Mercurial > repos > q2d2 > qiime2_core__tools__import
changeset 8:b2c99f2353b6 draft default tip
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 22:08:00 +0000 |
| parents | 65ea76686e11 |
| children | |
| files | qiime2_core__tools__import.xml |
| diffstat | 1 files changed, 112 insertions(+), 112 deletions(-) [+] |
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--- 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 @@ -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 import" id="qiime2_core__tools__import" version="2025.4.0+dist.h1147124e" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2025.7.0+dist.h44bd78f6" 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:2025.4</container> + <container type="docker">quay.io/qiime2/amplicon:2025.7</container> </requirements> <command>q2galaxy run tools import '$inputs'</command> <configfiles> @@ -3342,35 +3342,6 @@ -------- 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<tab>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". - SampleIdIndexedSingleEndPerSampleDirFmt *************************************** Single-end reads in fastq.gz files where base filename is the sample id @@ -3381,16 +3352,6 @@ * `xyz.fastq.gz` is `xyz` * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001` -PressedProfileHmmsDirectoryFmt -****************************** - -The <hmmfile>.h3m file contains the profile HMMs -and their annotation in a binary format. The <hmmfile>.h3i file is an -SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains -precomputed data structures for the fast heuristic filter -(the MSV filter). The <hmmfile>.h3p file contains precomputed data -structures for the rest of each profile. - QIIME1DemuxFormat ***************** QIIME 1 demultiplexed FASTA format. @@ -3438,6 +3399,21 @@ 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<tab>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 ******************** @@ -3453,100 +3429,124 @@ - diff: differentially abundant boolean (i.e. q < 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 <hmmfile>.h3m file contains the profile HMMs +and their annotation in a binary format. The <hmmfile>.h3i file is an +SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains +precomputed data structures for the fast heuristic filter +(the MSV filter). The <hmmfile>.h3p file contains precomputed data +structures for the rest of each profile. + Additional formats without documentation: ***************************************** - - BooleanSeriesFormat - - MixedCaseAlignedDNAFASTAFormat - - ProcrustesStatisticsFmt - - BAMDirFmt - - BLAST6Format - - PlacementsFormat - - SingleLanePerSampleSingleEndFastqDirFmt - - RNAFASTAFormat - - SILVATaxidMapFormat - - EMPPairedEndDirFmt - - EggnogProteinSequencesDirFmt - - SingleLanePerSamplePairedEndFastqDirFmt - - SampleEstimatorDirFmt - - DeblurStatsFmt - - EggnogRefDirFmt - - BIOMV100Format - - MAGtoContigsFormat - - MultiBAMDirFmt - - QualityFilterStatsFmt - - NewickFormat - - EMPSingleEndCasavaDirFmt - - ImportanceFormat - - OrdinationFormat - - Kraken2ReportDirectoryFormat - - AlignedRNAFASTAFormat - - SingleEndFastqManifestPhred33 + - PredictionsFormat - DiamondDatabaseFileFmt - - FirstDifferencesFormat - - LSMatFormat - - MixedCaseRNAFASTAFormat - - ArtificialGroupingFormat - - SingleEndFastqManifestPhred33V2 - - EMPPairedEndCasavaDirFmt - - TaxonomicClassiferTemporaryPickleDirFmt - - ProteinSingleProfileHmmDirectoryFmt - - MAGSequencesDirFmt - - TableJSONLFileFormat - - ProteinFASTAFormat - - ProbabilitiesFormat - - SingleEndFastqManifestPhred64 - - LociDirectoryFormat - - SingleEndFastqManifestPhred64V2 - - ProteinMultipleProfileHmmDirectoryFmt + - Kraken2DBReportFormat - MultiFASTADirectoryFormat - CasavaOneEightLanelessPerSampleDirFmt - - BLASTDBDirFmtV5 - - DecontamScoreFormat + - Kraken2OutputDirectoryFormat - MixedCaseAlignedRNAFASTAFormat - PairedEndFastqManifestPhred33 + - SeedOrthologDirFmt - DNAFASTAFormat - - MultiplexedPairedEndBarcodeInSequenceDirFmt - - Kraken2OutputDirectoryFormat - - ProteinsDirectoryFormat - - Kraken2DBReportFormat - - GenomeSequencesDirectoryFormat + - Kraken2DBDirectoryFormat + - PlacementsFormat + - DeblurStatsFmt - PairedDNASequencesDirectoryFormat - - BIOMV210Format - AlphaDiversityFormat - - DNASingleProfileHmmDirectoryFmt + - OrdinationFormat + - BIOMV100Format - MultiMAGSequencesDirFmt - AlignedProteinFASTAFormat - - GenesDirectoryFormat + - EMPPairedEndDirFmt - PairedEndFastqManifestPhred64 + - OrthologAnnotationDirFmt + - UchimeStatsFmt + - LSMatFormat - PairedRNASequencesDirectoryFormat - PairedEndFastqManifestPhred33V2 - MultiBowtie2IndexDirFmt - - SILVATaxonomyFormat - - BrackenDBDirectoryFormat - DifferentialFormat - - MultiplexedFastaQualDirFmt - - DADA2StatsFormat - - Kraken2DBDirectoryFormat + - ImmutableMetadataFormat - Bowtie2IndexDirFmt - - SeedOrthologDirFmt - AlignedDNAFASTAFormat - PairedEndFastqManifestPhred64V2 - - RNASingleProfileHmmDirectoryFmt - ContigSequencesDirFmt - - ImmutableMetadataFormat + - EMPPairedEndCasavaDirFmt + - EggnogProteinSequencesDirFmt + - CasavaOneEightSingleLanePerSampleDirFmt + - MixedCaseDNAFASTAFormat + - BooleanSeriesFormat + - EMPSingleEndDirFmt + - ProteinSingleProfileHmmDirectoryFmt + - ProbabilitiesFormat + - DADA2StatsFormat + - ImportanceFormat + - GenesDirectoryFormat - SeppReferenceDirFmt - - CasavaOneEightSingleLanePerSampleDirFmt + - SingleEndFastqManifestPhred64V2 + - SILVATaxonomyFormat + - BrackenDBDirectoryFormat + - BIOMV210Format + - ProteinMultipleProfileHmmDirectoryFmt + - QualityFilterStatsFmt + - MixedCaseAlignedDNAFASTAFormat - NCBITaxonomyDirFmt - - MixedCaseDNAFASTAFormat + - Kraken2ReportDirectoryFormat + - BAMDirFmt + - BLAST6Format + - ProteinsDirectoryFormat + - NewickFormat + - SingleLanePerSampleSingleEndFastqDirFmt + - DataLoafPackageDirFmt + - RNAFASTAFormat + - ProcrustesStatisticsFmt + - DNASingleProfileHmmDirectoryFmt + - SingleLanePerSamplePairedEndFastqDirFmt + - TaxonomicClassiferTemporaryPickleDirFmt + - MAGtoContigsFormat + - ArtificialGroupingFormat + - MultiBAMDirFmt + - FirstDifferencesFormat + - KaijuDBDirectoryFormat + - DecontamScoreFormat + - LociDirectoryFormat + - DNAMultipleProfileHmmDirectoryFmt + - TableJSONLFileFormat + - AlignedRNAFASTAFormat + - SingleEndFastqManifestPhred33 + - BLASTDBDirFmtV5 + - MAGSequencesDirFmt + - MixedCaseRNAFASTAFormat + - GenomeSequencesDirectoryFormat + - SingleEndFastqManifestPhred33V2 + - SampleEstimatorDirFmt + - RNASingleProfileHmmDirectoryFmt + - ProteinFASTAFormat - ErrorCorrectionDetailsFmt - - DataLoafPackageDirFmt - - OrthologAnnotationDirFmt - - PredictionsFormat + - EMPSingleEndCasavaDirFmt + - MultiplexedFastaQualDirFmt + - SingleEndFastqManifestPhred64 + - EggnogRefDirFmt + - SILVATaxidMapFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt - RNAMultipleProfileHmmDirectoryFmt - - DNAMultipleProfileHmmDirectoryFmt - - UchimeStatsFmt - - EMPSingleEndDirFmt - - KaijuDBDirectoryFormat </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>