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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
|---|---|
| date | Mon, 29 Aug 2022 20:37:34 +0000 |
| parents | |
| children | d3b1853c4efd |
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<?xml version='1.0' encoding='utf-8'?> <!-- Copyright (c) 2022, 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: 2022.8.1) for: qiime2 (version: 2022.8.1) --> <tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2022.8.1+dist.h91e3be72.2" profile="22.05" license="BSD-3-Clause"> <description>Export data from a QIIME 2 artifact</description> <requirements> <container type="docker">quay.io/qiime2/core:2022.8</container> </requirements> <command>q2galaxy run tools export '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> <inputs> <param name="input" type="data" format="qza" label="input: The path to the artifact you want to export"/> <param name="type_peek" type="select" label="The type of your input qza is:" display="radio"> <options> <filter type="data_meta" key="semantic_type" ref="input"/> </options> </param> <param name="fmt_peek" type="select" label="The current QIIME 2 format is:" display="radio"> <options> <filter type="data_meta" key="format" ref="input"/> </options> </param> <conditional name="fmt_finder"> <param name="type" type="select" label="To change the format, select the type indicated above:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="Bowtie2Index">Bowtie2Index</option> <option value="DeblurStats">DeblurStats</option> <option value="DistanceMatrix">DistanceMatrix</option> <option value="EMPPairedEndSequences">EMPPairedEndSequences</option> <option value="EMPSingleEndSequences">EMPSingleEndSequences</option> <option value="ErrorCorrectionDetails">ErrorCorrectionDetails</option> <option value="FeatureData__ob__AlignedProteinSequence__cb__">FeatureData[AlignedProteinSequence]</option> <option value="FeatureData__ob__AlignedRNASequence__cb__">FeatureData[AlignedRNASequence]</option> <option value="FeatureData__ob__AlignedSequence__cb__">FeatureData[AlignedSequence]</option> <option value="FeatureData__ob__BLAST6__cb__">FeatureData[BLAST6]</option> <option value="FeatureData__ob__Differential__cb__">FeatureData[Differential]</option> <option value="FeatureData__ob__Importance__cb__">FeatureData[Importance]</option> <option value="FeatureData__ob__PairedEndRNASequence__cb__">FeatureData[PairedEndRNASequence]</option> <option value="FeatureData__ob__PairedEndSequence__cb__">FeatureData[PairedEndSequence]</option> <option value="FeatureData__ob__ProteinSequence__cb__">FeatureData[ProteinSequence]</option> <option value="FeatureData__ob__RNASequence__cb__">FeatureData[RNASequence]</option> <option value="FeatureData__ob__Sequence__cb__">FeatureData[Sequence]</option> <option value="FeatureData__ob__Taxonomy__cb__">FeatureData[Taxonomy]</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> <option value="FeatureTable__ob__Frequency__cb__">FeatureTable[Frequency]</option> <option value="FeatureTable__ob__PercentileNormalized__cb__">FeatureTable[PercentileNormalized]</option> <option value="FeatureTable__ob__PresenceAbsence__cb__">FeatureTable[PresenceAbsence]</option> <option value="FeatureTable__ob__RelativeFrequency__cb__">FeatureTable[RelativeFrequency]</option> <option value="Hierarchy">Hierarchy</option> <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option> <option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option> <option value="PCoAResults">PCoAResults</option> <option value="Phylogeny__ob__Rooted__cb__">Phylogeny[Rooted]</option> <option value="Phylogeny__ob__Unrooted__cb__">Phylogeny[Unrooted]</option> <option value="Placements">Placements</option> <option value="ProcrustesStatistics">ProcrustesStatistics</option> <option value="QualityFilterStats">QualityFilterStats</option> <option value="RawSequences">RawSequences</option> <option value="SampleData__ob__AlphaDiversity__cb__">SampleData[AlphaDiversity]</option> <option value="SampleData__ob__ArtificialGrouping__cb__">SampleData[ArtificialGrouping]</option> <option value="SampleData__ob__BooleanSeries__cb__">SampleData[BooleanSeries]</option> <option value="SampleData__ob__ClassifierPredictions__cb__">SampleData[ClassifierPredictions]</option> <option value="SampleData__ob__DADA2Stats__cb__">SampleData[DADA2Stats]</option> <option value="SampleData__ob__FirstDifferences__cb__">SampleData[FirstDifferences]</option> <option value="SampleData__ob__JoinedSequencesWithQuality__cb__">SampleData[JoinedSequencesWithQuality]</option> <option value="SampleData__ob__PairedEndSequencesWithQuality__cb__">SampleData[PairedEndSequencesWithQuality]</option> <option value="SampleData__ob__Probabilities__cb__">SampleData[Probabilities]</option> <option value="SampleData__ob__RegressorPredictions__cb__">SampleData[RegressorPredictions]</option> <option value="SampleData__ob__SequencesWithQuality__cb__">SampleData[SequencesWithQuality]</option> <option value="SampleData__ob__Sequences__cb__">SampleData[Sequences]</option> <option value="SampleData__ob__TrueTargets__cb__">SampleData[TrueTargets]</option> <option value="SampleEstimator__ob__Classifier__cb__">SampleEstimator[Classifier]</option> <option value="SampleEstimator__ob__Regressor__cb__">SampleEstimator[Regressor]</option> <option value="SeppReferenceDatabase">SeppReferenceDatabase</option> <option value="TaxonomicClassifier">TaxonomicClassifier</option> <option value="UchimeStats">UchimeStats</option> </param> <when value="None"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> </param> </when> <when value="Bowtie2Index"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="Bowtie2IndexDirFmt">Bowtie2 Index Directory Format</option> </param> </when> <when value="DeblurStats"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="DeblurStatsFmt">Deblur Stats Format</option> </param> </when> <when value="DistanceMatrix"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="LSMatFormat">LS Mat Format</option> </param> </when> <when value="EMPPairedEndSequences"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="EMPPairedEndDirFmt">EMP Paired End Directory Format</option> </param> </when> <when value="EMPSingleEndSequences"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="EMPSingleEndDirFmt">EMP Single End Directory Format</option> </param> </when> <when value="ErrorCorrectionDetails"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> </param> </when> <when value="FeatureData__ob__AlignedProteinSequence__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="AlignedProteinFASTAFormat">Aligned Protein FASTA Format</option> </param> </when> <when value="FeatureData__ob__AlignedRNASequence__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="AlignedRNAFASTAFormat">Aligned RNAFASTA Format</option> </param> </when> <when value="FeatureData__ob__AlignedSequence__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="AlignedDNAFASTAFormat">Aligned DNAFASTA Format</option> </param> </when> <when value="FeatureData__ob__BLAST6__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="BLAST6Format">BLAST6 Format</option> </param> </when> <when value="FeatureData__ob__Differential__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="DifferentialFormat">Differential Format</option> </param> </when> <when value="FeatureData__ob__Importance__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="ImportanceFormat">Importance Format</option> </param> </when> <when value="FeatureData__ob__PairedEndRNASequence__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="PairedRNASequencesDirectoryFormat">Paired RNA Sequences Directory Format</option> </param> </when> <when value="FeatureData__ob__PairedEndSequence__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="PairedDNASequencesDirectoryFormat">Paired DNA Sequences Directory Format</option> </param> </when> <when value="FeatureData__ob__ProteinSequence__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="ProteinFASTAFormat">Protein FASTA Format</option> </param> </when> <when value="FeatureData__ob__RNASequence__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="RNAFASTAFormat">RNAFASTA Format</option> </param> </when> <when value="FeatureData__ob__Sequence__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="DNAFASTAFormat">DNAFASTA Format</option> </param> </when> <when value="FeatureData__ob__Taxonomy__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> </param> </when> <when value="FeatureTable__ob__Balance__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="BIOMV210Format">BIOMV210 Format</option> <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> </param> </when> <when value="FeatureTable__ob__Composition__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="BIOMV210Format">BIOMV210 Format</option> <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> </param> </when> <when value="FeatureTable__ob__Design__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="BIOMV210Format">BIOMV210 Format</option> <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> </param> </when> <when value="FeatureTable__ob__Frequency__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="BIOMV210Format">BIOMV210 Format</option> <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> </param> </when> <when value="FeatureTable__ob__PercentileNormalized__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="BIOMV210Format">BIOMV210 Format</option> <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> </param> </when> <when value="FeatureTable__ob__PresenceAbsence__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="BIOMV210Format">BIOMV210 Format</option> <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> </param> </when> <when value="FeatureTable__ob__RelativeFrequency__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="BIOMV210Format">BIOMV210 Format</option> <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> </param> </when> <when value="Hierarchy"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="NewickFormat">Newick Format</option> </param> </when> <when value="MultiplexedPairedEndBarcodeInSequence"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="MultiplexedPairedEndBarcodeInSequenceDirFmt">Multiplexed Paired End Barcode In Sequence Directory Format</option> </param> </when> <when value="MultiplexedSingleEndBarcodeInSequence"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="FastqGzFormat">Fastq Gz Format</option> </param> </when> <when value="PCoAResults"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="OrdinationFormat">Ordination Format</option> </param> </when> <when value="Phylogeny__ob__Rooted__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="NewickFormat">Newick Format</option> </param> </when> <when value="Phylogeny__ob__Unrooted__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="NewickFormat">Newick Format</option> </param> </when> <when value="Placements"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="PlacementsFormat">Placements Format</option> </param> </when> <when value="ProcrustesStatistics"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="ProcrustesStatisticsFmt">Procrustes Statistics Format</option> </param> </when> <when value="QualityFilterStats"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="QualityFilterStatsFmt">Quality Filter Stats Format</option> </param> </when> <when value="RawSequences"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="EMPSingleEndDirFmt">EMP Single End Directory Format</option> </param> </when> <when value="SampleData__ob__AlphaDiversity__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="AlphaDiversityFormat">Alpha Diversity Format</option> </param> </when> <when value="SampleData__ob__ArtificialGrouping__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="ArtificialGroupingFormat">Artificial Grouping Format</option> </param> </when> <when value="SampleData__ob__BooleanSeries__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="BooleanSeriesFormat">Boolean Series Format</option> </param> </when> <when value="SampleData__ob__ClassifierPredictions__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="PredictionsFormat">Predictions Format</option> </param> </when> <when value="SampleData__ob__DADA2Stats__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="DADA2StatsFormat">DADA2 Stats Format</option> </param> </when> <when value="SampleData__ob__FirstDifferences__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="FirstDifferencesFormat">First Differences Format</option> </param> </when> <when value="SampleData__ob__JoinedSequencesWithQuality__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="CasavaOneEightSingleLanePerSampleDirFmt">Casava One Eight Single Lane Per Sample Directory Format</option> <option value="QIIME1DemuxFormat">QIIME1 Demux Format</option> <option value="SingleLanePerSampleSingleEndFastqDirFmt">Single Lane Per Sample Single End Fastq Directory Format</option> </param> </when> <when value="SampleData__ob__PairedEndSequencesWithQuality__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="CasavaOneEightSingleLanePerSampleDirFmt">Casava One Eight Single Lane Per Sample Directory Format</option> <option value="SingleLanePerSamplePairedEndFastqDirFmt">Single Lane Per Sample Paired End Fastq Directory Format</option> <option value="SingleLanePerSampleSingleEndFastqDirFmt">Single Lane Per Sample Single End Fastq Directory Format</option> </param> </when> <when value="SampleData__ob__Probabilities__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="ProbabilitiesFormat">Probabilities Format</option> </param> </when> <when value="SampleData__ob__RegressorPredictions__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="PredictionsFormat">Predictions Format</option> </param> </when> <when value="SampleData__ob__SequencesWithQuality__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="CasavaOneEightSingleLanePerSampleDirFmt">Casava One Eight Single Lane Per Sample Directory Format</option> <option value="QIIME1DemuxFormat">QIIME1 Demux Format</option> <option value="SingleLanePerSampleSingleEndFastqDirFmt">Single Lane Per Sample Single End Fastq Directory Format</option> </param> </when> <when value="SampleData__ob__Sequences__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="QIIME1DemuxFormat">QIIME1 Demux Format</option> </param> </when> <when value="SampleData__ob__TrueTargets__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="PredictionsFormat">Predictions Format</option> </param> </when> <when value="SampleEstimator__ob__Classifier__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="SampleEstimatorDirFmt">Sample Estimator Directory Format</option> </param> </when> <when value="SampleEstimator__ob__Regressor__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="SampleEstimatorDirFmt">Sample Estimator Directory Format</option> </param> </when> <when value="SeppReferenceDatabase"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="SeppReferenceDirFmt">Sepp Reference Directory Format</option> </param> </when> <when value="TaxonomicClassifier"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="TaxonomicClassiferTemporaryPickleDirFmt">Taxonomic Classifer Temporary Pickle Directory Format</option> </param> </when> <when value="UchimeStats"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> <option value="UchimeStatsFmt">Uchime Stats Format</option> </param> </when> </conditional> </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 {'NewickFormat', 'DADA2StatsFormat', 'AlignedProteinFASTAFormat', 'QualityFilterStatsDirFmt', 'ProbabilitiesFormat', 'OrdinationFormat', 'SingleLanePerSamplePairedEndFastqDirFmt', 'EMPPairedEndDirFmt', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'AlignedDNASequencesDirectoryFormat', 'TSVTaxonomyDirectoryFormat', 'AlignedRNAFASTAFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'BooleanSeriesFormat', 'QualityFilterStatsFmt', 'BIOMV210DirFmt', 'EMPSingleEndDirFmt', 'Bowtie2IndexDirFmt', 'PlacementsFormat', 'TrueTargetsDirectoryFormat', 'AlignedRNASequencesDirectoryFormat', 'ProbabilitiesDirectoryFormat', 'ArtificialGroupingDirectoryFormat', 'DifferentialDirectoryFormat', 'AlignedDNAFASTAFormat', 'LSMatFormat', 'FastqGzFormat', 'RNASequencesDirectoryFormat', 'ProteinSequencesDirectoryFormat', 'DADA2StatsDirFmt', 'SeppReferenceDirFmt', 'DNAFASTAFormat', 'QIIME1DemuxDirFmt', 'BooleanSeriesDirectoryFormat', 'PairedRNASequencesDirectoryFormat', 'AlphaDiversityFormat', 'PlacementsDirFmt', 'ProcrustesStatisticsDirFmt', 'ImportanceFormat', 'NewickDirectoryFormat', 'TSVTaxonomyFormat', 'DifferentialFormat', 'QIIME1DemuxFormat', 'CasavaOneEightSingleLanePerSampleDirFmt', 'BLAST6Format', 'UchimeStatsFmt', 'FirstDifferencesFormat', 'PredictionsDirectoryFormat', 'ProcrustesStatisticsFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'AlignedProteinSequencesDirectoryFormat', 'SampleEstimatorDirFmt', 'RNAFASTAFormat', 'ProteinFASTAFormat', 'ArtificialGroupingFormat', 'AlphaDiversityDirectoryFormat', 'UchimeStatsDirFmt', 'TaxonomicClassiferTemporaryPickleDirFmt', 'PairedDNASequencesDirectoryFormat', 'DNASequencesDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'DeblurStatsFmt', 'DeblurStatsDirFmt', 'ErrorCorrectionDetailsDirFmt', 'OrdinationDirectoryFormat', 'BLAST6DirectoryFormat', 'BIOMV210Format', 'PredictionsFormat', 'ImportanceDirectoryFormat', 'FirstDifferencesDirectoryFormat'}</filter> <discover_datasets pattern="__designation_and_ext__" visible="false"/> </collection> <data name="AlignedDNAFASTAFormat" label="${tool.name} on ${on_string} as AlignedDNAFASTAFormat"> <filter>fmt_finder['output_format'] == 'AlignedDNAFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'AlignedDNAFASTAFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <data name="AlignedDNASequencesDirectoryFormat" label="${tool.name} on ${on_string} as AlignedDNASequencesDirectoryFormat"> <filter>fmt_finder['output_format'] == 'AlignedDNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'AlignedDNASequencesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>aligned-dna-sequences)\.(?P<ext>fasta)" visible="true"/> </data> <data name="AlignedProteinFASTAFormat" label="${tool.name} on ${on_string} as AlignedProteinFASTAFormat"> <filter>fmt_finder['output_format'] == 'AlignedProteinFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'AlignedProteinFASTAFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <data name="AlignedProteinSequencesDirectoryFormat" label="${tool.name} on ${on_string} as AlignedProteinSequencesDirectoryFormat"> <filter>fmt_finder['output_format'] == 'AlignedProteinSequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'AlignedProteinSequencesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>aligned-protein-sequences)\.(?P<ext>fasta)" visible="true"/> </data> <data name="AlignedRNAFASTAFormat" label="${tool.name} on ${on_string} as AlignedRNAFASTAFormat"> <filter>fmt_finder['output_format'] == 'AlignedRNAFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'AlignedRNAFASTAFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <data name="AlignedRNASequencesDirectoryFormat" label="${tool.name} on ${on_string} as AlignedRNASequencesDirectoryFormat"> <filter>fmt_finder['output_format'] == 'AlignedRNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'AlignedRNASequencesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>aligned-rna-sequences)\.(?P<ext>fasta)" visible="true"/> </data> <data name="AlphaDiversityDirectoryFormat" label="${tool.name} on ${on_string} as AlphaDiversityDirectoryFormat"> <filter>fmt_finder['output_format'] == 'AlphaDiversityDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'AlphaDiversityDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>alpha-diversity)\.(?P<ext>tsv)" visible="true"/> </data> <data name="AlphaDiversityFormat" label="${tool.name} on ${on_string} as AlphaDiversityFormat"> <filter>fmt_finder['output_format'] == 'AlphaDiversityFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek 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visible="true"/> </data> <data name="BLAST6Format" label="${tool.name} on ${on_string} as BLAST6Format"> <filter>fmt_finder['output_format'] == 'BLAST6Format' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BLAST6Format')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <data name="BooleanSeriesDirectoryFormat" label="${tool.name} on ${on_string} as BooleanSeriesDirectoryFormat"> <filter>fmt_finder['output_format'] == 'BooleanSeriesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BooleanSeriesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>outliers)\.(?P<ext>tsv)" visible="true"/> </data> <data name="BooleanSeriesFormat" label="${tool.name} on ${on_string} as BooleanSeriesFormat"> <filter>fmt_finder['output_format'] == 'BooleanSeriesFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BooleanSeriesFormat')</filter> 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type="list" label="${tool.name} on ${on_string} as CasavaOneEightSingleLanePerSampleDirFmt (sequences)"> <filter>fmt_finder['output_format'] == 'CasavaOneEightSingleLanePerSampleDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'CasavaOneEightSingleLanePerSampleDirFmt')</filter> <discover_datasets pattern="(?P<designation>.+_.+_L[0-9][0-9][0-9]_R[12]_001)\.(?P<ext>fastq\.gz)" visible="false"/> </collection> <data name="DADA2StatsDirFmt" label="${tool.name} on ${on_string} as DADA2StatsDirFmt"> <filter>fmt_finder['output_format'] == 'DADA2StatsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DADA2StatsDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>stats)\.(?P<ext>tsv)" visible="true"/> </data> <data name="DADA2StatsFormat" label="${tool.name} on ${on_string} as DADA2StatsFormat"> <filter>fmt_finder['output_format'] == 'DADA2StatsFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 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label="${tool.name} on ${on_string} as DifferentialFormat"> <filter>fmt_finder['output_format'] == 'DifferentialFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DifferentialFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <data name="DistanceMatrixDirectoryFormat" label="${tool.name} on ${on_string} as DistanceMatrixDirectoryFormat"> <filter>fmt_finder['output_format'] == 'DistanceMatrixDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DistanceMatrixDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>distance-matrix)\.(?P<ext>tsv)" visible="true"/> </data> <data name="EMPPairedEndDirFmt" label="${tool.name} on ${on_string} as EMPPairedEndDirFmt"> <filter>fmt_finder['output_format'] == 'EMPPairedEndDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'EMPPairedEndDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>forward)\.(?P<ext>fastq.gz)" visible="true"/> <discover_datasets pattern="(?P<designation>reverse)\.(?P<ext>fastq.gz)" visible="true"/> <discover_datasets pattern="(?P<designation>barcodes)\.(?P<ext>fastq.gz)" visible="true"/> </data> <data name="EMPSingleEndDirFmt" label="${tool.name} on ${on_string} as EMPSingleEndDirFmt"> <filter>fmt_finder['output_format'] == 'EMPSingleEndDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'EMPSingleEndDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>sequences)\.(?P<ext>fastq.gz)" visible="true"/> <discover_datasets pattern="(?P<designation>barcodes)\.(?P<ext>fastq.gz)" visible="true"/> </data> <data name="ErrorCorrectionDetailsDirFmt" label="${tool.name} on ${on_string} as ErrorCorrectionDetailsDirFmt"> <filter>fmt_finder['output_format'] == 'ErrorCorrectionDetailsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 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visible="true"/> </data> <data name="LSMatFormat" label="${tool.name} on ${on_string} as LSMatFormat"> <filter>fmt_finder['output_format'] == 'LSMatFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'LSMatFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <data name="MultiplexedPairedEndBarcodeInSequenceDirFmt" label="${tool.name} on ${on_string} as MultiplexedPairedEndBarcodeInSequenceDirFmt"> <filter>fmt_finder['output_format'] == 'MultiplexedPairedEndBarcodeInSequenceDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiplexedPairedEndBarcodeInSequenceDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>forward)\.(?P<ext>fastq.gz)" visible="true"/> <discover_datasets pattern="(?P<designation>reverse)\.(?P<ext>fastq.gz)" visible="true"/> </data> <data name="MultiplexedSingleEndBarcodeInSequenceDirFmt" label="${tool.name} on ${on_string} as MultiplexedSingleEndBarcodeInSequenceDirFmt"> <filter>fmt_finder['output_format'] == 'MultiplexedSingleEndBarcodeInSequenceDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiplexedSingleEndBarcodeInSequenceDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>forward)\.(?P<ext>fastq.gz)" visible="true"/> </data> <data name="NewickDirectoryFormat" label="${tool.name} on ${on_string} as NewickDirectoryFormat"> <filter>fmt_finder['output_format'] == 'NewickDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'NewickDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>tree)\.(?P<ext>nwk)" visible="true"/> </data> <data name="NewickFormat" label="${tool.name} on ${on_string} as NewickFormat"> <filter>fmt_finder['output_format'] == 'NewickFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'NewickFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <data name="OrdinationDirectoryFormat" label="${tool.name} on ${on_string} as OrdinationDirectoryFormat"> <filter>fmt_finder['output_format'] == 'OrdinationDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'OrdinationDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>ordination)\.(?P<ext>txt)" visible="true"/> </data> <data name="OrdinationFormat" label="${tool.name} on ${on_string} as OrdinationFormat"> <filter>fmt_finder['output_format'] == 'OrdinationFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'OrdinationFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <data name="PairedDNASequencesDirectoryFormat" label="${tool.name} on ${on_string} as PairedDNASequencesDirectoryFormat"> <filter>fmt_finder['output_format'] == 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<filter>fmt_finder['output_format'] == 'PlacementsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PlacementsDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>placements)\.(?P<ext>json)" visible="true"/> </data> <data name="PlacementsFormat" label="${tool.name} on ${on_string} as PlacementsFormat"> <filter>fmt_finder['output_format'] == 'PlacementsFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PlacementsFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <data name="PredictionsDirectoryFormat" label="${tool.name} on ${on_string} as PredictionsDirectoryFormat"> <filter>fmt_finder['output_format'] == 'PredictionsDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PredictionsDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>predictions)\.(?P<ext>tsv)" visible="true"/> </data> <data name="PredictionsFormat" label="${tool.name} on ${on_string} as PredictionsFormat"> <filter>fmt_finder['output_format'] == 'PredictionsFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PredictionsFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <data name="ProbabilitiesDirectoryFormat" label="${tool.name} on ${on_string} as ProbabilitiesDirectoryFormat"> <filter>fmt_finder['output_format'] == 'ProbabilitiesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProbabilitiesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>class_probabilities)\.(?P<ext>tsv)" visible="true"/> </data> <data name="ProbabilitiesFormat" label="${tool.name} on ${on_string} as ProbabilitiesFormat"> <filter>fmt_finder['output_format'] == 'ProbabilitiesFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 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ProteinFASTAFormat"> <filter>fmt_finder['output_format'] == 'ProteinFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinFASTAFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <data name="ProteinSequencesDirectoryFormat" label="${tool.name} on ${on_string} as ProteinSequencesDirectoryFormat"> <filter>fmt_finder['output_format'] == 'ProteinSequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinSequencesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>protein-sequences)\.(?P<ext>fasta)" visible="true"/> </data> <data name="QIIME1DemuxDirFmt" label="${tool.name} on ${on_string} as QIIME1DemuxDirFmt"> <filter>fmt_finder['output_format'] == 'QIIME1DemuxDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'QIIME1DemuxDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>seqs)\.(?P<ext>fna)" visible="true"/> </data> <data name="QIIME1DemuxFormat" label="${tool.name} on ${on_string} as QIIME1DemuxFormat"> <filter>fmt_finder['output_format'] == 'QIIME1DemuxFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'QIIME1DemuxFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <data name="QualityFilterStatsDirFmt" label="${tool.name} on ${on_string} as QualityFilterStatsDirFmt"> <filter>fmt_finder['output_format'] == 'QualityFilterStatsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'QualityFilterStatsDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>stats)\.(?P<ext>csv)" visible="true"/> </data> <data name="QualityFilterStatsFmt" label="${tool.name} on ${on_string} as QualityFilterStatsFmt"> <filter>fmt_finder['output_format'] == 'QualityFilterStatsFmt' or (fmt_finder['output_format'] == 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<filter>fmt_finder['output_format'] == 'SampleEstimatorDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SampleEstimatorDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>sklearn_version)\.(?P<ext>json)" visible="true"/> <discover_datasets pattern="(?P<designation>sklearn_pipeline)\.(?P<ext>tar)" visible="true"/> </data> <data name="SeppReferenceDirFmt" label="${tool.name} on ${on_string} as SeppReferenceDirFmt"> <filter>fmt_finder['output_format'] == 'SeppReferenceDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SeppReferenceDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>aligned-dna-sequences)\.(?P<ext>fasta)" visible="true"/> <discover_datasets pattern="(?P<designation>tree)\.(?P<ext>nwk)" visible="true"/> <discover_datasets pattern="(?P<designation>raxml-info)\.(?P<ext>txt)" visible="true"/> </data> <collection name="SingleLanePerSamplePairedEndFastqDirFmt_sequences" type="list" label="${tool.name} on ${on_string} as SingleLanePerSamplePairedEndFastqDirFmt (sequences)"> <filter>fmt_finder['output_format'] == 'SingleLanePerSamplePairedEndFastqDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SingleLanePerSamplePairedEndFastqDirFmt')</filter> <discover_datasets pattern="(?P<designation>.+_.+_L[0-9][0-9][0-9]_R[12]_001)\.(?P<ext>fastq\.gz)" visible="false"/> </collection> <data name="SingleLanePerSamplePairedEndFastqDirFmt" label="${tool.name} on ${on_string} as SingleLanePerSamplePairedEndFastqDirFmt"> <filter>fmt_finder['output_format'] == 'SingleLanePerSamplePairedEndFastqDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SingleLanePerSamplePairedEndFastqDirFmt')</filter> <discover_datasets assign_primary_output="true" ext="txt" pattern="(?P<designation>MANIFEST)" visible="true"/> <discover_datasets pattern="(?P<designation>metadata)\.(?P<ext>yml)" visible="true"/> </data> <collection name="SingleLanePerSampleSingleEndFastqDirFmt_sequences" type="list" label="${tool.name} on ${on_string} as SingleLanePerSampleSingleEndFastqDirFmt (sequences)"> <filter>fmt_finder['output_format'] == 'SingleLanePerSampleSingleEndFastqDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SingleLanePerSampleSingleEndFastqDirFmt')</filter> <discover_datasets pattern="(?P<designation>.+_.+_L[0-9][0-9][0-9]_R[12]_001)\.(?P<ext>fastq\.gz)" visible="false"/> </collection> <data name="SingleLanePerSampleSingleEndFastqDirFmt" label="${tool.name} on ${on_string} as SingleLanePerSampleSingleEndFastqDirFmt"> <filter>fmt_finder['output_format'] == 'SingleLanePerSampleSingleEndFastqDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SingleLanePerSampleSingleEndFastqDirFmt')</filter> <discover_datasets assign_primary_output="true" ext="txt" pattern="(?P<designation>MANIFEST)" visible="true"/> <discover_datasets pattern="(?P<designation>metadata)\.(?P<ext>yml)" visible="true"/> </data> <data name="TSVTaxonomyDirectoryFormat" label="${tool.name} on ${on_string} as TSVTaxonomyDirectoryFormat"> <filter>fmt_finder['output_format'] == 'TSVTaxonomyDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TSVTaxonomyDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>taxonomy)\.(?P<ext>tsv)" visible="true"/> </data> <data name="TSVTaxonomyFormat" label="${tool.name} on ${on_string} as TSVTaxonomyFormat"> <filter>fmt_finder['output_format'] == 'TSVTaxonomyFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TSVTaxonomyFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> <data name="TaxonomicClassiferTemporaryPickleDirFmt" label="${tool.name} on ${on_string} as TaxonomicClassiferTemporaryPickleDirFmt"> <filter>fmt_finder['output_format'] == 'TaxonomicClassiferTemporaryPickleDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TaxonomicClassiferTemporaryPickleDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>sklearn_version)\.(?P<ext>json)" visible="true"/> <discover_datasets pattern="(?P<designation>sklearn_pipeline)\.(?P<ext>tar)" visible="true"/> </data> <data name="TrueTargetsDirectoryFormat" label="${tool.name} on ${on_string} as TrueTargetsDirectoryFormat"> <filter>fmt_finder['output_format'] == 'TrueTargetsDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TrueTargetsDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>true_targets)\.(?P<ext>tsv)" visible="true"/> </data> <data name="UchimeStatsDirFmt" label="${tool.name} on ${on_string} as UchimeStatsDirFmt"> <filter>fmt_finder['output_format'] == 'UchimeStatsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'UchimeStatsDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>stats)\.(?P<ext>tsv)" visible="true"/> </data> <data name="UchimeStatsFmt" label="${tool.name} on ${on_string} as UchimeStatsFmt"> <filter>fmt_finder['output_format'] == 'UchimeStatsFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'UchimeStatsFmt')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> </outputs> <help> QIIME 2: tools export ===================== Export a QIIME 2 artifact to different formats Instructions ------------ 1. Select the QZA you would like to export. Once selected, two fields will update indicating the type and format of this QZA. 2. If you wish to change the output format, first provide the same type as the QZA (which is shown above). This will filter the avaiable formats. 3. Select the format you desire. Some limited documentation is available on these formats below. **IMPORTANT:** if you select the wrong type when exporting, you will recieve an error suggesting "No transformation from <X> to <Y>". Formats: -------- 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. QIIME1DemuxFormat ***************** QIIME 1 demultiplexed FASTA format. The QIIME 1 demultiplexed FASTA format is the default output format of ``split_libraries.py`` and ``split_libraries_fastq.py``. The file output by QIIME 1 is named ``seqs.fna``; this filename is sometimes associated with the file format itself due to its widespread usage in QIIME 1. The format is documented here: http://qiime.org/documentation/file_formats.html#demultiplexed-sequences Format details: - FASTA file with exactly two lines per record: header and sequence. Each sequence must span exactly one line and cannot be split across multiple lines. - The ID in each header must follow the format ``<sample-id>_<seq-id>``. ``<sample-id>`` is the identifier of the sample the sequence belongs to, and ``<seq-id>`` is an identifier for the sequence *within* its sample. In QIIME 1, ``<seq-id>`` is typically an incrementing integer starting from zero, but any non-empty value can be used here, as long as the header IDs remain unique throughout the file. Note: ``<sample-id>`` may contain sample IDs that contain underscores; the rightmost underscore will used to delimit sample and sequence IDs. - Descriptions in headers are permitted and ignored. - Header IDs must be unique within the file. - Each sequence must be DNA and cannot be empty. FastqGzFormat ************* A gzipped fastq file. Additional formats without documentation: ***************************************** - AlignedRNASequencesDirectoryFormat - MultiplexedSingleEndBarcodeInSequenceDirFmt - AlignedDNASequencesDirectoryFormat - NewickFormat - SeppReferenceDirFmt - ProcrustesStatisticsDirFmt - PairedRNASequencesDirectoryFormat - BIOMV210DirFmt - EMPPairedEndDirFmt - DistanceMatrixDirectoryFormat - AlphaDiversityDirectoryFormat - OrdinationDirectoryFormat - ArtificialGroupingFormat - BLAST6Format - RNASequencesDirectoryFormat - ProbabilitiesFormat - PlacementsFormat - DADA2StatsFormat - SampleEstimatorDirFmt - ImportanceFormat - AlignedProteinFASTAFormat - DNASequencesDirectoryFormat - BIOMV210Format - TSVTaxonomyDirectoryFormat - QualityFilterStatsDirFmt - SingleLanePerSampleSingleEndFastqDirFmt - CasavaOneEightSingleLanePerSampleDirFmt - ProteinFASTAFormat - ProbabilitiesDirectoryFormat - DADA2StatsDirFmt - Bowtie2IndexDirFmt - DifferentialFormat - QIIME1DemuxDirFmt - UchimeStatsFmt - DeblurStatsFmt - DeblurStatsDirFmt - AlignedRNAFASTAFormat - NewickDirectoryFormat - EMPSingleEndDirFmt - PredictionsDirectoryFormat - AlignedDNAFASTAFormat - ArtificialGroupingDirectoryFormat - FirstDifferencesDirectoryFormat - ProcrustesStatisticsFmt - FirstDifferencesFormat - BLAST6DirectoryFormat - PairedDNASequencesDirectoryFormat - ErrorCorrectionDetailsDirFmt - MultiplexedPairedEndBarcodeInSequenceDirFmt - LSMatFormat - AlphaDiversityFormat - PlacementsDirFmt - OrdinationFormat - BooleanSeriesFormat - ImportanceDirectoryFormat - AlignedProteinSequencesDirectoryFormat - RNAFASTAFormat - SingleLanePerSamplePairedEndFastqDirFmt - TaxonomicClassiferTemporaryPickleDirFmt - PredictionsFormat - TrueTargetsDirectoryFormat - ProteinSequencesDirectoryFormat - DNAFASTAFormat - QualityFilterStatsFmt - BooleanSeriesDirectoryFormat - DifferentialDirectoryFormat - UchimeStatsDirFmt </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations> </tool>