Mercurial > repos > q2d2 > qiime2_core__tools__export
changeset 0:0214b9ae8a6e draft
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 |
| files | qiime2_core__tools__export.xml test-data/.gitkeep |
| diffstat | 1 files changed, 891 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2_core__tools__export.xml Mon Aug 29 20:37:34 2022 +0000 @@ -0,0 +1,891 @@ +<?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 ${on_string} as AlignedProteinFASTAFormat"> + <filter>fmt_finder['output_format'] == 'AlignedProteinFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'AlignedProteinFASTAFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <data name="AlignedProteinSequencesDirectoryFormat" 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(fmt_finder['output_format'] == 'None' and fmt_peek == 'AlignedRNASequencesDirectoryFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>aligned-rna-sequences)\.(?P<ext>fasta)" visible="true"/> + </data> + <data name="AlphaDiversityDirectoryFormat" label="${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 ${on_string} as AlphaDiversityFormat"> + <filter>fmt_finder['output_format'] == 'AlphaDiversityFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'AlphaDiversityFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <data name="ArtificialGroupingDirectoryFormat" label="${tool.name} on ${on_string} as ArtificialGroupingDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'ArtificialGroupingDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ArtificialGroupingDirectoryFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>artificial-groupings)\.(?P<ext>tsv)" visible="true"/> + </data> + <data name="ArtificialGroupingFormat" label="${tool.name} on ${on_string} as ArtificialGroupingFormat"> + <filter>fmt_finder['output_format'] == 'ArtificialGroupingFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ArtificialGroupingFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <data name="BIOMV210DirFmt" label="${tool.name} on ${on_string} as BIOMV210DirFmt"> + 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<discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <data name="Bowtie2IndexDirFmt" label="${tool.name} on ${on_string} as Bowtie2IndexDirFmt"> + <filter>fmt_finder['output_format'] == 'Bowtie2IndexDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Bowtie2IndexDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>.+(?<!\.rev)\.1)\.(?P<ext>bt2l?)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+(?<!\.rev)\.2)\.(?P<ext>bt2l?)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+\.3)\.(?P<ext>bt2l?)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+\.4)\.(?P<ext>bt2l?)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+\.rev\.1)\.(?P<ext>bt2l?)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+\.rev\.2)\.(?P<ext>bt2l?)" visible="true"/> + </data> + <collection 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or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DADA2StatsFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <data name="DNAFASTAFormat" label="${tool.name} on ${on_string} as DNAFASTAFormat"> + <filter>fmt_finder['output_format'] == 'DNAFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNAFASTAFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <data name="DNASequencesDirectoryFormat" label="${tool.name} on ${on_string} as DNASequencesDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'DNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNASequencesDirectoryFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>dna-sequences)\.(?P<ext>fasta)" visible="true"/> + </data> + <data name="DeblurStatsDirFmt" label="${tool.name} on ${on_string} as DeblurStatsDirFmt"> + <filter>fmt_finder['output_format'] == 'DeblurStatsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DeblurStatsDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>stats)\.(?P<ext>csv)" visible="true"/> + </data> + <data name="DeblurStatsFmt" label="${tool.name} on ${on_string} as DeblurStatsFmt"> + <filter>fmt_finder['output_format'] == 'DeblurStatsFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DeblurStatsFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <data name="DifferentialDirectoryFormat" label="${tool.name} on ${on_string} as DifferentialDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'DifferentialDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DifferentialDirectoryFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>differentials)\.(?P<ext>tsv)" visible="true"/> + </data> + <data name="DifferentialFormat" label="${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"> + 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on ${on_string} as ErrorCorrectionDetailsDirFmt"> + <filter>fmt_finder['output_format'] == 'ErrorCorrectionDetailsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ErrorCorrectionDetailsDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>details)\.(?P<ext>tsv)" visible="true"/> + </data> + <data name="FastqGzFormat" label="${tool.name} on ${on_string} as FastqGzFormat"> + <filter>fmt_finder['output_format'] == 'FastqGzFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'FastqGzFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <data name="FirstDifferencesDirectoryFormat" label="${tool.name} on ${on_string} as FirstDifferencesDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'FirstDifferencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'FirstDifferencesDirectoryFormat')</filter> + <discover_datasets 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<filter>fmt_finder['output_format'] == 'ImportanceFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ImportanceFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <data name="LSMatFormat" label="${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 ${on_string} as MultiplexedPairedEndBarcodeInSequenceDirFmt"> + <filter>fmt_finder['output_format'] == 'MultiplexedPairedEndBarcodeInSequenceDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiplexedPairedEndBarcodeInSequenceDirFmt')</filter> + <discover_datasets assign_primary_output="true" 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pattern="(?P<designation>tree)\.(?P<ext>nwk)" visible="true"/> + </data> + <data name="NewickFormat" label="${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 ${on_string} as PairedDNASequencesDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'PairedDNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PairedDNASequencesDirectoryFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>left-dna-sequences)\.(?P<ext>fasta)" visible="true"/> + <discover_datasets pattern="(?P<designation>right-dna-sequences)\.(?P<ext>fasta)" visible="true"/> + </data> + <data name="PairedRNASequencesDirectoryFormat" label="${tool.name} on ${on_string} as PairedRNASequencesDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'PairedRNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 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+ <data name="PredictionsDirectoryFormat" label="${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 ${on_string} as ProbabilitiesDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'ProbabilitiesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek 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'QualityFilterStatsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'QualityFilterStatsDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>stats)\.(?P<ext>csv)" visible="true"/> + </data> + <data name="QualityFilterStatsFmt" label="${tool.name} on ${on_string} as QualityFilterStatsFmt"> + <filter>fmt_finder['output_format'] == 'QualityFilterStatsFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'QualityFilterStatsFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <data name="RNAFASTAFormat" label="${tool.name} on ${on_string} as RNAFASTAFormat"> + <filter>fmt_finder['output_format'] == 'RNAFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNAFASTAFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <data name="RNASequencesDirectoryFormat" label="${tool.name} on ${on_string} as RNASequencesDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'RNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNASequencesDirectoryFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>rna-sequences)\.(?P<ext>fasta)" visible="true"/> + </data> + <data name="SampleEstimatorDirFmt" label="${tool.name} on ${on_string} as SampleEstimatorDirFmt"> + <filter>fmt_finder['output_format'] == 'SampleEstimatorDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SampleEstimatorDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>sklearn_version)\.(?P<ext>json)" visible="true"/> + <discover_datasets pattern="(?P<designation>sklearn_pipeline)\.(?P<ext>tar)" visible="true"/> + </data> + <data name="SeppReferenceDirFmt" label="${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>