# HG changeset patch
# User q2d2
# Date 1714080488 0
# Node ID e96704fc516dfe733b261bcfe84a594643810a3c
# Parent  f47ed6c69f5d2ee04dfd5bc37e789c3d7454f440
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

diff -r f47ed6c69f5d -r e96704fc516d qiime2_core__tools__export.xml
--- a/qiime2_core__tools__export.xml	Thu Feb 01 21:22:13 2024 +0000
+++ b/qiime2_core__tools__export.xml	Thu Apr 25 21:28:08 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 export" id="qiime2_core__tools__export" version="2023.5.0+dist.h193f7cc9.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2024.2.1+dist.he188c3c2" profile="22.05" license="BSD-3-Clause">
     <description>Export data from 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 export '$inputs'</command>
+    <command>q2galaxy run tools export '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
@@ -34,6 +34,7 @@
         <conditional name="fmt_finder">
             <param name="type" type="select" label="To change the format, select the type indicated above:">
                 <option value="None" selected="true">export as is (no conversion)</option>
+                <option value="BLASTDB">BLASTDB</option>
                 <option value="Bowtie2Index">Bowtie2Index</option>
                 <option value="DeblurStats">DeblurStats</option>
                 <option value="DistanceMatrix">DistanceMatrix</option>
@@ -52,8 +53,11 @@
                 <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>
@@ -61,6 +65,10 @@
                 <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>
@@ -72,18 +80,25 @@
                 <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>
@@ -96,6 +111,12 @@
                     <option value="None" selected="true">export as is (no conversion)</option>
                 </param>
             </when>
+            <when value="BLASTDB">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="BLASTDBDirFmtV5">BLASTDB Directory Format V5</option>
+                </param>
+            </when>
             <when value="Bowtie2Index">
                 <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
                     <option value="None" selected="true">export as is (no conversion)</option>
@@ -200,9 +221,22 @@
             <when value="FeatureData__ob__RNASequence__cb__">
                 <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
                     <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="DNAFASTAFormat">DNAFASTA Format</option>
                     <option value="RNAFASTAFormat">RNAFASTA Format</option>
                 </param>
             </when>
+            <when value="FeatureData__ob__SILVATaxidMap__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="SILVATaxidMapFormat">SILVA Taxid Map Format</option>
+                </param>
+            </when>
+            <when value="FeatureData__ob__SILVATaxonomy__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="SILVATaxonomyFormat">SILVA Taxonomy Format</option>
+                </param>
+            </when>
             <when value="FeatureData__ob__Sequence__cb__">
                 <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
                     <option value="None" selected="true">export as is (no conversion)</option>
@@ -215,6 +249,12 @@
                     <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option>
                 </param>
             </when>
+            <when value="FeatureMap__ob__MAGtoContigs__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="MAGtoContigsFormat">MA Gto Contigs Format</option>
+                </param>
+            </when>
             <when value="FeatureTable__ob__Balance__cb__">
                 <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
                     <option value="None" selected="true">export as is (no conversion)</option>
@@ -264,6 +304,30 @@
                     <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option>
                 </param>
             </when>
+            <when value="GenomeData__ob__BLAST6__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="SeedOrthologDirFmt">Seed Ortholog Directory Format</option>
+                </param>
+            </when>
