Mercurial > repos > q2d2 > qiime2_coretoolsimport

--- a/qiime2_core__tools__import.xml	Sat Nov 01 17:33:53 2025 +0000
+++ b/qiime2_core__tools__import.xml	Wed Jan 28 16:39:32 2026 +0000
@@ -1,22 +1,22 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2025, QIIME 2 development team.
+Copyright (c) 2026, 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: 2025.10.0)
+    q2galaxy (version: 2026.1.0)
 for:
-    qiime2 (version: 2025.10.0)
+    qiime2 (version: 2026.1.0)
 -->
-<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2025.10.0+dist.hbfe50fe0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2026.1.0+dist.h02a552c2" 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:2025.10</container>
+        <container type="docker">quay.io/qiime2/amplicon:2026.1</container>
     </requirements>
     <command>q2galaxy run tools import '$inputs'</command>
     <configfiles>
@@ -106,7 +106,9 @@
                 <option value="FeatureData__ob__Sequence__cb__">FeatureData[Sequence]</option>
                 <option value="FeatureData__ob__SingleBowtie2Index__cb__">FeatureData[SingleBowtie2Index]</option>
                 <option value="FeatureData__ob__Taxonomy__cb__">FeatureData[Taxonomy]</option>
+                <option value="FeatureMap__ob__FunctionToContigs__cb__">FeatureMap[FunctionToContigs]</option>
                 <option value="FeatureMap__ob__MAGtoContigs__cb__">FeatureMap[MAGtoContigs]</option>
+                <option value="FeatureMap__ob__TaxonomyToContigs__cb__">FeatureMap[TaxonomyToContigs]</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>
@@ -613,6 +615,7 @@
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
                         <option value="AlignedProteinFASTAFormat" selected="true">Aligned Protein FASTA Format</option>
+                        <option value="FASTAFormat" selected="false">FASTA Format</option>
                     </param>
                     <when value="AlignedProteinFASTAFormat">
                         <section name="import" expanded="true" title="Import">
@@ -620,6 +623,12 @@
                             <param name="data" type="data" format="data" help="This data should be formatted as a AlignedProteinFASTAFormat. See the documentation below for more information."/>
                         </section>
                     </when>
+                    <when value="FASTAFormat">
+                        <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 FASTAFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
                 </conditional>
             </when>
             <when value="FeatureData__ob__AlignedRNASequence__cb__">
@@ -646,6 +655,7 @@
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
                         <option value="AlignedDNAFASTAFormat" selected="true">Aligned DNAFASTA Format</option>
+                        <option value="FASTAFormat" selected="false">FASTA Format</option>
                         <option value="MixedCaseAlignedDNAFASTAFormat" selected="false">Mixed Case Aligned DNAFASTA Format</option>
                     </param>
                     <when value="AlignedDNAFASTAFormat">
@@ -654,6 +664,12 @@
                             <param name="data" type="data" format="data" help="This data should be formatted as a AlignedDNAFASTAFormat. See the documentation below for more information."/>
                         </section>
                     </when>
+                    <when value="FASTAFormat">
+                        <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 FASTAFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
                     <when value="MixedCaseAlignedDNAFASTAFormat">
                         <section name="import" expanded="true" title="Import">
                             <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
@@ -1158,6 +1174,19 @@
                     </when>
                 </conditional>
             </when>
+            <when value="FeatureMap__ob__FunctionToContigs__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="FeatureMapFormat" selected="true">Feature Map Format</option>
+                    </param>
+                    <when value="FeatureMapFormat">
+                        <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 FeatureMapFormat. See the documentation below for more information."/>
+                        </section>
+                    </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:">
@@ -1171,6 +1200,19 @@
                     </when>
                 </conditional>
             </when>
+            <when value="FeatureMap__ob__TaxonomyToContigs__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="FeatureMapFormat" selected="true">Feature Map Format</option>
+                    </param>
+                    <when value="FeatureMapFormat">
+                        <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 FeatureMapFormat. 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:">
@@ -3405,20 +3447,20 @@
 --------
 These formats have documentation available.

-SRAFailedIDsFormat
-******************
+TSVTaxonomyFormat
+*****************
+Format for a 2+ column TSV file with an expected minimal header.

-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.
+The only header recognized by this format is:

-NCBIAccessionIDsFormat
-**********************
+    Feature ID&lt;tab&gt;Taxon
+
+Optionally followed by other arbitrary columns.

-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.
+This format supports blank lines. The expected header must be the first
+non-blank line. In addition to the header, there must be at least one line
+of data.
+

 SequenceCharacteristicsFormat
 *****************************
@@ -3434,15 +3476,13 @@
 "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
+NCBIAccessionIDsFormat
+**********************

-    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`
+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.

