# HG changeset patch
# User q2d2
# Date 1762018433 0
# Node ID 52a1f79f0941e3c931a4258c721d29010cf9c27b
# Parent  b2c99f2353b6eb579ee2f08569acc9e7ef175ec5
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

diff -r b2c99f2353b6 -r 52a1f79f0941 qiime2_core__tools__import.xml
--- a/qiime2_core__tools__import.xml	Tue Jul 15 22:08:00 2025 +0000
+++ b/qiime2_core__tools__import.xml	Sat Nov 01 17:33:53 2025 +0000
@@ -6,17 +6,17 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2025.7.0)
+    q2galaxy (version: 2025.10.0)
 for:
-    qiime2 (version: 2025.7.0)
+    qiime2 (version: 2025.10.0)
 -->
-<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2025.7.0+dist.h44bd78f6" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2025.10.0+dist.hbfe50fe0" profile="22.05" license="BSD-3-Clause">
     <description>Import data into a QIIME 2 artifact</description>
     <xrefs>
         <xref type="bio.tools">qiime2</xref>
     </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2025.7</container>
+        <container type="docker">quay.io/qiime2/amplicon:2025.10</container>
     </requirements>
     <command>q2galaxy run tools import '$inputs'</command>
     <configfiles>
@@ -66,6 +66,7 @@
                 <option value="BLASTDB">BLASTDB</option>
                 <option value="Bowtie2Index">Bowtie2Index</option>
                 <option value="BrackenDB">BrackenDB</option>
+                <option value="DADA2BaseTransitionStats">DADA2BaseTransitionStats</option>
                 <option value="DeblurStats">DeblurStats</option>
                 <option value="Dist1D__ob__Multi__comma__ Independent__cb__">Dist1D[Multi, Independent]</option>
                 <option value="Dist1D__ob__Multi__comma__ Matched__cb__">Dist1D[Multi, Matched]</option>
@@ -127,6 +128,7 @@
                 <option value="Kraken2DBReport">Kraken2DBReport</option>
                 <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option>
                 <option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option>
+                <option value="NCBIAccessionIDs">NCBIAccessionIDs</option>
                 <option value="PCoAResults">PCoAResults</option>
                 <option value="Phylogeny__ob__Rooted__cb__">Phylogeny[Rooted]</option>
                 <option value="Phylogeny__ob__Unrooted__cb__">Phylogeny[Unrooted]</option>
@@ -147,6 +149,8 @@
                 <option value="ReferenceDB__ob__EggnogProteinSequences__cb__">ReferenceDB[EggnogProteinSequences]</option>
                 <option value="ReferenceDB__ob__Eggnog__cb__">ReferenceDB[Eggnog]</option>
                 <option value="ReferenceDB__ob__NCBITaxonomy__cb__">ReferenceDB[NCBITaxonomy]</option>
+                <option value="SRAFailedIDs">SRAFailedIDs</option>
+                <option value="SRAMetadata">SRAMetadata</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>
@@ -318,6 +322,19 @@
                     </when>
                 </conditional>
             </when>
+            <when value="DADA2BaseTransitionStats">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="DADA2BaseTransitionStatsFormat" selected="true">DADA2 Base Transition Stats Format</option>
+                    </param>
+                    <when value="DADA2BaseTransitionStatsFormat">
+                        <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 DADA2BaseTransitionStatsFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="DeblurStats">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -1666,6 +1683,26 @@
                     </when>
                 </conditional>
             </when>
+            <when value="NCBIAccessionIDs">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="NCBIAccessionIDsFormat" selected="true">NCBI Accession I Ds Format</option>
+                        <option value="SRAMetadataFormat" selected="false">SRA Metadata Format</option>
+                    </param>
+                    <when value="NCBIAccessionIDsFormat">
+                        <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 NCBIAccessionIDsFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                    <when value="SRAMetadataFormat">
+                        <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 SRAMetadataFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="PCoAResults">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -2050,6 +2087,32 @@
                     </when>
                 </conditional>
             </when>
+            <when value="SRAFailedIDs">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="SRAFailedIDsFormat" selected="true">SRA Failed I Ds Format</option>
+                    </param>
+                    <when value="SRAFailedIDsFormat">
+                        <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 SRAFailedIDsFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="SRAMetadata">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="SRAMetadataFormat" selected="true">SRA Metadata Format</option>
+                    </param>
+                    <when value="SRAMetadataFormat">
+                        <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 SRAMetadataFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="SampleData__ob__AlignmentMap__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -3342,6 +3405,35 @@
 --------
 These formats have documentation available.
