Mercurial > repos > q2d2 > qiime2_core__tools__export

changeset 8:61fb1a11e004 draft default tip

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 9436cc47c72b58a6a3d3a5c2ee075689c2926ef0
author q2d2
date Tue, 15 Jul 2025 22:07:57 +0000
parents f83fcc984626
children
files qiime2_core__tools__export.xml
diffstat 1 files changed, 139 insertions(+), 139 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2_core__tools__export.xml	Mon May 05 19:06:10 2025 +0000
+++ b/qiime2_core__tools__export.xml	Tue Jul 15 22:07:57 2025 +0000
@@ -6,17 +6,17 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2025.4.0)
+    q2galaxy (version: 2025.7.0)
 for:
-    qiime2 (version: 2025.4.0)
+    qiime2 (version: 2025.7.0)
 -->
-<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2025.4.0+dist.h1147124e" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2025.7.0+dist.h44bd78f6" profile="22.05" license="BSD-3-Clause">
     <description>Export data from a QIIME 2 artifact</description>
     <xrefs>
         <xref type="bio.tools">qiime2</xref>
     </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2025.4</container>
+        <container type="docker">quay.io/qiime2/amplicon:2025.7</container>
     </requirements>
     <command>q2galaxy run tools export '$inputs'</command>
     <configfiles>
@@ -862,7 +862,7 @@
     </inputs>
     <outputs>
         <collection name="exported" type="list" label="${tool.name} on ${on_string} as ${fmt_peek}">
-            <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'DiamondDatabaseFileFmt', 'UchimeStatsDirFmt', 'PredictionsDirectoryFormat', 'SILVATaxidMapFormat', 'SequenceCharacteristicsFormat', 'DecontamScoreFormat', 'NCBITaxonomyDirFmt', 'ProteinMultipleProfileHmmDirectoryFmt', 'FastqGzFormat', 'ContigSequencesDirFmt', 'Bowtie2IndexDirFmt', 'MultiBowtie2IndexDirFmt', 'BooleanSeriesFormat', 'EMPPairedEndDirFmt', 'Kraken2DBReportDirectoryFormat', 'ProteinsDirectoryFormat', 'PlacementsDirFmt', 'DecontamScoreDirFmt', 'RNAFASTAFormat', 'OrdinationFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'Kraken2DBDirectoryFormat', 'AlignedDNAFASTAFormat', 'ImportanceDirectoryFormat', 'EggnogProteinSequencesDirFmt', 'DataLoafPackageDirFmt', 'DifferentialFormat', 'CasavaOneEightSingleLanePerSampleDirFmt', 'AlignedDNASequencesDirectoryFormat', 'FirstDifferencesFormat', 'ErrorCorrectionDetailsFmt', 'MAGSequencesDirFmt', 'LSMatFormat', 'BrackenDBDirectoryFormat', 'UchimeStatsFmt', 'PredictionsFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'PlacementsFormat', 'ANCOMBC2OutputDirFmt', 'TableJSONLDirFmt', 'MultiBAMDirFmt', 'QIIME1DemuxDirFmt', 'ProteinSequencesDirectoryFormat', 'BLAST6DirectoryFormat', 'BLAST6Format', 'SingleLanePerSamplePairedEndFastqDirFmt', 'Kraken2ReportDirectoryFormat', 'ArtificialGroupingFormat', 'DADA2StatsFormat', 'ProcrustesStatisticsDirFmt', 'ProbabilitiesFormat', 'AlphaDiversityFormat', 'PairedRNASequencesDirectoryFormat', 