+            <when value="GenomeData__ob__Genes__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="GenesDirectoryFormat">Genes Directory Format</option>
+                </param>
+            </when>
+            <when value="GenomeData__ob__Loci__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="LociDirectoryFormat">Loci Directory Format</option>
+                </param>
+            </when>
+            <when value="GenomeData__ob__Proteins__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="ProteinsDirectoryFormat">Proteins Directory Format</option>
+                </param>
+            </when>
             <when value="Hierarchy">
                 <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
                     <option value="None" selected="true">export as is (no conversion)</option>
@@ -330,6 +394,12 @@
                     <option value="EMPSingleEndDirFmt">EMP Single End Directory Format</option>
                 </param>
             </when>
+            <when value="SampleData__ob__AlignmentMap__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="BAMDirFmt">BAM Directory Format</option>
+                </param>
+            </when>
             <when value="SampleData__ob__AlphaDiversity__cb__">
                 <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
                     <option value="None" selected="true">export as is (no conversion)</option>
@@ -342,6 +412,12 @@
                     <option value="ArtificialGroupingFormat">Artificial Grouping Format</option>
                 </param>
             </when>
+            <when value="SampleData__ob__BLAST6__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="SeedOrthologDirFmt">Seed Ortholog Directory Format</option>
+                </param>
+            </when>
             <when value="SampleData__ob__BooleanSeries__cb__">
                 <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
                     <option value="None" selected="true">export as is (no conversion)</option>
@@ -354,6 +430,12 @@
                     <option value="PredictionsFormat">Predictions Format</option>
                 </param>
             </when>
+            <when value="SampleData__ob__Contigs__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="ContigSequencesDirFmt">Contig Sequences Directory Format</option>
+                </param>
+            </when>
             <when value="SampleData__ob__DADA2Stats__cb__">
                 <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
                     <option value="None" selected="true">export as is (no conversion)</option>
@@ -374,6 +456,24 @@
                     <option value="SingleLanePerSampleSingleEndFastqDirFmt">Single Lane Per Sample Single End Fastq Directory Format</option>
                 </param>
             </when>
+            <when value="SampleData__ob__MAGs__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="MultiMAGSequencesDirFmt">Multi MAG Sequences Directory Format</option>
+                </param>
+            </when>
+            <when value="SampleData__ob__MultiAlignmentMap__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="MultiBAMDirFmt">Multi BAM Directory Format</option>
+                </param>
+            </when>
+            <when value="SampleData__ob__MultiBowtie2Index__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="MultiBowtie2IndexDirFmt">Multi Bowtie2 Index Directory Format</option>
+                </param>
+            </when>
             <when value="SampleData__ob__PairedEndSequencesWithQuality__cb__">
                 <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
                     <option value="None" selected="true">export as is (no conversion)</option>
@@ -408,6 +508,12 @@
                     <option value="QIIME1DemuxFormat">QIIME1 Demux Format</option>
                 </param>
             </when>
+            <when value="SampleData__ob__SingleBowtie2Index__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="Bowtie2IndexDirFmt">Bowtie2 Index Directory Format</option>
+                </param>
+            </when>
             <when value="SampleData__ob__TrueTargets__cb__">
                 <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