 
+SRAFailedIDsFormat
+******************
+
+This is a "fake" format only used to store a list of failed SRA IDs,
+which can be converted to QIIME's metadata and input into any fondue
+action.
+
+NCBIAccessionIDsFormat
+**********************
+
+This is a format used to store a list of SRA accession IDs (run,
+study, BioProject, sample and experiment IDs), which can be converted
+to QIIME's metadata. Artifacts containing of run, study and BioProject
+IDs can be input into any fondue action.
+
+SequenceCharacteristicsFormat
+*****************************
+
+Format for a TSV file with information about sequences like length of a
+feature. The first column contains feature identifiers and is followed by
+other optional columns.
+
+The file cannot be empty and must have at least two columns.
+
+Validation for additional columns can be added with a semantic validator
+tied to a property. For example the "validate_seq_char_len" validator for
+"FeatureData[SequenceCharacteristics % Properties("length")]"
+adds validation for a numerical column called "length".
+
 SampleIdIndexedSingleEndPerSampleDirFmt
 ***************************************
 Single-end reads in fastq.gz files where base filename is the sample id
@@ -3352,6 +3444,37 @@
      * `xyz.fastq.gz` is `xyz`
      * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001`
 
+ANCOMBC2OutputDirFmt
+********************
+
+Stores the model statistics and optionally the structural zeros table=
+output by the ANCOMBC2 method.
+
+The slices are:
+    - lfc: log-fold change
+    - se: standard error
+    - W: lfc / se (the test statistic)
+    - p: p-value
+    - q: adjusted p-value
+    - diff: differentially abundant boolean (i.e. q &lt; alpha)
+    - passed_ss: whether sensitivity analysis was passed
+
+FastqGzFormat
+*************
+
+A gzipped fastq file.
+
+
+PressedProfileHmmsDirectoryFmt
+******************************
+
+The  &lt;hmmfile&gt;.h3m file contains the profile HMMs
+and their annotation in a binary format. The &lt;hmmfile&gt;.h3i file is an
+SSI index for the &lt;hmmfile&gt;.h3m file.  The &lt;hmmfile&gt;.h3f file contains
+precomputed data structures for the fast heuristic filter
+(the MSV filter).  The &lt;hmmfile&gt;.h3p file contains precomputed data
+structures for the rest of each profile.
+
 QIIME1DemuxFormat
 *****************
 QIIME 1 demultiplexed FASTA format.
@@ -3386,12 +3509,6 @@
 - Each sequence must be DNA and cannot be empty.
 
 
-FastqGzFormat
-*************
-
-A gzipped fastq file.
-
-
 HeaderlessTSVTaxonomyFormat
 ***************************
 Format for a 2+ column TSV file without a header.
@@ -3414,139 +3531,102 @@
 of data.
 
 
-ANCOMBC2OutputDirFmt
-********************
-
-Stores the model statistics and optionally the structural zeros table=
-output by the ANCOMBC2 method.
-
-The slices are:
-    - lfc: log-fold change
-    - se: standard error
-    - W: lfc / se (the test statistic)
-    - p: p-value
-    - q: adjusted p-value
-    - diff: differentially abundant boolean (i.e. q &lt; alpha)
-    - passed_ss: whether sensitivity analysis was passed
-
-SequenceCharacteristicsFormat
-*****************************
-
-Format for a TSV file with information about sequences like length of a
-feature. The first column contains feature identifiers and is followed by
-other optional columns.
-
-The file cannot be empty and must have at least two columns.
-
-Validation for additional columns can be added with a semantic validator
-tied to a property. For example the "validate_seq_char_len" validator for
-"FeatureData[SequenceCharacteristics % Properties("length")]"
-adds validation for a numerical column called "length".
