAMDirFmt">
+                        <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="SampleData__ob__MultiBowtie2Index__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="MultiBowtie2IndexDirFmt" selected="true">Multi Bowtie2 Index Directory Format</option>
+                    </param>
+                    <when value="MultiBowtie2IndexDirFmt">
+                        <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="SampleData__ob__PairedEndSequencesWithQuality__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -1147,7 +1688,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz" 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>
@@ -1178,7 +1719,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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>
@@ -1233,7 +1774,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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>
@@ -1313,7 +1854,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz" 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>
@@ -1344,7 +1885,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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>
@@ -1375,7 +1916,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+\.fastq\.gz" 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>
@@ -1430,7 +1971,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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>
@@ -1469,7 +2010,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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>
@@ -1522,7 +2063,7 @@
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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>
@@ -1555,6 +2096,51 @@
                     </when>
                 </conditional>
             </when>
+            <when value="SampleData__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="SampleData__ob__TrueTargets__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -1658,64 +2244,6 @@
     <outputs>
         <data name="imported_data" format="qza" from_work_dir="imported_data.qza"/>
     </outputs>
-    <tests>
-        <test>
-            <conditional name="import_root">
-                <param name="type" value="SampleData__ob__PairedEndSequencesWithQuality__cb__"/>
-                <conditional name="__q2galaxy__GUI__cond__format__">
-                    <param name="format" value="CasavaOneEightLanelessPerSampleDirFmt"/>
-                    <section name="import_sequences">
-                    <conditional name="__q2galaxy__GUI__cond__sequences__">
-                        <param name="__q2galaxy__GUI__select__picker__" value="collection"/>
-                        <param name="elements">
-                            <collection type="list">
-                                <element name="YY_S49_R1_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R1_001.fastq.gz" />
-                                <element name="YY_S49_R2_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R2_001.fastq.gz" />
-                            </collection>
-                        </param>
-                        <conditional name="__q2galaxy__GUI__cond__add_ext__">
-                            <param name="__q2galaxy__GUI__select__ext_pick__" value="yes"/>
-                            <param name="ext" label="fastq.gz"/>
-                        </conditional>
-                    </conditional>
-                </section>
-                </conditional>
-            </conditional>
-            <output name="imported_data">
-                <assert_contents>
-                    <has_size min="1"/>
-                </assert_contents>
-            </output>
-        </test>
-        <test>
-            <conditional name="import_root">
-                <param name="type" value="SampleData__ob__PairedEndSequencesWithQuality__cb__"/>
-                <conditional name="__q2galaxy__GUI__cond__format__">
-                    <param name="format" value="CasavaOneEightSingleLanePerSampleDirFmt"/>
-                    <section name="import_sequences">
-                    <conditional name="__q2galaxy__GUI__cond__sequences__">
-                        <param name="__q2galaxy__GUI__select__picker__" value="collection"/>
-                        <param name="elements">
-                            <collection type="list">
-                                <element name="YY_S49_L001_R1_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R1_001.fastq.gz" />
-                                <element name="YY_S49_L001_R2_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R2_001.fastq.gz" />
-                            </collection>
-                        </param>
-                        <conditional name="__q2galaxy__GUI__cond__add_ext__">
-                            <param name="__q2galaxy__GUI__select__ext_pick__" value="yes"/>
-                            <param name="ext" label="fastq.gz"/>
-                        </conditional>
-                    </conditional>
-                </section>
-                </conditional>
-            </conditional>
-            <output name="imported_data">
-                <assert_contents>
-                    <has_size min="1"/>
-                </assert_contents>
-            </output>
-        </test>
-    </tests>
     <help>
 QIIME 2: tools import
 =====================
@@ -1747,6 +2275,29 @@
 --------
 These formats have documentation available.
 
+HeaderlessTSVTaxonomyFormat
+***************************
+Format for a 2+ column TSV file without a header.
+
+This format supports comment lines starting with #, and blank lines.
+
+
+SampleIdIndexedSingleEndPerSampleDirFmt
+***************************************
+Single-end reads in fastq.gz files where base filename is the sample id
+
+    The full file name, minus the extension (`.fastq.gz`) is the sample id.
+    For example, the sample id for the file:
+     * `sample-1.fastq.gz` is `sample-1`
+     * `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.
@@ -1796,89 +2347,80 @@
 of data.
 
 
-HeaderlessTSVTaxonomyFormat
-***************************
-Format for a 2+ column TSV file without a header.
-
-This format supports comment lines starting with #, and blank lines.
-
-
-FastqGzFormat
-*************
-
-A gzipped fastq file.
-
-
-SampleIdIndexedSingleEndPerSampleDirFmt
-***************************************
-Single-end reads in fastq.gz files where base filename is the sample id
-
-    The full file name, minus the extension (`.fastq.gz`) is the sample id.