'AlignedRNASequencesDirectoryFormat', 'SeedOrthologDirFmt', 'AlignedProteinSequencesDirectoryFormat', 'TSVTaxonomyDirectoryFormat', 'SequenceCharacteristicsDirectoryFormat', 'PressedProfileHmmsDirectoryFmt', 'RNASequencesDirectoryFormat', 'GenesDirectoryFormat', 'SILVATaxonomyFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'MAGtoContigsFormat', 'RNAMultipleProfileHmmDirectoryFmt', 'ProteinFASTAFormat', 'DiamondDatabaseDirFmt', 'LociDirectoryFormat', 'ProcrustesStatisticsFmt', 'DNASingleProfileHmmDirectoryFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'QualityFilterStatsDirFmt', 'RNASingleProfileHmmDirectoryFmt', 'ImmutableMetadataFormat', 'DADA2StatsDirFmt', 'KaijuDBDirectoryFormat', 'QIIME1DemuxFormat', 'SILVATaxidMapDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'DifferentialDirectoryFormat', 'BIOMV210Format', 'FirstDifferencesDirectoryFormat', 'OrdinationDirectoryFormat', 'SILVATaxonomyDirectoryFormat', 'TSVTaxonomyFormat', 'ProbabilitiesDirectoryFormat', 'BLASTDBDirFmtV5', 'ArtificialGroupingDirectoryFormat', 'TableJSONLFileFormat', 'Kraken2OutputDirectoryFormat', 'GenomeSequencesDirectoryFormat', 'AlignedRNAFASTAFormat', 'Kraken2DBReportFormat', 'ErrorCorrectionDetailsDirFmt', 'QualityFilterStatsFmt', 'SampleEstimatorDirFmt', 'BAMDirFmt', 'DNASequencesDirectoryFormat', 'DNAMultipleProfileHmmDirectoryFmt', 'TrueTargetsDirectoryFormat', 'DNAFASTAFormat', 'BooleanSeriesDirectoryFormat', 'OrthologAnnotationDirFmt', 'ImportanceFormat', 'MAGtoContigsDirFmt', 'ProteinSingleProfileHmmDirectoryFmt', 'DeblurStatsFmt', 'NewickDirectoryFormat', 'AlphaDiversityDirectoryFormat', 'NewickFormat', 'EggnogRefDirFmt', 'PairedDNASequencesDirectoryFormat', 'DeblurStatsDirFmt', 'MultiFASTADirectoryFormat', 'EMPSingleEndDirFmt', 'MultiMAGSequencesDirFmt', 'ImmutableMetadataDirectoryFormat', 'AlignedProteinFASTAFormat', 'SeppReferenceDirFmt', 'BIOMV210DirFmt'}</filter>
+            <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'SingleLanePerSampleSingleEndFastqDirFmt', 'BooleanSeriesDirectoryFormat', 'ProteinSingleProfileHmmDirectoryFmt', 'DifferentialFormat', 'NewickDirectoryFormat', 'MultiBAMDirFmt', 'ProbabilitiesFormat', 'NCBITaxonomyDirFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'LSMatFormat', 'RNAFASTAFormat', 'NewickFormat', 'ProteinMultipleProfileHmmDirectoryFmt', 'TableJSONLFileFormat', 'ProcrustesStatisticsDirFmt', 'GenomeSequencesDirectoryFormat', 'SILVATaxidMapFormat', 'KaijuDBDirectoryFormat', 'GenesDirectoryFormat', 'ImmutableMetadataDirectoryFormat', 'DeblurStatsDirFmt', 'ANCOMBC2OutputDirFmt', 'BAMDirFmt', 'TrueTargetsDirectoryFormat', 'PlacementsFormat', 'Bowtie2IndexDirFmt', 'PairedRNASequencesDirectoryFormat', 'ImportanceFormat', 'BLAST6DirectoryFormat', 'DiamondDatabaseDirFmt', 'Kraken2ReportDirectoryFormat', 'SeppReferenceDirFmt', 'ProcrustesStatisticsFmt', 'AlignedDNAFASTAFormat', 'QualityFilterStatsDirFmt', 'ContigSequencesDirFmt', 