 ANCOMBC2OutputDirFmt
 ********************
@@ -3459,12 +3499,6 @@
     - diff: differentially abundant boolean (i.e. q &lt; alpha)
     - passed_ss: whether sensitivity analysis was passed

-FastqGzFormat
-*************
-
-A gzipped fastq file.
-
-
 PressedProfileHmmsDirectoryFmt
 ******************************

@@ -3475,6 +3509,36 @@
 (the MSV filter).  The &lt;hmmfile&gt;.h3p file contains precomputed data
 structures for the rest of each profile.

+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.
+
+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`
+
 QIIME1DemuxFormat
 *****************
 QIIME 1 demultiplexed FASTA format.
@@ -3509,124 +3573,104 @@
 - Each sequence must be DNA and cannot be empty.


-HeaderlessTSVTaxonomyFormat
-***************************
-Format for a 2+ column TSV file without a header.
-
-This format supports comment lines starting with #, and blank lines.
-
-
-TSVTaxonomyFormat
-*****************
-Format for a 2+ column TSV file with an expected minimal header.
-
-The only header recognized by this format is:
-
-    Feature ID&lt;tab&gt;Taxon
-
-Optionally followed by other arbitrary columns.
-
-This format supports blank lines. The expected header must be the first
-non-blank line. In addition to the header, there must be at least one line
-of data.
-
-
 Additional formats without documentation:
 *****************************************
- - ContigSequencesDirFmt
- - BrackenDBDirectoryFormat
- - MixedCaseAlignedDNAFASTAFormat
- - SILVATaxidMapFormat
- - EggnogRefDirFmt
- - CasavaOneEightSingleLanePerSampleDirFmt
+ - FASTAFormat
+ - ArtificialGroupingFormat
+ - EMPPairedEndCasavaDirFmt
+ - AlignedRNAFASTAFormat
+ - SILVATaxonomyFormat
  - RNAMultipleProfileHmmDirectoryFmt
- - BLAST6Format
- - LSMatFormat
- - MultiplexedFastaQualDirFmt
- - RNAFASTAFormat
+ - SeppReferenceDirFmt
  - NewickFormat
+ - MixedCaseRNAFASTAFormat
+ - ContigSequencesDirFmt
+ - ProteinFASTAFormat
+ - QualityFilterStatsFmt
+ - CasavaOneEightSingleLanePerSampleDirFmt
+ - OrdinationFormat
+ - FirstDifferencesFormat
+ - PredictionsFormat
+ - TableJSONLFileFormat
+ - Kraken2ReportDirectoryFormat
+ - GenesDirectoryFormat
  - MAGSequencesDirFmt
- - DiamondDatabaseFileFmt
- - OrthologAnnotationDirFmt
- - DeblurStatsFmt
+ - ProbabilitiesFormat
+ - MixedCaseAlignedRNAFASTAFormat
+ - EggnogProteinSequencesDirFmt
+ - SILVATaxidMapFormat
+ - DNAFASTAFormat
+ - SingleEndFastqManifestPhred33V2
+ - ImmutableMetadataFormat
+ - ErrorCorrectionDetailsFmt
+ - BrackenDBDirectoryFormat
+ - FeatureMapFormat
+ - BooleanSeriesFormat
+ - DataLoafPackageDirFmt
+ - ProteinSingleProfileHmmDirectoryFmt
+ - AlphaDiversityFormat
+ - PairedDNASequencesDirectoryFormat
+ - Kraken2DBReportFormat
  - BAMDirFmt
  - BIOMV100Format
- - AlignedRNAFASTAFormat
+ - AlignedProteinFASTAFormat
  - ProteinsDirectoryFormat
+ - ProcrustesStatisticsFmt
+ - SingleEndFastqManifestPhred64V2
  - MAGtoContigsFormat
+ - ProteinMultipleProfileHmmDirectoryFmt
+ - SRAMetadataFormat
+ - PairedRNASequencesDirectoryFormat
+ - BIOMV210Format
+ - MultiBAMDirFmt
+ - ImportanceFormat
+ - DifferentialFormat
+ - KaijuDBDirectoryFormat
+ - DNASingleProfileHmmDirectoryFmt
+ - AlignedDNAFASTAFormat
