Mercurial > repos > q2d2 > qiime2_core__tools__import
changeset 6:8a0db69428c7 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 5f71b597c9495eae67a447744fded834f56ca1f7
| author | q2d2 |
|---|---|
| date | Wed, 30 Oct 2024 20:00:15 +0000 |
| parents | f9e68fa06585 |
| children | |
| files | qiime2_core__tools__import.xml |
| diffstat | 1 files changed, 653 insertions(+), 259 deletions(-) [+] |
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--- a/qiime2_core__tools__import.xml Mon Jun 03 23:32:49 2024 +0000 +++ b/qiime2_core__tools__import.xml Wed Oct 30 20:00:15 2024 +0000 @@ -6,14 +6,17 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2024.5.0) + q2galaxy (version: 2024.10.0) for: - qiime2 (version: 2024.5.0) + qiime2 (version: 2024.10.1) --> -<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2024.5.0+dist.he540b0b0" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2024.10.0+dist.h3d8a7e27" profile="22.05" license="BSD-3-Clause"> <description>Import data into a QIIME 2 artifact</description> + <xrefs> + <xref type="bio.tools">qiime2</xref> + </xrefs> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2024.5</container> + <container type="docker">quay.io/qiime2/amplicon:2024.10</container> </requirements> <command>q2galaxy run tools import '$inputs'</command> <configfiles> @@ -64,6 +67,16 @@ <option value="Bowtie2Index">Bowtie2Index</option> <option value="BrackenDB">BrackenDB</option> <option value="DeblurStats">DeblurStats</option> + <option value="Dist1D__ob__Multi__comma__ Independent__cb__">Dist1D[Multi, Independent]</option> + <option value="Dist1D__ob__Multi__comma__ Matched__cb__">Dist1D[Multi, Matched]</option> + <option value="Dist1D__ob__NestedOrdered__comma__ Independent__cb__">Dist1D[NestedOrdered, Independent]</option> + <option value="Dist1D__ob__NestedOrdered__comma__ Matched__cb__">Dist1D[NestedOrdered, Matched]</option> + <option value="Dist1D__ob__NestedUnordered__comma__ Independent__cb__">Dist1D[NestedUnordered, Independent]</option> + <option value="Dist1D__ob__NestedUnordered__comma__ Matched__cb__">Dist1D[NestedUnordered, Matched]</option> + <option value="Dist1D__ob__Ordered__comma__ Independent__cb__">Dist1D[Ordered, Independent]</option> + <option value="Dist1D__ob__Ordered__comma__ Matched__cb__">Dist1D[Ordered, Matched]</option> + <option value="Dist1D__ob__Unordered__comma__ Independent__cb__">Dist1D[Unordered, Independent]</option> + <option value="Dist1D__ob__Unordered__comma__ Matched__cb__">Dist1D[Unordered, Matched]</option> <option value="DistanceMatrix">DistanceMatrix</option> <option value="EMPPairedEndSequences">EMPPairedEndSequences</option> <option value="EMPSingleEndSequences">EMPSingleEndSequences</option> @@ -78,12 +91,9 @@ <option value="FeatureData__ob__DifferentialAbundance__cb__">FeatureData[DifferentialAbundance]</option> <option value="FeatureData__ob__Differential__cb__">FeatureData[Differential]</option> <option value="FeatureData__ob__Importance__cb__">FeatureData[Importance]</option> - <option value="FeatureData__ob__KEGG__cb__">FeatureData[KEGG]</option> <option value="FeatureData__ob__Kraken2Output__cb__">FeatureData[Kraken2Output]</option> <option value="FeatureData__ob__Kraken2Report__cb__">FeatureData[Kraken2Report]</option> <option value="FeatureData__ob__MAG__cb__">FeatureData[MAG]</option> - <option value="FeatureData__ob__NOG__cb__">FeatureData[NOG]</option> - <option value="FeatureData__ob__OG__cb__">FeatureData[OG]</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> @@ -99,12 +109,15 @@ <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__Normalized__cb__">FeatureTable[Normalized]</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="GenomeData__ob__BLAST6__cb__">GenomeData[BLAST6]</option> + <option value="GenomeData__ob__DNASequence__cb__">GenomeData[DNASequence]</option> <option value="GenomeData__ob__Genes__cb__">GenomeData[Genes]</option> <option value="GenomeData__ob__Loci__cb__">GenomeData[Loci]</option> + <option value="GenomeData__ob__NOG__cb__">GenomeData[NOG]</option> + <option value="GenomeData__ob__Orthologs__cb__">GenomeData[Orthologs]</option> <option value="GenomeData__ob__Proteins__cb__">GenomeData[Proteins]</option> <option value="Hierarchy">Hierarchy</option> <option value="ImmutableMetadata">ImmutableMetadata</option> @@ -118,6 +131,15 @@ <option value="Phylogeny__ob__Unrooted__cb__">Phylogeny[Unrooted]</option> <option value="Placements">Placements</option> <option value="ProcrustesStatistics">ProcrustesStatistics</option> + <option value="ProfileHMM__ob__MultipleDNA__cb__">ProfileHMM[MultipleDNA]</option> + <option value="ProfileHMM__ob__MultipleProtein__cb__">ProfileHMM[MultipleProtein]</option> + <option value="ProfileHMM__ob__MultipleRNA__cb__">ProfileHMM[MultipleRNA]</option> + <option value="ProfileHMM__ob__PressedDNA__cb__">ProfileHMM[PressedDNA]</option> + <option value="ProfileHMM__ob__PressedProtein__cb__">ProfileHMM[PressedProtein]</option> + <option value="ProfileHMM__ob__PressedRNA__cb__">ProfileHMM[PressedRNA]</option> + <option value="ProfileHMM__ob__SingleDNA__cb__">ProfileHMM[SingleDNA]</option> + <option