-    For example, the sample id for the file:
-     * `sample-1.fastq.gz` is `sample-1`
-     * `xyz.fastq.gz` is `xyz`
-     * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001`
-
 Additional formats without documentation:
 *****************************************
+ - BAMDirFmt
+ - TaxonomicClassiferTemporaryPickleDirFmt
+ - BooleanSeriesFormat
+ - SingleEndFastqManifestPhred33
+ - SampleEstimatorDirFmt
+ - MultiBAMDirFmt
+ - MAGtoContigsFormat
+ - MixedCaseAlignedRNAFASTAFormat
+ - PlacementsFormat
+ - PredictionsFormat
+ - SingleEndFastqManifestPhred64
+ - MultiplexedPairedEndBarcodeInSequenceDirFmt
+ - SingleLanePerSampleSingleEndFastqDirFmt
+ - AlignedProteinFASTAFormat
+ - PairedDNASequencesDirectoryFormat
+ - DataLoafPackageDirFmt
+ - ArtificialGroupingFormat
+ - PairedEndFastqManifestPhred33
+ - DNAFASTAFormat
+ - EMPSingleEndDirFmt
+ - SingleLanePerSamplePairedEndFastqDirFmt
+ - PairedRNASequencesDirectoryFormat
+ - SeppReferenceDirFmt
+ - DifferentialFormat
+ - UchimeStatsFmt
+ - SILVATaxonomyFormat
+ - PairedEndFastqManifestPhred64
+ - GenesDirectoryFormat
+ - MultiFASTADirectoryFormat
+ - EMPPairedEndDirFmt
+ - CasavaOneEightLanelessPerSampleDirFmt
+ - AlignedDNAFASTAFormat
+ - SILVATaxidMapFormat
+ - PairedEndFastqManifestPhred33V2
+ - SingleEndFastqManifestPhred33V2
+ - MixedCaseDNAFASTAFormat
+ - ProteinsDirectoryFormat
+ - MultiMAGSequencesDirFmt
+ - EMPSingleEndCasavaDirFmt
+ - QualityFilterStatsFmt
+ - LSMatFormat
+ - ImmutableMetadataFormat
+ - DeblurStatsFmt
+ - PairedEndFastqManifestPhred64V2
+ - SingleEndFastqManifestPhred64V2
+ - AlphaDiversityFormat
+ - MultiBowtie2IndexDirFmt
+ - EMPPairedEndCasavaDirFmt
+ - ImportanceFormat
  - FirstDifferencesFormat
  - MixedCaseAlignedDNAFASTAFormat
- - SingleLanePerSamplePairedEndFastqDirFmt
- - EMPPairedEndDirFmt
- - ImmutableMetadataFormat
- - PairedEndFastqManifestPhred64V2
- - DataLoafPackageDirFmt
- - AlignedDNAFASTAFormat
- - BIOMV100Format
- - UchimeStatsFmt
- - BLAST6Format
- - PairedDNASequencesDirectoryFormat
- - SingleEndFastqManifestPhred33V2
- - QualityFilterStatsFmt
+ - MultiplexedFastaQualDirFmt
  - DADA2StatsFormat
- - AlignedProteinFASTAFormat
- - MixedCaseRNAFASTAFormat
- - PlacementsFormat
- - NewickFormat
- - PairedEndFastqManifestPhred64
+ - OrdinationFormat
+ - CasavaOneEightSingleLanePerSampleDirFmt
  - ProteinFASTAFormat
  - RNAFASTAFormat
- - BooleanSeriesFormat
- - SingleEndFastqManifestPhred64
- - LSMatFormat
- - DeblurStatsFmt
- - ErrorCorrectionDetailsFmt
- - MixedCaseDNAFASTAFormat
- - TaxonomicClassiferTemporaryPickleDirFmt
- - DNAFASTAFormat
- - ProcrustesStatisticsFmt
- - CasavaOneEightLanelessPerSampleDirFmt
- - EMPSingleEndDirFmt
- - DecontamScoreFormat
- - OrdinationFormat
- - SingleLanePerSampleSingleEndFastqDirFmt
- - Bowtie2IndexDirFmt
+ - BIOMV100Format
+ - ContigSequencesDirFmt
+ - NewickFormat
+ - BLAST6Format
+ - LociDirectoryFormat
  - BIOMV210Format
- - PairedEndFastqManifestPhred33V2
- - SampleEstimatorDirFmt
- - EMPSingleEndCasavaDirFmt
- - PairedRNASequencesDirectoryFormat
- - EMPPairedEndCasavaDirFmt
- - CasavaOneEightSingleLanePerSampleDirFmt
- - SingleEndFastqManifestPhred64V2
- - MultiplexedFastaQualDirFmt
- - DifferentialFormat
- - AlphaDiversityFormat
- - MultiplexedPairedEndBarcodeInSequenceDirFmt
- - PairedEndFastqManifestPhred33
- - ArtificialGroupingFormat
  - ProbabilitiesFormat
- - SeppReferenceDirFmt
- - MixedCaseAlignedRNAFASTAFormat
- - SingleEndFastqManifestPhred33
- - ImportanceFormat
+ - ErrorCorrectionDetailsFmt
+ - BLASTDBDirFmtV5
+ - DecontamScoreFormat
  - AlignedRNAFASTAFormat
- - PredictionsFormat
+ - ProcrustesStatisticsFmt
+ - SeedOrthologDirFmt
+ - Bowtie2IndexDirFmt
+ - MixedCaseRNAFASTAFormat
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>
diff -r 10447a4b0cc3 -r 9dbdf05beaa9 test-data/YY/YY_S49_R1_001.fastq.gz
Binary file test-data/YY/YY_S49_R1_001.fastq.gz has changed
diff -r 10447a4b0cc3 -r 9dbdf05beaa9 test-data/YY/YY_S49_R2_001.fastq.gz
Binary file test-data/YY/YY_S49_R2_001.fastq.gz has changed