'BIOMV210Format', 'EggnogRefDirFmt', 'FirstDifferencesDirectoryFormat', 'PlacementsDirFmt', 'ArtificialGroupingDirectoryFormat', 'DNAMultipleProfileHmmDirectoryFmt', 'OrdinationFormat', 'ImportanceDirectoryFormat', 'PressedProfileHmmsDirectoryFmt', 'MAGtoContigsDirFmt', 'OrthologAnnotationDirFmt', 'DeblurStatsFmt', 'Kraken2DBDirectoryFormat', 'QualityFilterStatsFmt', 'SILVATaxonomyDirectoryFormat', 'UchimeStatsDirFmt', 'UchimeStatsFmt', 'MultiBowtie2IndexDirFmt', 'DataLoafPackageDirFmt', 'EggnogProteinSequencesDirFmt', 'EMPSingleEndDirFmt', 'DNAFASTAFormat', 'QIIME1DemuxFormat', 'AlignedDNASequencesDirectoryFormat', 'DADA2StatsFormat', 'AlignedProteinFASTAFormat', 'DecontamScoreFormat', 'RNASequencesDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'RNAMultipleProfileHmmDirectoryFmt', 'EMPPairedEndDirFmt', 'ProteinFASTAFormat', 'BooleanSeriesFormat', 'MultiFASTADirectoryFormat', 'AlignedRNASequencesDirectoryFormat', 'DifferentialDirectoryFormat', 'FastqGzFormat', 'BrackenDBDirectoryFormat', 'ImmutableMetadataFormat', 'PairedDNASequencesDirectoryFormat', 'OrdinationDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'AlignedProteinSequencesDirectoryFormat', 'SILVATaxidMapDirectoryFormat', 'DADA2StatsDirFmt', 'MAGtoContigsFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'BIOMV210DirFmt', 'SequenceCharacteristicsFormat', 'ProteinSequencesDirectoryFormat', 'SequenceCharacteristicsDirectoryFormat', 'Kraken2DBReportFormat', 'DiamondDatabaseFileFmt', 'AlignedRNAFASTAFormat', 'PredictionsFormat', 'SILVATaxonomyFormat', 'AlphaDiversityFormat', 'ProbabilitiesDirectoryFormat', 'ErrorCorrectionDetailsFmt', 'ProteinsDirectoryFormat', 'DNASequencesDirectoryFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'LociDirectoryFormat', 'DecontamScoreDirFmt', 'ErrorCorrectionDetailsDirFmt', 'RNASingleProfileHmmDirectoryFmt', 'TSVTaxonomyFormat', 'PredictionsDirectoryFormat', 'FirstDifferencesFormat', 'MultiMAGSequencesDirFmt', 'SingleLanePerSamplePairedEndFastqDirFmt', 'MAGSequencesDirFmt', 'ArtificialGroupingFormat', 'BLAST6Format', 'BLASTDBDirFmtV5', 'AlphaDiversityDirectoryFormat', 'TableJSONLDirFmt', 'SampleEstimatorDirFmt', 'Kraken2DBReportDirectoryFormat', 'Kraken2OutputDirectoryFormat', 'SeedOrthologDirFmt', 'QIIME1DemuxDirFmt', 'DNASingleProfileHmmDirectoryFmt', 'TSVTaxonomyDirectoryFormat'}</filter>
             <discover_datasets pattern="__designation_and_ext__" visible="false"/>
         </collection>
         <data name="ANCOMBC2OutputDirFmt" label="${tool.name} on ${on_string} as ANCOMBC2OutputDirFmt">
@@ -1432,45 +1432,6 @@
 --------
 These formats have documentation available.
 
-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.
-
-
-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.
-
 QIIME1DemuxFormat
 *****************
 QIIME 1 demultiplexed FASTA format.
@@ -1511,6 +1472,21 @@
 A gzipped fastq file.
 
 
+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.
