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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 9436cc47c72b58a6a3d3a5c2ee075689c2926ef0 |
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modified:
qiime2_core__tools__import.xml |
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| diff -r 65ea76686e11 -r b2c99f2353b6 qiime2_core__tools__import.xml --- a/qiime2_core__tools__import.xml Mon May 05 19:06:07 2025 +0000 +++ b/qiime2_core__tools__import.xml Tue Jul 15 22:08:00 2025 +0000 |
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| b'@@ -6,17 +6,17 @@\n -->\n <!--\n This tool was automatically generated by:\n- q2galaxy (version: 2025.4.0)\n+ q2galaxy (version: 2025.7.0)\n for:\n- qiime2 (version: 2025.4.0)\n+ qiime2 (version: 2025.7.0)\n -->\n-<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2025.4.0+dist.h1147124e" profile="22.05" license="BSD-3-Clause">\n+<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2025.7.0+dist.h44bd78f6" profile="22.05" license="BSD-3-Clause">\n <description>Import data into a QIIME 2 artifact</description>\n <xrefs>\n <xref type="bio.tools">qiime2</xref>\n </xrefs>\n <requirements>\n- <container type="docker">quay.io/qiime2/amplicon:2025.4</container>\n+ <container type="docker">quay.io/qiime2/amplicon:2025.7</container>\n </requirements>\n <command>q2galaxy run tools import \'$inputs\'</command>\n <configfiles>\n@@ -3342,35 +3342,6 @@\n --------\n These formats have documentation available.\n \n-TSVTaxonomyFormat\n-*****************\n-Format for a 2+ column TSV file with an expected minimal header.\n-\n-The only header recognized by this format is:\n-\n- Feature ID<tab>Taxon\n-\n-Optionally followed by other arbitrary columns.\n-\n-This format supports blank lines. The expected header must be the first\n-non-blank line. In addition to the header, there must be at least one line\n-of data.\n-\n-\n-SequenceCharacteristicsFormat\n-*****************************\n-\n-Format for a TSV file with information about sequences like length of a\n-feature. The first column contains feature identifiers and is followed by\n-other optional columns.\n-\n-The file cannot be empty and must have at least two columns.\n-\n-Validation for additional columns can be added with a semantic validator\n-tied to a property. For example the "validate_seq_char_len" validator for\n-"FeatureData[SequenceCharacteristics % Properties("length")]"\n-adds validation for a numerical column called "length".\n-\n SampleIdIndexedSingleEndPerSampleDirFmt\n ***************************************\n Single-end reads in fastq.gz files where base filename is the sample id\n@@ -3381,16 +3352,6 @@\n * `xyz.fastq.gz` is `xyz`\n * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001`\n \n-PressedProfileHmmsDirectoryFmt\n-******************************\n-\n-The <hmmfile>.h3m file contains the profile HMMs\n-and their annotation in a binary format. The <hmmfile>.h3i file is an\n-SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains\n-precomputed data structures for the fast heuristic filter\n-(the MSV filter). The <hmmfile>.h3p file contains precomputed data\n-structures for the rest of each profile.\n-\n QIIME1DemuxFormat\n *****************\n QIIME 1 demultiplexed FASTA format.\n@@ -3438,6 +3399,21 @@\n This format supports comment lines starting with #, and blank lines.\n \n \n+TSVTaxonomyFormat\n+*****************\n+Format for a 2+ column TSV file with an expected minimal header.\n+\n+The only header recognized by this format is:\n+\n+ Feature ID<tab>Taxon\n+\n+Optionally followed by other arbitrary columns.\n+\n+This format supports blank lines. The expected header must be the first\n+non-blank line. In addition to the header, there must be at least one line\n+of data.\n+\n+\n ANCOMBC2OutputDirFmt\n ********************\n \n@@ -3453,100 +3429,124 @@\n - diff: differentially abundant boolean (i.e. q < alpha)\n - passed_ss: whether sensitivity analysis was passed\n \n+SequenceCharacteristicsFormat\n+*****************************\n+\n+Format for a TSV file with information about sequences like length of a\n+feature. The first column contains feature identifiers and is followed by\n+other optional columns.\n+\n+The file cannot be empty and must have at least two columns.\n+\n+Validation for additional columns can be added with a semantic validator\n+tied to a property. For example the "validate_seq_char_len" validator for\n+"FeatureData[SequenceCharacteristics % Properties("length")'..b'nedRNAFASTAFormat\n- - SingleEndFastqManifestPhred33\n+ - PredictionsFormat\n - DiamondDatabaseFileFmt\n- - FirstDifferencesFormat\n- - LSMatFormat\n- - MixedCaseRNAFASTAFormat\n- - ArtificialGroupingFormat\n- - SingleEndFastqManifestPhred33V2\n- - EMPPairedEndCasavaDirFmt\n- - TaxonomicClassiferTemporaryPickleDirFmt\n- - ProteinSingleProfileHmmDirectoryFmt\n- - MAGSequencesDirFmt\n- - TableJSONLFileFormat\n- - ProteinFASTAFormat\n- - ProbabilitiesFormat\n- - SingleEndFastqManifestPhred64\n- - LociDirectoryFormat\n- - SingleEndFastqManifestPhred64V2\n- - ProteinMultipleProfileHmmDirectoryFmt\n+ - Kraken2DBReportFormat\n - MultiFASTADirectoryFormat\n - CasavaOneEightLanelessPerSampleDirFmt\n- - BLASTDBDirFmtV5\n- - DecontamScoreFormat\n+ - Kraken2OutputDirectoryFormat\n - MixedCaseAlignedRNAFASTAFormat\n - PairedEndFastqManifestPhred33\n+ - SeedOrthologDirFmt\n - DNAFASTAFormat\n- - MultiplexedPairedEndBarcodeInSequenceDirFmt\n- - Kraken2OutputDirectoryFormat\n- - ProteinsDirectoryFormat\n- - Kraken2DBReportFormat\n- - GenomeSequencesDirectoryFormat\n+ - Kraken2DBDirectoryFormat\n+ - PlacementsFormat\n+ - DeblurStatsFmt\n - PairedDNASequencesDirectoryFormat\n- - BIOMV210Format\n - AlphaDiversityFormat\n- - DNASingleProfileHmmDirectoryFmt\n+ - OrdinationFormat\n+ - BIOMV100Format\n - MultiMAGSequencesDirFmt\n - AlignedProteinFASTAFormat\n- - GenesDirectoryFormat\n+ - EMPPairedEndDirFmt\n - PairedEndFastqManifestPhred64\n+ - OrthologAnnotationDirFmt\n+ - UchimeStatsFmt\n+ - LSMatFormat\n - PairedRNASequencesDirectoryFormat\n - PairedEndFastqManifestPhred33V2\n - MultiBowtie2IndexDirFmt\n- - SILVATaxonomyFormat\n- - BrackenDBDirectoryFormat\n - DifferentialFormat\n- - MultiplexedFastaQualDirFmt\n- - DADA2StatsFormat\n- - Kraken2DBDirectoryFormat\n+ - ImmutableMetadataFormat\n - Bowtie2IndexDirFmt\n- - SeedOrthologDirFmt\n - AlignedDNAFASTAFormat\n - PairedEndFastqManifestPhred64V2\n- - RNASingleProfileHmmDirectoryFmt\n - ContigSequencesDirFmt\n- - ImmutableMetadataFormat\n+ - EMPPairedEndCasavaDirFmt\n+ - EggnogProteinSequencesDirFmt\n+ - CasavaOneEightSingleLanePerSampleDirFmt\n+ - MixedCaseDNAFASTAFormat\n+ - BooleanSeriesFormat\n+ - EMPSingleEndDirFmt\n+ - ProteinSingleProfileHmmDirectoryFmt\n+ - ProbabilitiesFormat\n+ - DADA2StatsFormat\n+ - ImportanceFormat\n+ - GenesDirectoryFormat\n - SeppReferenceDirFmt\n- - CasavaOneEightSingleLanePerSampleDirFmt\n+ - SingleEndFastqManifestPhred64V2\n+ - SILVATaxonomyFormat\n+ - BrackenDBDirectoryFormat\n+ - BIOMV210Format\n+ - ProteinMultipleProfileHmmDirectoryFmt\n+ - QualityFilterStatsFmt\n+ - MixedCaseAlignedDNAFASTAFormat\n - NCBITaxonomyDirFmt\n- - MixedCaseDNAFASTAFormat\n+ - Kraken2ReportDirectoryFormat\n+ - BAMDirFmt\n+ - BLAST6Format\n+ - ProteinsDirectoryFormat\n+ - NewickFormat\n+ - SingleLanePerSampleSingleEndFastqDirFmt\n+ - DataLoafPackageDirFmt\n+ - RNAFASTAFormat\n+ - ProcrustesStatisticsFmt\n+ - DNASingleProfileHmmDirectoryFmt\n+ - SingleLanePerSamplePairedEndFastqDirFmt\n+ - TaxonomicClassiferTemporaryPickleDirFmt\n+ - MAGtoContigsFormat\n+ - ArtificialGroupingFormat\n+ - MultiBAMDirFmt\n+ - FirstDifferencesFormat\n+ - KaijuDBDirectoryFormat\n+ - DecontamScoreFormat\n+ - LociDirectoryFormat\n+ - DNAMultipleProfileHmmDirectoryFmt\n+ - TableJSONLFileFormat\n+ - AlignedRNAFASTAFormat\n+ - SingleEndFastqManifestPhred33\n+ - BLASTDBDirFmtV5\n+ - MAGSequencesDirFmt\n+ - MixedCaseRNAFASTAFormat\n+ - GenomeSequencesDirectoryFormat\n+ - SingleEndFastqManifestPhred33V2\n+ - SampleEstimatorDirFmt\n+ - RNASingleProfileHmmDirectoryFmt\n+ - ProteinFASTAFormat\n - ErrorCorrectionDetailsFmt\n- - DataLoafPackageDirFmt\n- - OrthologAnnotationDirFmt\n- - PredictionsFormat\n+ - EMPSingleEndCasavaDirFmt\n+ - MultiplexedFastaQualDirFmt\n+ - SingleEndFastqManifestPhred64\n+ - EggnogRefDirFmt\n+ - SILVATaxidMapFormat\n+ - MultiplexedPairedEndBarcodeInSequenceDirFmt\n - RNAMultipleProfileHmmDirectoryFmt\n- - DNAMultipleProfileHmmDirectoryFmt\n- - UchimeStatsFmt\n- - EMPSingleEndDirFmt\n- - KaijuDBDirectoryFormat\n </help>\n <citations>\n <citation type="doi">10.1038/s41587-019-0209-9</citation>\n' |