-
-PressedProfileHmmsDirectoryFmt
-******************************
-
-The  &lt;hmmfile&gt;.h3m file contains the profile HMMs
-and their annotation in a binary format. The &lt;hmmfile&gt;.h3i file is an
-SSI index for the &lt;hmmfile&gt;.h3m file.  The &lt;hmmfile&gt;.h3f file contains
-precomputed data structures for the fast heuristic filter
-(the MSV filter).  The &lt;hmmfile&gt;.h3p file contains precomputed data
-structures for the rest of each profile.
-
 Additional formats without documentation:
 *****************************************
- - PredictionsFormat
+ - ContigSequencesDirFmt
+ - BrackenDBDirectoryFormat
+ - MixedCaseAlignedDNAFASTAFormat
+ - SILVATaxidMapFormat
+ - EggnogRefDirFmt
+ - CasavaOneEightSingleLanePerSampleDirFmt
+ - RNAMultipleProfileHmmDirectoryFmt
+ - BLAST6Format
+ - LSMatFormat
+ - MultiplexedFastaQualDirFmt
+ - RNAFASTAFormat
+ - NewickFormat
+ - MAGSequencesDirFmt
  - DiamondDatabaseFileFmt
- - Kraken2DBReportFormat
- - MultiFASTADirectoryFormat
- - CasavaOneEightLanelessPerSampleDirFmt
- - Kraken2OutputDirectoryFormat
- - MixedCaseAlignedRNAFASTAFormat
- - PairedEndFastqManifestPhred33
- - SeedOrthologDirFmt
- - DNAFASTAFormat
- - Kraken2DBDirectoryFormat
- - PlacementsFormat
+ - OrthologAnnotationDirFmt
  - DeblurStatsFmt
- - PairedDNASequencesDirectoryFormat
- - AlphaDiversityFormat
- - OrdinationFormat
+ - BAMDirFmt
  - BIOMV100Format
- - MultiMAGSequencesDirFmt
- - AlignedProteinFASTAFormat
- - EMPPairedEndDirFmt
- - PairedEndFastqManifestPhred64
- - OrthologAnnotationDirFmt
- - UchimeStatsFmt
- - LSMatFormat
- - PairedRNASequencesDirectoryFormat
- - PairedEndFastqManifestPhred33V2
- - MultiBowtie2IndexDirFmt
- - DifferentialFormat
- - ImmutableMetadataFormat
- - Bowtie2IndexDirFmt
- - AlignedDNAFASTAFormat
- - PairedEndFastqManifestPhred64V2
- - ContigSequencesDirFmt
- - EMPPairedEndCasavaDirFmt
- - EggnogProteinSequencesDirFmt
- - CasavaOneEightSingleLanePerSampleDirFmt
- - MixedCaseDNAFASTAFormat
- - BooleanSeriesFormat
+ - AlignedRNAFASTAFormat
+ - ProteinsDirectoryFormat
+ - MAGtoContigsFormat
+ - DecontamScoreFormat
+ - SingleEndFastqManifestPhred33V2
  - EMPSingleEndDirFmt
  - ProteinSingleProfileHmmDirectoryFmt
  - ProbabilitiesFormat
- - DADA2StatsFormat
+ - MixedCaseRNAFASTAFormat
+ - ProteinFASTAFormat
+ - MultiBAMDirFmt
+ - BIOMV210Format
+ - Kraken2DBReportFormat
  - ImportanceFormat
- - GenesDirectoryFormat
- - SeppReferenceDirFmt
+ - SeedOrthologDirFmt
  - SingleEndFastqManifestPhred64V2
- - SILVATaxonomyFormat
- - BrackenDBDirectoryFormat
- - BIOMV210Format
+ - EMPPairedEndDirFmt
+ - ArtificialGroupingFormat
  - ProteinMultipleProfileHmmDirectoryFmt
- - QualityFilterStatsFmt
- - MixedCaseAlignedDNAFASTAFormat
- - NCBITaxonomyDirFmt
- - Kraken2ReportDirectoryFormat
- - BAMDirFmt
- - BLAST6Format
- - ProteinsDirectoryFormat
- - NewickFormat
- - SingleLanePerSampleSingleEndFastqDirFmt
- - DataLoafPackageDirFmt
- - RNAFASTAFormat
- - ProcrustesStatisticsFmt
+ - SampleEstimatorDirFmt
+ - SingleEndFastqManifestPhred33
+ - Kraken2OutputDirectoryFormat
+ - EggnogProteinSequencesDirFmt
+ - MixedCaseAlignedRNAFASTAFormat
+ - DNAFASTAFormat
+ - EMPSingleEndCasavaDirFmt
+ - OrdinationFormat
  - DNASingleProfileHmmDirectoryFmt
  - SingleLanePerSamplePairedEndFastqDirFmt
+ - PairedDNASequencesDirectoryFormat
+ - ImmutableMetadataFormat
+ - AlphaDiversityFormat
+ - SingleEndFastqManifestPhred64
+ - AlignedProteinFASTAFormat
+ - GenesDirectoryFormat
+ - DADA2BaseTransitionStatsFormat
  - TaxonomicClassiferTemporaryPickleDirFmt
- - MAGtoContigsFormat
- - ArtificialGroupingFormat
- - MultiBAMDirFmt
+ - SILVATaxonomyFormat
+ - EMPPairedEndCasavaDirFmt
+ - DNAMultipleProfileHmmDirectoryFmt
+ - BLASTDBDirFmtV5
+ - PlacementsFormat
+ - MultiFASTADirectoryFormat
+ - CasavaOneEightLanelessPerSampleDirFmt
+ - PairedRNASequencesDirectoryFormat
+ - BooleanSeriesFormat
+ - SRAMetadataFormat
+ - PairedEndFastqManifestPhred33
+ - RNASingleProfileHmmDirectoryFmt
+ - DifferentialFormat
+ - GenomeSequencesDirectoryFormat
+ - ProcrustesStatisticsFmt
+ - MultiMAGSequencesDirFmt
+ - AlignedDNAFASTAFormat
+ - PairedEndFastqManifestPhred64
+ - DADA2StatsFormat
+ - MultiplexedPairedEndBarcodeInSequenceDirFmt
+ - TableJSONLFileFormat
+ - MixedCaseDNAFASTAFormat
+ - PredictionsFormat
+ - Kraken2ReportDirectoryFormat
+ - SeppReferenceDirFmt
+ - PairedEndFastqManifestPhred33V2
+ - LociDirectoryFormat
+ - Bowtie2IndexDirFmt
+ - UchimeStatsFmt
+ - MultiBowtie2IndexDirFmt
+ - ErrorCorrectionDetailsFmt
+ - NCBITaxonomyDirFmt
+ - QualityFilterStatsFmt
+ - Kraken2DBDirectoryFormat
+ - DataLoafPackageDirFmt
+ - SingleLanePerSampleSingleEndFastqDirFmt
+ - PairedEndFastqManifestPhred64V2
  - FirstDifferencesFormat
  - KaijuDBDirectoryFormat
- - DecontamScoreFormat
- - LociDirectoryFormat
- - DNAMultipleProfileHmmDirectoryFmt
- - TableJSONLFileFormat
- - AlignedRNAFASTAFormat
- - SingleEndFastqManifestPhred33
- - BLASTDBDirFmtV5
- - MAGSequencesDirFmt
- - MixedCaseRNAFASTAFormat
- - GenomeSequencesDirectoryFormat
- - SingleEndFastqManifestPhred33V2
- - SampleEstimatorDirFmt
- - RNASingleProfileHmmDirectoryFmt
- - ProteinFASTAFormat
- - ErrorCorrectionDetailsFmt
- - EMPSingleEndCasavaDirFmt
- - MultiplexedFastaQualDirFmt
- - SingleEndFastqManifestPhred64
- - EggnogRefDirFmt
- - SILVATaxidMapFormat
- - MultiplexedPairedEndBarcodeInSequenceDirFmt
- - RNAMultipleProfileHmmDirectoryFmt
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>