value="ProfileHMM__ob__SingleProtein__cb__">ProfileHMM[SingleProtein]</option> + <option value="ProfileHMM__ob__SingleRNA__cb__">ProfileHMM[SingleRNA]</option> <option value="QualityFilterStats">QualityFilterStats</option> <option value="RawSequences">RawSequences</option> <option value="ReferenceDB__ob__Diamond__cb__">ReferenceDB[Diamond]</option> @@ -127,7 +149,6 @@ <option value="SampleData__ob__AlignmentMap__cb__">SampleData[AlignmentMap]</option> <option value="SampleData__ob__AlphaDiversity__cb__">SampleData[AlphaDiversity]</option> <option value="SampleData__ob__ArtificialGrouping__cb__">SampleData[ArtificialGrouping]</option> - <option value="SampleData__ob__BLAST6__cb__">SampleData[BLAST6]</option> <option value="SampleData__ob__BooleanSeries__cb__">SampleData[BooleanSeries]</option> <option value="SampleData__ob__ClassifierPredictions__cb__">SampleData[ClassifierPredictions]</option> <option value="SampleData__ob__Contigs__cb__">SampleData[Contigs]</option> @@ -139,6 +160,8 @@ <option value="SampleData__ob__MAGs__cb__">SampleData[MAGs]</option> <option value="SampleData__ob__MultiAlignmentMap__cb__">SampleData[MultiAlignmentMap]</option> <option value="SampleData__ob__MultiBowtie2Index__cb__">SampleData[MultiBowtie2Index]</option> + <option value="SampleData__ob__NOG__cb__">SampleData[NOG]</option> + <option value="SampleData__ob__Orthologs__cb__">SampleData[Orthologs]</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> @@ -149,6 +172,7 @@ <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="StatsTable__ob__Pairwise__cb__">StatsTable[Pairwise]</option> <option value="TaxonomicClassifier">TaxonomicClassifier</option> <option value="UchimeStats">UchimeStats</option> </param> @@ -306,6 +330,136 @@ </when> </conditional> </when> + <when value="Dist1D__ob__Multi__comma__ Independent__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option> + </param> + <when value="TableJSONLFileFormat"> + <section name="import" expanded="true" title="Import"> + <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> + <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Dist1D__ob__Multi__comma__ Matched__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option> + </param> + <when value="TableJSONLFileFormat"> + <section name="import" expanded="true" title="Import"> + <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> + <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Dist1D__ob__NestedOrdered__comma__ Independent__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option> + </param> + <when value="TableJSONLFileFormat"> + <section name="import" expanded="true" title="Import"> + <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> + <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Dist1D__ob__NestedOrdered__comma__ Matched__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option> + </param> + <when value="TableJSONLFileFormat"> + <section name="import" expanded="true" title="Import"> + <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> + <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Dist1D__ob__NestedUnordered__comma__ Independent__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option> + </param> + <when value="TableJSONLFileFormat"> + <section name="import" expanded="true" title="Import"> + <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> + <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Dist1D__ob__NestedUnordered__comma__ Matched__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option> + </param> + <when value="TableJSONLFileFormat"> + <section name="import" expanded="true" title="Import"> + <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> + <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Dist1D__ob__Ordered__comma__ Independent__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option> + </param> + <when value="TableJSONLFileFormat"> + <section name="import" expanded="true" title="Import"> + <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> + <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Dist1D__ob__Ordered__comma__ Matched__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option> + </param> + <when value="TableJSONLFileFormat"> + <section name="import" expanded="true" title="Import"> + <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> + <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Dist1D__ob__Unordered__comma__ Independent__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option> + </param> + <when value="TableJSONLFileFormat"> + <section name="import" expanded="true" title="Import"> + <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> + <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Dist1D__ob__Unordered__comma__ Matched__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option> + </param> + <when value="TableJSONLFileFormat"> + <section name="import" expanded="true" title="Import"> + <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> + <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="DistanceMatrix"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -619,44 +773,6 @@ </when> </conditional> </when> - <when value="FeatureData__ob__KEGG__cb__"> - <conditional name="__q2galaxy__GUI__cond__format__"> - <param name="format" type="select" label="QIIME 2 file format to import from:"> - <option value="OrthologAnnotationDirFmt" selected="true">Ortholog Annotation Directory Format</option> - </param> - <when value="OrthologAnnotationDirFmt"> - <section name="import_annotations" expanded="true" title="Import annotations"> - <conditional name="__q2galaxy__GUI__cond__annotations__"> - <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> - <option value="collection" selected="true">Use collection to import</option> - <option value="individual">Associate individual files</option> - </param> - <when value="collection"> - <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .+\.annotations" collection_type="list"/> - <conditional name="__q2galaxy__GUI__cond__add_ext__"> - <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> - <option value="no">No, use element identifiers as is</option> - <option value="yes">Yes, append an extension</option> - </param> - <when value="yes"> - <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> - </when> - <when value="no"/> - </conditional> - </when> - <when value="individual"> - <repeat name="elements" min="1" title="Add Elements"> - <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.annotations"> - <validator type="regex" message="This filename doesn't match the regex.">.+\.annotations</validator> - </param> - <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/> - </repeat> - </when> - </conditional> - </section> - </when> - </conditional> - </when> <when value="FeatureData__ob__Kraken2Output__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -771,82 +887,6 @@ </when> </conditional> </when> - <when value="FeatureData__ob__NOG__cb__"> - <conditional name="__q2galaxy__GUI__cond__format__"> - <param name="format" type="select" label="QIIME 2 file format to import from:"> - <option value="OrthologAnnotationDirFmt" selected="true">Ortholog Annotation Directory Format</option> - </param> - <when value="OrthologAnnotationDirFmt"> - <section name="import_annotations" expanded="true" title="Import annotations"> - <conditional name="__q2galaxy__GUI__cond__annotations__"> - <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> - <option value="collection" selected="true">Use collection to import</option> - <option value="individual">Associate individual files</option> - </param> - <when value="collection"> - <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .+\.annotations" collection_type="list"/> - <conditional name="__q2galaxy__GUI__cond__add_ext__"> - <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> - <option value="no">No, use element identifiers as is</option> - <option value="yes">Yes, append an extension</option> - </param> - <when value="yes"> - <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> - </when> - <when value="no"/> - </conditional> - </when> - <when value="individual"> - <repeat name="elements" min="1" title="Add Elements"> - <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.annotations"> - <validator type="regex" message="This filename doesn't match the regex.">.+\.annotations</validator> - </param> - <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/> - </repeat> - </when> - </conditional> - </section> - </when> - </conditional> - </when> - <when value="FeatureData__ob__OG__cb__"> - <conditional name="__q2galaxy__GUI__cond__format__"> - <param name="format" type="select" label="QIIME 2 file format to import from:"> - <option value="OrthologAnnotationDirFmt" selected="true">Ortholog Annotation Directory Format</option> - </param> - <when value="OrthologAnnotationDirFmt"> - <section name="import_annotations" expanded="true" title="Import annotations"> - <conditional name="__q2galaxy__GUI__cond__annotations__"> - <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> - <option value="collection" selected="true">Use collection to import</option> - <option value="individual">Associate individual files</option> - </param> - <when value="collection"> - <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .+\.annotations" collection_type="list"/> - <conditional name="__q2galaxy__GUI__cond__add_ext__"> - <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> - <option value="no">No, use element identifiers as is</option> - <option value="yes">Yes, append an extension</option> - </param> - <when value="yes"> - <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> - </when> - <when value="no"/> - </conditional> - </when> - <when value="individual"> - <repeat name="elements" min="1" title="Add Elements"> - <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.annotations"> - <validator type="regex" message="This filename doesn't match the regex.">.+\.annotations</validator> - </param> - <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/> - </repeat> - </when> - </conditional> - </section> - </when> - </conditional> - </when> <when value="FeatureData__ob__PairedEndRNASequence__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -1152,6 +1192,26 @@ </when> </conditional> </when> + <when value="FeatureTable__ob__Normalized__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="BIOMV100Format" selected="false">BIOMV100 Format</option> + <option value="BIOMV210Format" selected="true">BIOMV210 Format</option> + </param> + <when value="BIOMV100Format"> + <section name="import" expanded="true" title="Import"> + <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> + <param name="data" type="data" format="data" help="This data should be formatted as a BIOMV100Format. See the documentation below for more information."/> + </section> + </when> + <when value="BIOMV210Format"> + <section name="import" expanded="true" title="Import"> + <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> + <param name="data" type="data" format="data" help="This data should be formatted as a BIOMV210Format. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="FeatureTable__ob__PercentileNormalized__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -1212,20 +1272,20 @@ </when> </conditional> </when> - <when value="GenomeData__ob__BLAST6__cb__"> + <when value="GenomeData__ob__DNASequence__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> - <option value="SeedOrthologDirFmt" selected="true">Seed Ortholog Directory Format</option> + <option value="GenomeSequencesDirectoryFormat" selected="true">Genome Sequences Directory Format</option> </param> - <when value="SeedOrthologDirFmt"> - <section name="import_seed_orthologs" expanded="true" title="Import seed_orthologs"> - <conditional name="__q2galaxy__GUI__cond__seed_orthologs__"> + <when value="GenomeSequencesDirectoryFormat"> + <section name="import_genomes" expanded="true" title="Import genomes"> + <conditional name="__q2galaxy__GUI__cond__genomes__"> <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> <option value="collection" selected="true">Use collection to import</option> <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .*\..*\.seed_orthologs" collection_type="list"/> + <param name="elements" type="data_collection" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information. Elements must match regex: .+\.(fasta|fa)$" collection_type="list"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1239,10 +1299,10 @@ </when> <when value="individual"> <repeat name="elements" min="1" title="Add Elements"> - <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\..*\.seed_orthologs"> - <validator type="regex" message="This filename doesn't match the regex.">.*\..*\.seed_orthologs</validator> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.(fasta|fa)$"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.(fasta|fa)$</validator> </param> - <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/> + <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/> </repeat> </when> </conditional> @@ -1326,6 +1386,82 @@ </when> </conditional> </when> + <when value="GenomeData__ob__NOG__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="OrthologAnnotationDirFmt" selected="true">Ortholog Annotation Directory Format</option> + </param> + <when value="OrthologAnnotationDirFmt"> + <section name="import_annotations" expanded="true" title="Import annotations"> + <conditional name="__q2galaxy__GUI__cond__annotations__"> + <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> + <option value="collection" selected="true">Use collection to import</option> + <option value="individual">Associate individual files</option> + </param> + <when value="collection"> + <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .+\.annotations" collection_type="list"/> + <conditional name="__q2galaxy__GUI__cond__add_ext__"> + <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> + <option value="no">No, use element identifiers as is</option> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="individual"> + <repeat name="elements" min="1" title="Add Elements"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.annotations"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.annotations</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> + <when value="GenomeData__ob__Orthologs__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="SeedOrthologDirFmt" selected="true">Seed Ortholog Directory Format</option> + </param> + <when value="SeedOrthologDirFmt"> + <section name="import_seed_orthologs" expanded="true" title="Import seed_orthologs"> + <conditional name="__q2galaxy__GUI__cond__seed_orthologs__"> + <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> + <option value="collection" selected="true">Use collection to import</option> + <option value="individual">Associate individual files</option> + </param> + <when value="collection"> + <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .*\..*\.seed_orthologs" collection_type="list"/> + <conditional name="__q2galaxy__GUI__cond__add_ext__"> + <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> + <option value="no">No, use element identifiers as is</option> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="individual"> + <repeat name="elements" min="1" title="Add Elements"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\..*\.seed_orthologs"> + <validator type="regex" message="This filename doesn't match the regex.">.*\..*\.seed_orthologs</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> <when value="GenomeData__ob__Proteins__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -1553,6 +1689,195 @@ </when> </conditional> </when> + <when value="ProfileHMM__ob__MultipleDNA__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="DNAMultipleProfileHmmDirectoryFmt" selected="true">DNA Multiple Profile Hmm Directory Format</option> + </param> + <when value="DNAMultipleProfileHmmDirectoryFmt"> + <section name="import_profiles" expanded="true" title="Import profiles"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a DNAMultipleProfileHmmFileFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="ProfileHMM__ob__MultipleProtein__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="ProteinMultipleProfileHmmDirectoryFmt" selected="true">Protein Multiple Profile Hmm Directory Format</option> + </param> + <when value="ProteinMultipleProfileHmmDirectoryFmt"> + <section name="import_profiles" expanded="true" title="Import profiles"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProteinMultipleProfileHmmFileFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="ProfileHMM__ob__MultipleRNA__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="RNAMultipleProfileHmmDirectoryFmt" selected="true">RNA Multiple Profile Hmm Directory Format</option> + </param> + <when value="RNAMultipleProfileHmmDirectoryFmt"> + <section name="import_profiles" expanded="true" title="Import profiles"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a RNAMultipleProfileHmmFileFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="ProfileHMM__ob__PressedDNA__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="PressedProfileHmmsDirectoryFmt" selected="true">Pressed Profile Hmms Directory Format</option> + </param> + <when value="PressedProfileHmmsDirectoryFmt"> + <section name="import_h3m" expanded="true" title="Import h3m"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3m"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3m</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/> + </section> + <section name="import_h3i" expanded="true" title="Import h3i"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3i"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3i</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/> + </section> + <section name="import_h3f" expanded="true" title="Import h3f"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3f"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3f</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/> + </section> + <section name="import_h3p" expanded="true" title="Import h3p"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3p"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3p</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="ProfileHMM__ob__PressedProtein__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="PressedProfileHmmsDirectoryFmt" selected="true">Pressed Profile Hmms Directory Format</option> + </param> + <when value="PressedProfileHmmsDirectoryFmt"> + <section name="import_h3m" expanded="true" title="Import h3m"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3m"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3m</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/> + </section> + <section name="import_h3i" expanded="true" title="Import h3i"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3i"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3i</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/> + </section> + <section name="import_h3f" expanded="true" title="Import h3f"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3f"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3f</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/> + </section> + <section name="import_h3p" expanded="true" title="Import h3p"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3p"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3p</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="ProfileHMM__ob__PressedRNA__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="PressedProfileHmmsDirectoryFmt" selected="true">Pressed Profile Hmms Directory Format</option> + </param> + <when value="PressedProfileHmmsDirectoryFmt"> + <section name="import_h3m" expanded="true" title="Import h3m"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3m"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3m</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/> + </section> + <section name="import_h3i" expanded="true" title="Import h3i"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3i"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3i</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/> + </section> + <section name="import_h3f" expanded="true" title="Import h3f"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3f"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3f</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/> + </section> + <section name="import_h3p" expanded="true" title="Import h3p"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm\.h3p"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm\.h3p</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProfileHmmBinaryFileFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="ProfileHMM__ob__SingleDNA__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="DNASingleProfileHmmDirectoryFmt" selected="true">DNA Single Profile Hmm Directory Format</option> + </param> + <when value="DNASingleProfileHmmDirectoryFmt"> + <section name="import_profile" expanded="true" title="Import profile"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a DNASingleProfileHmmFileFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="ProfileHMM__ob__SingleProtein__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="ProteinSingleProfileHmmDirectoryFmt" selected="true">Protein Single Profile Hmm Directory Format</option> + </param> + <when value="ProteinSingleProfileHmmDirectoryFmt"> + <section name="import_profile" expanded="true" title="Import profile"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProteinSingleProfileHmmFileFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="ProfileHMM__ob__SingleRNA__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="RNASingleProfileHmmDirectoryFmt" selected="true">RNA Single Profile Hmm Directory Format</option> + </param> + <when value="RNASingleProfileHmmDirectoryFmt"> + <section name="import_profile" expanded="true" title="Import profile"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\.hmm"> + <validator type="regex" message="This filename doesn't match the regex.">.*\.hmm</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a RNASingleProfileHmmFileFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="QualityFilterStats"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -1747,44 +2072,6 @@ </when> </conditional> </when> - <when value="SampleData__ob__BLAST6__cb__"> - <conditional name="__q2galaxy__GUI__cond__format__"> - <param name="format" type="select" label="QIIME 2 file format to import from:"> - <option value="SeedOrthologDirFmt" selected="true">Seed Ortholog Directory Format</option> - </param> - <when value="SeedOrthologDirFmt"> - <section name="import_seed_orthologs" expanded="true" title="Import seed_orthologs"> - <conditional name="__q2galaxy__GUI__cond__seed_orthologs__"> - <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> - <option value="collection" selected="true">Use collection to import</option> - <option value="individual">Associate individual files</option> - </param> - <when value="collection"> - <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .*\..*\.seed_orthologs" collection_type="list"/> - <conditional name="__q2galaxy__GUI__cond__add_ext__"> - <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> - <option value="no">No, use element identifiers as is</option> - <option value="yes">Yes, append an extension</option> - </param> - <when value="yes"> - <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> - </when> - <when value="no"/> - </conditional> - </when> - <when value="individual"> - <repeat name="elements" min="1" title="Add Elements"> - <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\..*\.seed_orthologs"> - <validator type="regex" message="This filename doesn't match the regex.">.*\..*\.seed_orthologs</validator> - </param> - <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/> - </repeat> - </when> - </conditional> - </section> - </when> - </conditional> - </when> <when value="SampleData__ob__BooleanSeries__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -2318,6 +2605,82 @@ </when> </conditional> </when> + <when value="SampleData__ob__NOG__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="OrthologAnnotationDirFmt" selected="true">Ortholog Annotation Directory Format</option> + </param> + <when value="OrthologAnnotationDirFmt"> + <section name="import_annotations" expanded="true" title="Import annotations"> + <conditional name="__q2galaxy__GUI__cond__annotations__"> + <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> + <option value="collection" selected="true">Use collection to import</option> + <option value="individual">Associate individual files</option> + </param> + <when value="collection"> + <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .+\.annotations" collection_type="list"/> + <conditional name="__q2galaxy__GUI__cond__add_ext__"> + <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> + <option value="no">No, use element identifiers as is</option> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="individual"> + <repeat name="elements" min="1" title="Add Elements"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.annotations"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.annotations</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> + <when value="SampleData__ob__Orthologs__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="SeedOrthologDirFmt" selected="true">Seed Ortholog Directory Format</option> + </param> + <when value="SeedOrthologDirFmt"> + <section name="import_seed_orthologs" expanded="true" title="Import seed_orthologs"> + <conditional name="__q2galaxy__GUI__cond__seed_orthologs__"> + <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> + <option value="collection" selected="true">Use collection to import</option> + <option value="individual">Associate individual files</option> + </param> + <when value="collection"> + <param name="elements" type="data_collection" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information. Elements must match regex: .*\..*\.seed_orthologs" collection_type="list"/> + <conditional name="__q2galaxy__GUI__cond__add_ext__"> + <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> + <option value="no">No, use element identifiers as is</option> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="individual"> + <repeat name="elements" min="1" title="Add Elements"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .*\..*\.seed_orthologs"> + <validator type="regex" message="This filename doesn't match the regex.">.*\..*\.seed_orthologs</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> <when value="SampleData__ob__PairedEndSequencesWithQuality__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -2858,6 +3221,19 @@ </when> </conditional> </when> + <when value="StatsTable__ob__Pairwise__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="TableJSONLFileFormat" selected="true">Table JSONL File Format</option> + </param> + <when value="TableJSONLFileFormat"> + <section name="import" expanded="true" title="Import"> + <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> + <param name="data" type="data" format="data" help="This data should be formatted as a TableJSONLFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="TaxonomicClassifier"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -2924,10 +3300,36 @@ -------- These formats have documentation available. -FastqGzFormat -************* +HeaderlessTSVTaxonomyFormat +*************************** +Format for a 2+ column TSV file without a header. + +This format supports comment lines starting with #, and blank lines. + + +PressedProfileHmmsDirectoryFmt +****************************** -A gzipped fastq file. +The <hmmfile>.h3m file contains the profile HMMs +and their annotation in a binary format. The <hmmfile>.h3i file is an +SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains +precomputed data structures for the fast heuristic filter +(the MSV filter). The <hmmfile>.h3p file contains precomputed data +structures for the rest of each profile. + +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. SampleIdIndexedSingleEndPerSampleDirFmt @@ -2974,13 +3376,6 @@ - Each sequence must be DNA and cannot be empty. -HeaderlessTSVTaxonomyFormat -*************************** -Format for a 2+ column TSV file without a header. - -This format supports comment lines starting with #, and blank lines. - - SequenceCharacteristicsFormat ***************************** @@ -2995,107 +3390,106 @@ "FeatureData[SequenceCharacteristics % Properties("length")]" adds validation for a numerical column called "length". -TSVTaxonomyFormat -***************** -Format for a 2+ column TSV file with an expected minimal header. - -The only header recognized by this format is: +FastqGzFormat +************* - 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. +A gzipped fastq file. Additional formats without documentation: ***************************************** - - DataLoafPackageDirFmt - - EggnogRefDirFmt - - NCBITaxonomyDirFmt - - SILVATaxonomyFormat - - MixedCaseAlignedRNAFASTAFormat - - MAGSequencesDirFmt + - DifferentialFormat - Kraken2OutputDirectoryFormat - - BAMDirFmt - - EggnogProteinSequencesDirFmt - - ImmutableMetadataFormat - - EMPPairedEndCasavaDirFmt - - LSMatFormat - - SingleLanePerSampleSingleEndFastqDirFmt - - AlignedProteinFASTAFormat - - PairedDNASequencesDirectoryFormat - - BooleanSeriesFormat - - MultiplexedPairedEndBarcodeInSequenceDirFmt - - DecontamScoreFormat - - OrthologAnnotationDirFmt - - GenesDirectoryFormat - MultiBAMDirFmt - - BIOMV210Format - - ErrorCorrectionDetailsFmt - - DiamondDatabaseFileFmt - - PairedRNASequencesDirectoryFormat - - DifferentialFormat - - Kraken2DBDirectoryFormat - - DADA2StatsFormat + - FirstDifferencesFormat + - SingleEndFastqManifestPhred33V2 - AlignedDNAFASTAFormat + - EggnogProteinSequencesDirFmt + - SingleEndFastqManifestPhred64 + - MAGSequencesDirFmt + - ProteinSingleProfileHmmDirectoryFmt + - MixedCaseDNAFASTAFormat - ImportanceFormat - - SingleEndFastqManifestPhred33 - - NewickFormat - - MultiplexedFastaQualDirFmt - - SingleLanePerSamplePairedEndFastqDirFmt + - ImmutableMetadataFormat + - ErrorCorrectionDetailsFmt + - ArtificialGroupingFormat + - OrthologAnnotationDirFmt + - DecontamScoreFormat + - SingleEndFastqManifestPhred64V2 + - QualityFilterStatsFmt - DeblurStatsFmt - - MixedCaseDNAFASTAFormat - - SingleEndFastqManifestPhred33V2 - - QualityFilterStatsFmt - - SingleEndFastqManifestPhred64 - - MultiFASTADirectoryFormat - - ProcrustesStatisticsFmt + - OrdinationFormat + - PairedEndFastqManifestPhred33 + - LSMatFormat + - ProteinMultipleProfileHmmDirectoryFmt + - SingleLanePerSamplePairedEndFastqDirFmt - CasavaOneEightLanelessPerSampleDirFmt - - SILVATaxidMapFormat - - SingleEndFastqManifestPhred64V2 - - Kraken2ReportDirectoryFormat + - