| Previous changeset 3:10447a4b0cc3 (2024-02-01) Next changeset 5:f9e68fa06585 (2024-06-03) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 389df0134cd0763dcf02aac6e623fc15f8861c1e |
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modified:
qiime2_core__tools__import.xml |
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removed:
test-data/YY/YY_S49_R1_001.fastq.gz test-data/YY/YY_S49_R2_001.fastq.gz |
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| diff -r 10447a4b0cc3 -r 9dbdf05beaa9 qiime2_core__tools__import.xml --- a/qiime2_core__tools__import.xml Thu Feb 01 21:22:08 2024 +0000 +++ b/qiime2_core__tools__import.xml Thu Apr 25 21:28:32 2024 +0000 |
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| b'@@ -1,21 +1,21 @@\n <?xml version=\'1.0\' encoding=\'utf-8\'?>\n <!--\n-Copyright (c) 2023, QIIME 2 development team.\n+Copyright (c) 2024, QIIME 2 development team.\n \n Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)\n -->\n <!--\n This tool was automatically generated by:\n- q2galaxy (version: 2023.5.0)\n+ q2galaxy (version: 2024.2.1)\n for:\n- qiime2 (version: 2023.5.1)\n+ qiime2 (version: 2024.2.0)\n -->\n-<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.3" profile="22.05" license="BSD-3-Clause">\n+<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2024.2.1+dist.he188c3c2" profile="22.05" license="BSD-3-Clause">\n <description>Import data into a QIIME 2 artifact</description>\n <requirements>\n- <container type="docker">quay.io/qiime2/core:2023.5</container>\n+ <container type="docker">quay.io/qiime2/amplicon:2024.2</container>\n </requirements>\n- <command detect_errors="exit_code">q2galaxy run tools import \'$inputs\'</command>\n+ <command>q2galaxy run tools import \'$inputs\'</command>\n <configfiles>\n <configfile name="inputs"><%\n # This is an exercise in cheating the Cheetah\n@@ -60,6 +60,7 @@\n <conditional name="import_root">\n <param name="type" type="select" label="Type of data to import:">\n <option value="None">Select a QIIME 2 type to import.</option>\n+ <option value="BLASTDB">BLASTDB</option>\n <option value="Bowtie2Index">Bowtie2Index</option>\n <option value="DeblurStats">DeblurStats</option>\n <option value="DistanceMatrix">DistanceMatrix</option>\n@@ -78,8 +79,11 @@\n <option value="FeatureData__ob__PairedEndSequence__cb__">FeatureData[PairedEndSequence]</option>\n <option value="FeatureData__ob__ProteinSequence__cb__">FeatureData[ProteinSequence]</option>\n <option value="FeatureData__ob__RNASequence__cb__">FeatureData[RNASequence]</option>\n+ <option value="FeatureData__ob__SILVATaxidMap__cb__">FeatureData[SILVATaxidMap]</option>\n+ <option value="FeatureData__ob__SILVATaxonomy__cb__">FeatureData[SILVATaxonomy]</option>\n <option value="FeatureData__ob__Sequence__cb__">FeatureData[Sequence]</option>\n <option value="FeatureData__ob__Taxonomy__cb__">FeatureData[Taxonomy]</option>\n+ <option value="FeatureMap__ob__MAGtoContigs__cb__">FeatureMap[MAGtoContigs]</option>\n <option value="FeatureTable__ob__Balance__cb__">FeatureTable[Balance]</option>\n <option value="FeatureTable__ob__Composition__cb__">FeatureTable[Composition]</option>\n <option value="FeatureTable__ob__Design__cb__">FeatureTable[Design]</option>\n@@ -87,6 +91,10 @@\n <option value="FeatureTable__ob__PercentileNormalized__cb__">FeatureTable[PercentileNormalized]</option>\n <option value="FeatureTable__ob__PresenceAbsence__cb__">FeatureTable[PresenceAbsence]</option>\n <option value="FeatureTable__ob__RelativeFrequency__cb__">FeatureTable[RelativeFrequency]</option>\n+ <option value="GenomeData__ob__BLAST6__cb__">GenomeData[BLAST6]</option>\n+ <option value="GenomeData__ob__Genes__cb__">GenomeData[Genes]</option>\n+ <option value="GenomeData__ob__Loci__cb__">GenomeData[Loci]</option>\n+ <option value="GenomeData__ob__Proteins__cb__">GenomeData[Proteins]</option>\n <option value="Hierarchy">Hierarchy</option>\n <option value="ImmutableMetadata">ImmutableMetadata</option>\n <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option>\n@@ -98,18 +106,25 @@\n <option value="ProcrustesStatistics">ProcrustesStatistics</option>\n <option value="QualityFilterStats"'..b'***************************************\n-Single-end reads in fastq.gz files where base filename is the sample id\n-\n- The full file name, minus the extension (`.fastq.gz`) is the sample id.