+ - SingleEndFastqManifestPhred33
  - DecontamScoreFormat
- - SingleEndFastqManifestPhred33V2
+ - LociDirectoryFormat
+ - MultiplexedFastaQualDirFmt
+ - MixedCaseDNAFASTAFormat
+ - PairedEndFastqManifestPhred33V2
+ - SingleLanePerSamplePairedEndFastqDirFmt
  - EMPSingleEndDirFmt
- - ProteinSingleProfileHmmDirectoryFmt
- - ProbabilitiesFormat
- - MixedCaseRNAFASTAFormat
- - ProteinFASTAFormat
- - MultiBAMDirFmt
- - BIOMV210Format
- - Kraken2DBReportFormat
- - ImportanceFormat
- - SeedOrthologDirFmt
- - SingleEndFastqManifestPhred64V2
+ - SingleEndFastqManifestPhred64
+ - Kraken2OutputDirectoryFormat
+ - GenomeSequencesDirectoryFormat
+ - LSMatFormat
+ - PairedEndFastqManifestPhred64V2
+ - MultiFASTADirectoryFormat
+ - DiamondDatabaseFileFmt
+ - CasavaOneEightLanelessPerSampleDirFmt
+ - BLASTDBDirFmtV5
  - EMPPairedEndDirFmt
- - ArtificialGroupingFormat
- - ProteinMultipleProfileHmmDirectoryFmt
- - SampleEstimatorDirFmt
- - SingleEndFastqManifestPhred33
- - Kraken2OutputDirectoryFormat
- - EggnogProteinSequencesDirFmt
- - MixedCaseAlignedRNAFASTAFormat
- - DNAFASTAFormat
- - EMPSingleEndCasavaDirFmt
- - OrdinationFormat
- - DNASingleProfileHmmDirectoryFmt
- - SingleLanePerSamplePairedEndFastqDirFmt
- - PairedDNASequencesDirectoryFormat
- - ImmutableMetadataFormat
- - AlphaDiversityFormat
- - SingleEndFastqManifestPhred64
- - AlignedProteinFASTAFormat
- - GenesDirectoryFormat
+ - MixedCaseAlignedDNAFASTAFormat
  - DADA2BaseTransitionStatsFormat
+ - DNAMultipleProfileHmmDirectoryFmt
+ - PairedEndFastqManifestPhred33
  - TaxonomicClassiferTemporaryPickleDirFmt
- - SILVATaxonomyFormat
- - EMPPairedEndCasavaDirFmt
- - DNAMultipleProfileHmmDirectoryFmt
- - BLASTDBDirFmtV5
- - PlacementsFormat
- - MultiFASTADirectoryFormat
- - CasavaOneEightLanelessPerSampleDirFmt
- - PairedRNASequencesDirectoryFormat
- - BooleanSeriesFormat
- - SRAMetadataFormat
- - PairedEndFastqManifestPhred33
- - RNASingleProfileHmmDirectoryFmt
- - DifferentialFormat
- - GenomeSequencesDirectoryFormat
- - ProcrustesStatisticsFmt
+ - BLAST6Format
+ - EggnogRefDirFmt
+ - UchimeStatsFmt
+ - SeedOrthologDirFmt
+ - RNAFASTAFormat
  - MultiMAGSequencesDirFmt
- - AlignedDNAFASTAFormat
- - PairedEndFastqManifestPhred64
- - DADA2StatsFormat
+ - Bowtie2IndexDirFmt
  - MultiplexedPairedEndBarcodeInSequenceDirFmt
- - TableJSONLFileFormat
- - MixedCaseDNAFASTAFormat
- - PredictionsFormat
- - Kraken2ReportDirectoryFormat
- - SeppReferenceDirFmt
- - PairedEndFastqManifestPhred33V2
- - LociDirectoryFormat
- - Bowtie2IndexDirFmt
- - UchimeStatsFmt
+ - NCBITaxonomyDirFmt
+ - EMPSingleEndCasavaDirFmt
+ - PairedEndFastqManifestPhred64
+ - Kraken2DBDirectoryFormat
+ - RNASingleProfileHmmDirectoryFmt
+ - DADA2StatsFormat
+ - PlacementsFormat
+ - OrthologAnnotationDirFmt
+ - SingleLanePerSampleSingleEndFastqDirFmt
  - MultiBowtie2IndexDirFmt
- - ErrorCorrectionDetailsFmt
- - NCBITaxonomyDirFmt
- - QualityFilterStatsFmt
- - Kraken2DBDirectoryFormat
- - DataLoafPackageDirFmt
- - SingleLanePerSampleSingleEndFastqDirFmt
- - PairedEndFastqManifestPhred64V2
- - FirstDifferencesFormat
- - KaijuDBDirectoryFormat
+ - DeblurStatsFmt
+ - SampleEstimatorDirFmt
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>