+
+
 ANCOMBC2OutputDirFmt
 ********************
 
@@ -1526,122 +1502,146 @@
     - 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:
 *****************************************
- - BooleanSeriesFormat
- - ProcrustesStatisticsFmt
- - DADA2StatsDirFmt
- - BAMDirFmt
- - ProbabilitiesDirectoryFormat
- - BLAST6Format
+ - DiamondDatabaseDirFmt
+ - PredictionsFormat
+ - DiamondDatabaseFileFmt
+ - Kraken2DBReportFormat
+ - MultiFASTADirectoryFormat
+ - Kraken2OutputDirectoryFormat
+ - ProcrustesStatisticsDirFmt
+ - SeedOrthologDirFmt
+ - DNAFASTAFormat
+ - Kraken2DBDirectoryFormat
+ - Kraken2DBReportDirectoryFormat
  - PlacementsFormat
- - BIOMV210DirFmt
- - SingleLanePerSampleSingleEndFastqDirFmt
- - RNAFASTAFormat
- - SILVATaxidMapFormat
- - EMPPairedEndDirFmt
- - EggnogProteinSequencesDirFmt
- - SingleLanePerSamplePairedEndFastqDirFmt
- - TSVTaxonomyDirectoryFormat
- - SampleEstimatorDirFmt
+ - FirstDifferencesDirectoryFormat
  - DeblurStatsFmt
- - EggnogRefDirFmt
- - MAGtoContigsFormat
- - MultiplexedSingleEndBarcodeInSequenceDirFmt
- - MultiBAMDirFmt
- - TrueTargetsDirectoryFormat
- - BLAST6DirectoryFormat
- - MAGtoContigsDirFmt
- - QualityFilterStatsFmt
- - RNASequencesDirectoryFormat
- - NewickFormat
- - ImportanceFormat
- - ProteinSequencesDirectoryFormat
- - ImportanceDirectoryFormat
+ - ErrorCorrectionDetailsDirFmt
+ - PairedDNASequencesDirectoryFormat
+ - PredictionsDirectoryFormat
+ - AlphaDiversityFormat
  - OrdinationFormat
- - DecontamScoreDirFmt
- - Kraken2ReportDirectoryFormat
- - AlignedRNAFASTAFormat
- - ArtificialGroupingDirectoryFormat
- - DiamondDatabaseFileFmt
- - FirstDifferencesFormat
- - LSMatFormat
- - ArtificialGroupingFormat
- - TaxonomicClassiferTemporaryPickleDirFmt
- - ProteinSingleProfileHmmDirectoryFmt
- - MAGSequencesDirFmt
- - TableJSONLFileFormat
- - ProteinFASTAFormat
- - ProbabilitiesFormat
- - AlignedRNASequencesDirectoryFormat
- - SequenceCharacteristicsDirectoryFormat
- - SILVATaxidMapDirectoryFormat
- - LociDirectoryFormat
- - DistanceMatrixDirectoryFormat
- - ProteinMultipleProfileHmmDirectoryFmt
- - MultiFASTADirectoryFormat
- - BLASTDBDirFmtV5
- - DecontamScoreFormat
- - DNAFASTAFormat
- - MultiplexedPairedEndBarcodeInSequenceDirFmt
- - Kraken2OutputDirectoryFormat
- - ProteinsDirectoryFormat
- - Kraken2DBReportFormat
  - PlacementsDirFmt
- - GenomeSequencesDirectoryFormat
- - PairedDNASequencesDirectoryFormat
- - BIOMV210Format
- - AlphaDiversityFormat
- - DNASingleProfileHmmDirectoryFmt
- - SILVATaxonomyDirectoryFormat
  - MultiMAGSequencesDirFmt
  - AlignedProteinFASTAFormat
- - ImmutableMetadataDirectoryFormat
- - GenesDirectoryFormat
- - UchimeStatsDirFmt
- - FirstDifferencesDirectoryFormat
- - NewickDirectoryFormat
+ - EMPPairedEndDirFmt
+ - OrthologAnnotationDirFmt
+ - UchimeStatsFmt
+ - LSMatFormat
+ - DeblurStatsDirFmt
+ - MAGtoContigsDirFmt
  - PairedRNASequencesDirectoryFormat
  - AlphaDiversityDirectoryFormat
  - MultiBowtie2IndexDirFmt
  - AlignedProteinSequencesDirectoryFormat
- - SILVATaxonomyFormat
- - BrackenDBDirectoryFormat
- - TableJSONLDirFmt
+ - ImmutableMetadataDirectoryFormat