\n- For example, the sample id for the file:\n- * `sample-1.fastq.gz` is `sample-1`\n- * `xyz.fastq.gz` is `xyz`\n- * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001`\n-\n Additional formats without documentation:\n *****************************************\n+ - BAMDirFmt\n+ - TaxonomicClassiferTemporaryPickleDirFmt\n+ - BooleanSeriesFormat\n+ - SingleEndFastqManifestPhred33\n+ - SampleEstimatorDirFmt\n+ - MultiBAMDirFmt\n+ - MAGtoContigsFormat\n+ - MixedCaseAlignedRNAFASTAFormat\n+ - PlacementsFormat\n+ - PredictionsFormat\n+ - SingleEndFastqManifestPhred64\n+ - MultiplexedPairedEndBarcodeInSequenceDirFmt\n+ - SingleLanePerSampleSingleEndFastqDirFmt\n+ - AlignedProteinFASTAFormat\n+ - PairedDNASequencesDirectoryFormat\n+ - DataLoafPackageDirFmt\n+ - ArtificialGroupingFormat\n+ - PairedEndFastqManifestPhred33\n+ - DNAFASTAFormat\n+ - EMPSingleEndDirFmt\n+ - SingleLanePerSamplePairedEndFastqDirFmt\n+ - PairedRNASequencesDirectoryFormat\n+ - SeppReferenceDirFmt\n+ - DifferentialFormat\n+ - UchimeStatsFmt\n+ - SILVATaxonomyFormat\n+ - PairedEndFastqManifestPhred64\n+ - GenesDirectoryFormat\n+ - MultiFASTADirectoryFormat\n+ - EMPPairedEndDirFmt\n+ - CasavaOneEightLanelessPerSampleDirFmt\n+ - AlignedDNAFASTAFormat\n+ - SILVATaxidMapFormat\n+ - PairedEndFastqManifestPhred33V2\n+ - SingleEndFastqManifestPhred33V2\n+ - MixedCaseDNAFASTAFormat\n+ - ProteinsDirectoryFormat\n+ - MultiMAGSequencesDirFmt\n+ - EMPSingleEndCasavaDirFmt\n+ - QualityFilterStatsFmt\n+ - LSMatFormat\n+ - ImmutableMetadataFormat\n+ - DeblurStatsFmt\n+ - PairedEndFastqManifestPhred64V2\n+ - SingleEndFastqManifestPhred64V2\n+ - AlphaDiversityFormat\n+ - MultiBowtie2IndexDirFmt\n+ - EMPPairedEndCasavaDirFmt\n+ - ImportanceFormat\n - FirstDifferencesFormat\n - MixedCaseAlignedDNAFASTAFormat\n- - SingleLanePerSamplePairedEndFastqDirFmt\n- - EMPPairedEndDirFmt\n- - ImmutableMetadataFormat\n- - PairedEndFastqManifestPhred64V2\n- - DataLoafPackageDirFmt\n- - AlignedDNAFASTAFormat\n- - BIOMV100Format\n- - UchimeStatsFmt\n- - BLAST6Format\n- - PairedDNASequencesDirectoryFormat\n- - SingleEndFastqManifestPhred33V2\n- - QualityFilterStatsFmt\n+ - MultiplexedFastaQualDirFmt\n - DADA2StatsFormat\n- - AlignedProteinFASTAFormat\n- - MixedCaseRNAFASTAFormat\n- - PlacementsFormat\n- - NewickFormat\n- - PairedEndFastqManifestPhred64\n+ - OrdinationFormat\n+ - CasavaOneEightSingleLanePerSampleDirFmt\n - ProteinFASTAFormat\n - RNAFASTAFormat\n- - BooleanSeriesFormat\n- - SingleEndFastqManifestPhred64\n- - LSMatFormat\n- - DeblurStatsFmt\n- - ErrorCorrectionDetailsFmt\n- - MixedCaseDNAFASTAFormat\n- - TaxonomicClassiferTemporaryPickleDirFmt\n- - DNAFASTAFormat\n- - ProcrustesStatisticsFmt\n- - CasavaOneEightLanelessPerSampleDirFmt\n- - EMPSingleEndDirFmt\n- - DecontamScoreFormat\n- - OrdinationFormat\n- - SingleLanePerSampleSingleEndFastqDirFmt\n- - Bowtie2IndexDirFmt\n+ - BIOMV100Format\n+ - ContigSequencesDirFmt\n+ - NewickFormat\n+ - BLAST6Format\n+ - LociDirectoryFormat\n - BIOMV210Format\n- - PairedEndFastqManifestPhred33V2\n- - SampleEstimatorDirFmt\n- - EMPSingleEndCasavaDirFmt\n- - PairedRNASequencesDirectoryFormat\n- - EMPPairedEndCasavaDirFmt\n- - CasavaOneEightSingleLanePerSampleDirFmt\n- - SingleEndFastqManifestPhred64V2\n- - MultiplexedFastaQualDirFmt\n- - DifferentialFormat\n- - AlphaDiversityFormat\n- - MultiplexedPairedEndBarcodeInSequenceDirFmt\n- - PairedEndFastqManifestPhred33\n- - ArtificialGroupingFormat\n - ProbabilitiesFormat\n- - SeppReferenceDirFmt\n- - MixedCaseAlignedRNAFASTAFormat\n- - SingleEndFastqManifestPhred33\n- - ImportanceFormat\n+ - ErrorCorrectionDetailsFmt\n+ - BLASTDBDirFmtV5\n+ - DecontamScoreFormat\n - AlignedRNAFASTAFormat\n- - PredictionsFormat\n+ - ProcrustesStatisticsFmt\n+ - SeedOrthologDirFmt\n+ - Bowtie2IndexDirFmt\n+ - MixedCaseRNAFASTAFormat\n </help>\n <citations>\n <citation type="doi">10.1038/s41587-019-0209-9</citation>\n' |
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| diff -r 10447a4b0cc3 -r 9dbdf05beaa9 test-data/YY/YY_S49_R1_001.fastq.gz |
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| diff -r 10447a4b0cc3 -r 9dbdf05beaa9 test-data/YY/YY_S49_R2_001.fastq.gz |
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