                     <option value="None" selected="true">export as is (no conversion)</option>
@@ -448,7 +554,7 @@
     </inputs>
     <outputs>
         <collection name="exported" type="list" label="${tool.name} on ${on_string} as ${fmt_peek}">
-            <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'QIIME1DemuxFormat', 'DNAFASTAFormat', 'PlacementsDirFmt', 'ImmutableMetadataFormat', 'Bowtie2IndexDirFmt', 'QIIME1DemuxDirFmt', 'AlignedDNASequencesDirectoryFormat', 'DADA2StatsDirFmt', 'AlignedRNASequencesDirectoryFormat', 'OrdinationFormat', 'ProteinFASTAFormat', 'LSMatFormat', 'PairedRNASequencesDirectoryFormat', 'DifferentialFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'AlignedProteinFASTAFormat', 'ArtificialGroupingDirectoryFormat', 'RNAFASTAFormat', 'SeppReferenceDirFmt', 'FastqGzFormat', 'ProcrustesStatisticsDirFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'QualityFilterStatsFmt', 'PlacementsFormat', 'ProbabilitiesDirectoryFormat', 'ImportanceDirectoryFormat', 'FirstDifferencesFormat', 'TrueTargetsDirectoryFormat', 'ImmutableMetadataDirectoryFormat', 'UchimeStatsDirFmt', 'NewickDirectoryFormat', 'DADA2StatsFormat', 'AlignedDNAFASTAFormat', 'PredictionsDirectoryFormat', 'AlphaDiversityDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'DeblurStatsDirFmt', 'DNASequencesDirectoryFormat', 'SingleLanePerSamplePairedEndFastqDirFmt', 'UchimeStatsFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'ErrorCorrectionDetailsDirFmt', 'BLAST6DirectoryFormat', 'DecontamScoreDirFmt', 'SampleEstimatorDirFmt', 'FirstDifferencesDirectoryFormat', 'QualityFilterStatsDirFmt', 'DistanceMatrixDirectoryFormat', 'DecontamScoreFormat', 'EMPSingleEndDirFmt', 'EMPPairedEndDirFmt', 'DataLoafPackageDirFmt', 'PairedDNASequencesDirectoryFormat', 'BIOMV210DirFmt', 'AlignedRNAFASTAFormat', 'OrdinationDirectoryFormat', 'BIOMV210Format', 'AlphaDiversityFormat', 'ArtificialGroupingFormat', 'DeblurStatsFmt', 'TSVTaxonomyDirectoryFormat', 'PredictionsFormat', 'BooleanSeriesFormat', 'DifferentialDirectoryFormat', 'ProcrustesStatisticsFmt', 'BooleanSeriesDirectoryFormat', 'AlignedProteinSequencesDirectoryFormat', 'TSVTaxonomyFormat', 'NewickFormat', 'ProteinSequencesDirectoryFormat', 'BLAST6Format', 'ImportanceFormat', 'RNASequencesDirectoryFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'ProbabilitiesFormat'}</filter>
+            <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'PairedDNASequencesDirectoryFormat', 'DataLoafPackageDirFmt', 'BIOMV210Format', 'BLAST6DirectoryFormat', 'ProteinFASTAFormat', 'ProbabilitiesFormat', 'MultiBowtie2IndexDirFmt', 'MultiMAGSequencesDirFmt', 'ImmutableMetadataFormat', 'DecontamScoreFormat', 'SILVATaxidMapFormat', 'AlignedProteinFASTAFormat', 'NewickFormat', 'PredictionsFormat', 'AlignedProteinSequencesDirectoryFormat', 'SeppReferenceDirFmt', 'TaxonomicClassiferTemporaryPickleDirFmt', 'PlacementsDirFmt', 'ImmutableMetadataDirectoryFormat', 'CasavaOneEightSingleLanePerSampleDirFmt', 'EMPPairedEndDirFmt', 'RNAFASTAFormat', 'EMPSingleEndDirFmt', 'ProcrustesStatisticsDirFmt', 'DADA2StatsDirFmt', 'ErrorCorrectionDetailsDirFmt', 'ProbabilitiesDirectoryFormat', 'MultiBAMDirFmt', 'SeedOrthologDirFmt', 'AlignedRNASequencesDirectoryFormat', 'MAGtoContigsDirFmt', 'DifferentialDirectoryFormat', 'QualityFilterStatsDirFmt', 'SILVATaxonomyFormat', 'DADA2StatsFormat', 'UchimeStatsFmt', 'DecontamScoreDirFmt', 'SingleLanePerSamplePairedEndFastqDirFmt', 'RNASequencesDirectoryFormat', 'SingleLanePerSampleSingleEndFastqDirFmt', 'DNAFASTAFormat', 'BooleanSeriesDirectoryFormat', 'LociDirectoryFormat', 'NewickDirectoryFormat', 'ProteinSequencesDirectoryFormat', 'DeblurStatsFmt', 'BooleanSeriesFormat', 'OrdinationFormat', 'AlphaDiversityFormat', 'TSVTaxonomyFormat', 'SampleEstimatorDirFmt', 'MAGtoContigsFormat', 'SILVATaxonomyDirectoryFormat', 'QIIME1DemuxDirFmt', 'BLASTDBDirFmtV5', 'ProteinsDirectoryFormat', 'LSMatFormat', 'PredictionsDirectoryFormat', 'DifferentialFormat', 'BAMDirFmt', 'ArtificialGroupingFormat', 'ImportanceDirectoryFormat', 'DNASequencesDirectoryFormat', 'SILVATaxidMapDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'QIIME1DemuxFormat', 'OrdinationDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'QualityFilterStatsFmt', 'PairedRNASequencesDirectoryFormat', 'DeblurStatsDirFmt', 'ContigSequencesDirFmt', 'GenesDirectoryFormat', 'ImportanceFormat', 'ProcrustesStatisticsFmt', 'ArtificialGroupingDirectoryFormat', 'FirstDifferencesDirectoryFormat', 'BLAST6Format', 'TSVTaxonomyDirectoryFormat', 'AlphaDiversityDirectoryFormat', 'BIOMV210DirFmt', 'TrueTargetsDirectoryFormat', 'AlignedDNASequencesDirectoryFormat', 'FastqGzFormat', 'AlignedRNAFASTAFormat', 'AlignedDNAFASTAFormat', 'FirstDifferencesFormat', 'Bowtie2IndexDirFmt', 'UchimeStatsDirFmt', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'PlacementsFormat'}</filter>