  - DifferentialFormat
+ - ImmutableMetadataFormat
  - DNASequencesDirectoryFormat
- - DeblurStatsDirFmt
- - DADA2StatsFormat
- - Kraken2DBDirectoryFormat
+ - TableJSONLDirFmt
+ - DistanceMatrixDirectoryFormat
  - Bowtie2IndexDirFmt
- - Kraken2DBReportDirectoryFormat
- - SeedOrthologDirFmt
- - QualityFilterStatsDirFmt
+ - ImportanceDirectoryFormat
  - AlignedDNAFASTAFormat
- - ProcrustesStatisticsDirFmt
- - RNASingleProfileHmmDirectoryFmt
+ - SILVATaxonomyDirectoryFormat
  - ContigSequencesDirFmt
- - ImmutableMetadataFormat
- - BooleanSeriesDirectoryFormat
- - DiamondDatabaseDirFmt
- - SeppReferenceDirFmt
+ - EggnogProteinSequencesDirFmt
  - DifferentialDirectoryFormat
  - CasavaOneEightSingleLanePerSampleDirFmt
- - NCBITaxonomyDirFmt
- - ErrorCorrectionDetailsFmt
- - DataLoafPackageDirFmt
- - OrthologAnnotationDirFmt
- - PredictionsFormat
- - OrdinationDirectoryFormat
+ - BooleanSeriesFormat
+ - EMPSingleEndDirFmt
+ - ProteinSingleProfileHmmDirectoryFmt
+ - ProbabilitiesFormat
+ - DADA2StatsFormat
+ - BIOMV210DirFmt
  - AlignedDNASequencesDirectoryFormat
- - PredictionsDirectoryFormat
- - RNAMultipleProfileHmmDirectoryFmt
+ - ImportanceFormat
+ - DADA2StatsDirFmt
+ - GenesDirectoryFormat
+ - SeppReferenceDirFmt
+ - SILVATaxonomyFormat
+ - SILVATaxidMapDirectoryFormat
+ - OrdinationDirectoryFormat
+ - BooleanSeriesDirectoryFormat
+ - BrackenDBDirectoryFormat
+ - BIOMV210Format
+ - ProteinMultipleProfileHmmDirectoryFmt
+ - ProbabilitiesDirectoryFormat
+ - QIIME1DemuxDirFmt
+ - QualityFilterStatsFmt
+ - NCBITaxonomyDirFmt
+ - Kraken2ReportDirectoryFormat
+ - BAMDirFmt
+ - BLAST6Format
+ - ProteinsDirectoryFormat
+ - NewickFormat
+ - SingleLanePerSampleSingleEndFastqDirFmt
+ - DataLoafPackageDirFmt
+ - RNAFASTAFormat
+ - UchimeStatsDirFmt
+ - ProcrustesStatisticsFmt
+ - DNASingleProfileHmmDirectoryFmt
+ - TrueTargetsDirectoryFormat
+ - SingleLanePerSamplePairedEndFastqDirFmt
+ - TSVTaxonomyDirectoryFormat
+ - TaxonomicClassiferTemporaryPickleDirFmt
+ - MAGtoContigsFormat
+ - ArtificialGroupingFormat
+ - MultiBAMDirFmt
+ - QualityFilterStatsDirFmt
+ - BLAST6DirectoryFormat
+ - FirstDifferencesFormat
+ - KaijuDBDirectoryFormat
+ - DecontamScoreFormat
+ - RNASequencesDirectoryFormat
+ - LociDirectoryFormat
  - DNAMultipleProfileHmmDirectoryFmt
- - UchimeStatsFmt
- - ErrorCorrectionDetailsDirFmt
- - EMPSingleEndDirFmt
- - KaijuDBDirectoryFormat
- - QIIME1DemuxDirFmt
+ - ProteinSequencesDirectoryFormat
+ - TableJSONLFileFormat
+ - AlignedRNAFASTAFormat
+ - BLASTDBDirFmtV5
+ - MAGSequencesDirFmt
+ - GenomeSequencesDirectoryFormat
+ - SampleEstimatorDirFmt
+ - RNASingleProfileHmmDirectoryFmt
+ - ArtificialGroupingDirectoryFormat
+ - NewickDirectoryFormat
+ - MultiplexedSingleEndBarcodeInSequenceDirFmt
+ - ProteinFASTAFormat
+ - ErrorCorrectionDetailsFmt
+ - AlignedRNASequencesDirectoryFormat
+ - DecontamScoreDirFmt
+ - EggnogRefDirFmt
+ - SequenceCharacteristicsDirectoryFormat
+ - SILVATaxidMapFormat
+ - MultiplexedPairedEndBarcodeInSequenceDirFmt
+ - RNAMultipleProfileHmmDirectoryFmt
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>