             <discover_datasets pattern="__designation_and_ext__" visible="false"/>
         </collection>
         <data name="AlignedDNAFASTAFormat" label="${tool.name} on ${on_string} as AlignedDNAFASTAFormat">
@@ -491,6 +597,10 @@
             <filter>fmt_finder['output_format'] == 'ArtificialGroupingFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ArtificialGroupingFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <collection name="BAMDirFmt_bams" type="list" label="${tool.name} on ${on_string} as BAMDirFmt (bams)">
+            <filter>fmt_finder['output_format'] == 'BAMDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BAMDirFmt')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;bam)" visible="false"/>
+        </collection>
         <data name="BIOMV210DirFmt" label="${tool.name} on ${on_string} as BIOMV210DirFmt">
             <filter>fmt_finder['output_format'] == 'BIOMV210DirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BIOMV210DirFmt')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;feature-table)\.(?P&lt;ext&gt;biom)" visible="true"/>
@@ -507,6 +617,17 @@
             <filter>fmt_finder['output_format'] == 'BLAST6Format' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BLAST6Format')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <data name="BLASTDBDirFmtV5" label="${tool.name} on ${on_string} as BLASTDBDirFmtV5">
+            <filter>fmt_finder['output_format'] == 'BLASTDBDirFmtV5' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BLASTDBDirFmtV5')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;ndb)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;nhr)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;nin)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;not)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;nsq)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;ntf)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;nto)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;njs)" visible="true"/>
+        </data>
         <data name="BooleanSeriesDirectoryFormat" label="${tool.name} on ${on_string} as BooleanSeriesDirectoryFormat">
             <filter>fmt_finder['output_format'] == 'BooleanSeriesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BooleanSeriesDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;outliers)\.(?P&lt;ext&gt;tsv)" visible="true"/>
@@ -528,6 +649,10 @@
             <filter>fmt_finder['output_format'] == 'CasavaOneEightSingleLanePerSampleDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'CasavaOneEightSingleLanePerSampleDirFmt')</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+_.+_L[0-9][0-9][0-9]_R[12]_001)\.(?P&lt;ext&gt;fastq\.gz)" visible="false"/>
         </collection>
+        <collection name="ContigSequencesDirFmt_sequences" type="list" label="${tool.name} on ${on_string} as ContigSequencesDirFmt (sequences)">
+            <filter>fmt_finder['output_format'] == 'ContigSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ContigSequencesDirFmt')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;[^)\.(?P&lt;ext&gt;].+_contigs.(fasta|fa)$)" visible="false"/>
+        </collection>
         <data name="DADA2StatsDirFmt" label="${tool.name} on ${on_string} as DADA2StatsDirFmt">
             <filter>fmt_finder['output_format'] == 'DADA2StatsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DADA2StatsDirFmt')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;stats)\.(?P&lt;ext&gt;tsv)" visible="true"/>
@@ -607,6 +732,10 @@
             <filter>fmt_finder['output_format'] == 'FirstDifferencesFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'FirstDifferencesFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <collection name="GenesDirectoryFormat_genes" type="list" label="${tool.name} on ${on_string} as GenesDirectoryFormat (genes)">
+            <filter>fmt_finder['output_format'] == 'GenesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'GenesDirectoryFormat')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;(.*\_)?genes[0-9]*)\.(?P&lt;ext&gt;(fa|fna|fasta)$)" visible="false"/>
+        </collection>
         <data name="ImmutableMetadataDirectoryFormat" label="${tool.name} on ${on_string} as ImmutableMetadataDirectoryFormat">
             <filter>fmt_finder['output_format'] == 'ImmutableMetadataDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ImmutableMetadataDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;metadata)\.(?P&lt;ext&gt;tsv)" visible="true"/>
@@ -627,6 +756,39 @@
             <filter>fmt_finder['output_format'] == 'LSMatFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'LSMatFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <collection name="LociDirectoryFormat_loci" type="list" label="${tool.name} on ${on_string} as LociDirectoryFormat (loci)">
+            <filter>fmt_finder['output_format'] == 'LociDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'LociDirectoryFormat')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;(.*\_)?loci[0-9]*)\.(?P&lt;ext&gt;gff$)" visible="false"/>
+        </collection>
+        <data name="MAGtoContigsDirFmt" label="${tool.name} on ${on_string} as MAGtoContigsDirFmt">
+            <filter>fmt_finder['output_format'] == 'MAGtoContigsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MAGtoContigsDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;mag-to-contigs)\.(?P&lt;ext&gt;json)" visible="true"/>
+        </data>
+        <data name="MAGtoContigsFormat" label="${tool.name} on ${on_string} as MAGtoContigsFormat">
+            <filter>fmt_finder['output_format'] == 'MAGtoContigsFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MAGtoContigsFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
+        </data>
+        <collection name="MultiBAMDirFmt_bams" type="list" label="${tool.name} on ${on_string} as MultiBAMDirFmt (bams)">
+            <filter>fmt_finder['output_format'] == 'MultiBAMDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiBAMDirFmt')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+\/.+)\.(?P&lt;ext&gt;bam)" visible="false"/>
+        </collection>
+        <data name="MultiBowtie2IndexDirFmt" label="${tool.name} on ${on_string} as MultiBowtie2IndexDirFmt">
+            <filter>fmt_finder['output_format'] == 'MultiBowtie2IndexDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiBowtie2IndexDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;.+(?&lt;!\.rev)\.1)\.(?P&lt;ext&gt;bt2l?)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+(?&lt;!\.rev)\.2)\.(?P&lt;ext&gt;bt2l?)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+\.3)\.(?P&lt;ext&gt;bt2l?)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+\.4)\.(?P&lt;ext&gt;bt2l?)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+\.rev\.1)\.(?P&lt;ext&gt;bt2l?)" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+\.rev\.2)\.(?P&lt;ext&gt;bt2l?)" visible="true"/>
+        </data>
+        <collection name="MultiMAGSequencesDirFmt_sequences" type="list" label="${tool.name} on ${on_string} as MultiMAGSequencesDirFmt (sequences)">
+            <filter>fmt_finder['output_format'] == 'MultiMAGSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiMAGSequencesDirFmt')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;(fa|fasta)$)" visible="false"/>
+        </collection>
+        <data name="MultiMAGSequencesDirFmt" label="${tool.name} on ${on_string} as MultiMAGSequencesDirFmt">
+            <filter>fmt_finder['output_format'] == 'MultiMAGSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiMAGSequencesDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" ext="txt" pattern="(?P&lt;designation&gt;MANIFEST)" visible="true"/>
+        </data>
         <data name="MultiplexedPairedEndBarcodeInSequenceDirFmt" label="${tool.name} on ${on_string} as MultiplexedPairedEndBarcodeInSequenceDirFmt">
             <filter>fmt_finder['output_format'] == 'MultiplexedPairedEndBarcodeInSequenceDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiplexedPairedEndBarcodeInSequenceDirFmt')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;forward)\.(?P&lt;ext&gt;fastq.gz)" visible="true"/>
@@ -702,6 +864,10 @@
             <filter>fmt_finder['output_format'] == 'ProteinSequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinSequencesDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;protein-sequences)\.(?P&lt;ext&gt;fasta)" visible="true"/>
         </data>
+        <collection name="ProteinsDirectoryFormat_proteins" type="list" label="${tool.name} on ${on_string} as ProteinsDirectoryFormat (proteins)">
+            <filter>fmt_finder['output_format'] == 'ProteinsDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinsDirectoryFormat')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;(.*\_)?proteins[0-9]*)\.(?P&lt;ext&gt;(fa|faa|fasta)$)" visible="false"/>
+        </collection>
         <data name="QIIME1DemuxDirFmt" label="${tool.name} on ${on_string} as QIIME1DemuxDirFmt">
             <filter>fmt_finder['output_format'] == 'QIIME1DemuxDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'QIIME1DemuxDirFmt')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;seqs)\.(?P&lt;ext&gt;fna)" visible="true"/>
@@ -726,11 +892,31 @@
             <filter>fmt_finder['output_format'] == 'RNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNASequencesDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;rna-sequences)\.(?P&lt;ext&gt;fasta)" visible="true"/>
         </data>
+        <data name="SILVATaxidMapDirectoryFormat" label="${tool.name} on ${on_string} as SILVATaxidMapDirectoryFormat">
+            <filter>fmt_finder['output_format'] == 'SILVATaxidMapDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SILVATaxidMapDirectoryFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;silva_taxmap)\.(?P&lt;ext&gt;tsv)" visible="true"/>
+        </data>
+        <data name="SILVATaxidMapFormat" label="${tool.name} on ${on_string} as SILVATaxidMapFormat">
+            <filter>fmt_finder['output_format'] == 'SILVATaxidMapFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SILVATaxidMapFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
+        </data>
+        <data name="SILVATaxonomyDirectoryFormat" label="${tool.name} on ${on_string} as SILVATaxonomyDirectoryFormat">
+            <filter>fmt_finder['output_format'] == 'SILVATaxonomyDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SILVATaxonomyDirectoryFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;silva_taxonomy)\.(?P&lt;ext&gt;tsv)" visible="true"/>
+        </data>
+        <data name="SILVATaxonomyFormat" label="${tool.name} on ${on_string} as SILVATaxonomyFormat">
+            <filter>fmt_finder['output_format'] == 'SILVATaxonomyFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SILVATaxonomyFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
+        </data>
         <data name="SampleEstimatorDirFmt" label="${tool.name} on ${on_string} as SampleEstimatorDirFmt">
             <filter>fmt_finder['output_format'] == 'SampleEstimatorDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SampleEstimatorDirFmt')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;sklearn_version)\.(?P&lt;ext&gt;json)" visible="true"/>
             <discover_datasets pattern="(?P&lt;designation&gt;sklearn_pipeline)\.(?P&lt;ext&gt;tar)" visible="true"/>
         </data>
+        <collection name="SeedOrthologDirFmt_seed_orthologs" type="list" label="${tool.name} on ${on_string} as SeedOrthologDirFmt (seed_orthologs)">
+            <filter>fmt_finder['output_format'] == 'SeedOrthologDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SeedOrthologDirFmt')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*\..*)\.(?P&lt;ext&gt;seed_orthologs)" visible="false"/>
+        </collection>
         <data name="SeppReferenceDirFmt" label="${tool.name} on ${on_string} as SeppReferenceDirFmt">
             <filter>fmt_finder['output_format'] == 'SeppReferenceDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SeppReferenceDirFmt')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;aligned-dna-sequences)\.(?P&lt;ext&gt;fasta)" visible="true"/>
@@ -805,6 +991,12 @@
 --------
 These formats have documentation available.
 
+FastqGzFormat
+*************
+
+A gzipped fastq file.
+
+
 QIIME1DemuxFormat
 *****************
 QIIME 1 demultiplexed FASTA format.
@@ -854,86 +1046,96 @@
 of data.
 
 
-FastqGzFormat
-*************
-
-A gzipped fastq file.
-
-
 Additional formats without documentation:
 *****************************************
- - FirstDifferencesFormat
- - DecontamScoreDirFmt
- - OrdinationDirectoryFormat
- - EMPPairedEndDirFmt
- - ImmutableMetadataFormat
- - PredictionsDirectoryFormat
- - AlphaDiversityDirectoryFormat
- - DataLoafPackageDirFmt
- - AlignedDNAFASTAFormat
- - DADA2StatsDirFmt
+ - BAMDirFmt
+ - TaxonomicClassiferTemporaryPickleDirFmt
+ - ProbabilitiesDirectoryFormat
+ - BooleanSeriesFormat
+ - ErrorCorrectionDetailsDirFmt
+ - AlignedRNASequencesDirectoryFormat
+ - ProcrustesStatisticsDirFmt
+ - DifferentialDirectoryFormat
+ - SampleEstimatorDirFmt
+ - PlacementsDirFmt
+ - SILVATaxidMapDirectoryFormat
+ - BIOMV210DirFmt
+ - MultiBAMDirFmt
+ - QualityFilterStatsDirFmt
  - TrueTargetsDirectoryFormat
- - UchimeStatsFmt
- - BLAST6Format
+ - MAGtoContigsFormat
+ - ArtificialGroupingDirectoryFormat
+ - BooleanSeriesDirectoryFormat
+ - PlacementsFormat
+ - PredictionsFormat
+ - MultiplexedPairedEndBarcodeInSequenceDirFmt
+ - DeblurStatsDirFmt
+ - SingleLanePerSampleSingleEndFastqDirFmt
+ - AlignedProteinFASTAFormat
  - PairedDNASequencesDirectoryFormat
- - QIIME1DemuxDirFmt
+ - UchimeStatsDirFmt
+ - DataLoafPackageDirFmt
+ - ArtificialGroupingFormat
+ - PredictionsDirectoryFormat
+ - SILVATaxonomyDirectoryFormat
+ - DNAFASTAFormat
+ - EMPSingleEndDirFmt
+ - SingleLanePerSamplePairedEndFastqDirFmt
+ - AlignedProteinSequencesDirectoryFormat
+ - PairedRNASequencesDirectoryFormat
+ - SeppReferenceDirFmt
+ - MAGtoContigsDirFmt
+ - DifferentialFormat
+ - UchimeStatsFmt
+ - SILVATaxonomyFormat
+ - FirstDifferencesDirectoryFormat
+ - DNASequencesDirectoryFormat
+ - GenesDirectoryFormat
+ - EMPPairedEndDirFmt
+ - AlignedDNAFASTAFormat
+ - SILVATaxidMapFormat
+ - ProteinsDirectoryFormat
+ - MultiMAGSequencesDirFmt
  - QualityFilterStatsFmt
+ - AlignedDNASequencesDirectoryFormat
+ - LSMatFormat
+ - ImmutableMetadataFormat
+ - DeblurStatsFmt
+ - AlphaDiversityFormat
+ - MultiBowtie2IndexDirFmt
+ - ImportanceFormat
+ - FirstDifferencesFormat
  - DADA2StatsFormat
- - AlignedProteinFASTAFormat
- - PlacementsFormat
- - NewickFormat
- - ProbabilitiesDirectoryFormat
- - ErrorCorrectionDetailsDirFmt
+ - DistanceMatrixDirectoryFormat
+ - ImmutableMetadataDirectoryFormat
+ - OrdinationFormat
+ - DecontamScoreDirFmt
+ - CasavaOneEightSingleLanePerSampleDirFmt
+ - MultiplexedSingleEndBarcodeInSequenceDirFmt
+ - AlphaDiversityDirectoryFormat
  - ProteinFASTAFormat
  - RNAFASTAFormat
- - MultiplexedSingleEndBarcodeInSequenceDirFmt
- - BooleanSeriesFormat
- - LSMatFormat
+ - ContigSequencesDirFmt
  - ImportanceDirectoryFormat
- - DeblurStatsFmt
- - AlignedRNASequencesDirectoryFormat
- - QualityFilterStatsDirFmt
- - TaxonomicClassiferTemporaryPickleDirFmt
- - BooleanSeriesDirectoryFormat
- - DifferentialDirectoryFormat
- - DNAFASTAFormat
- - ProcrustesStatisticsFmt
- - PlacementsDirFmt
- - EMPSingleEndDirFmt
- - DecontamScoreFormat
- - BIOMV210DirFmt
- - ImmutableMetadataDirectoryFormat
- - AlignedDNASequencesDirectoryFormat
+ - DADA2StatsDirFmt
+ - NewickFormat
+ - OrdinationDirectoryFormat
  - TSVTaxonomyDirectoryFormat
- - OrdinationFormat
- - FirstDifferencesDirectoryFormat
- - Bowtie2IndexDirFmt
- - BIOMV210Format
- - SingleLanePerSampleSingleEndFastqDirFmt
- - SampleEstimatorDirFmt
- - PairedRNASequencesDirectoryFormat
- - CasavaOneEightSingleLanePerSampleDirFmt
- - AlignedProteinSequencesDirectoryFormat
- - UchimeStatsDirFmt
- - NewickDirectoryFormat
- - SingleLanePerSamplePairedEndFastqDirFmt
- - DifferentialFormat
+ - BLAST6Format
+ - LociDirectoryFormat
  - ProteinSequencesDirectoryFormat
  - RNASequencesDirectoryFormat
- - MultiplexedPairedEndBarcodeInSequenceDirFmt
- - AlphaDiversityFormat
- - DistanceMatrixDirectoryFormat
- - ArtificialGroupingFormat
- - ArtificialGroupingDirectoryFormat
+ - BIOMV210Format
  - ProbabilitiesFormat
- - DeblurStatsDirFmt
- - SeppReferenceDirFmt
- - ImportanceFormat
+ - BLASTDBDirFmtV5
+ - DecontamScoreFormat
+ - AlignedRNAFASTAFormat
+ - NewickDirectoryFormat
+ - ProcrustesStatisticsFmt
  - BLAST6DirectoryFormat
- - AlignedRNAFASTAFormat
- - DNASequencesDirectoryFormat
- - ProcrustesStatisticsDirFmt
- - PredictionsFormat
+ - SeedOrthologDirFmt
+ - QIIME1DemuxDirFmt
+ - Bowtie2IndexDirFmt
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>
diff -r f47ed6c69f5d -r e96704fc516d test-data/YY/YY_S49_R1_001.fastq.gz
Binary file test-data/YY/YY_S49_R1_001.fastq.gz has changed
diff -r f47ed6c69f5d -r e96704fc516d test-data/YY/YY_S49_R2_001.fastq.gz
Binary file test-data/YY/YY_S49_R2_001.fastq.gz has changed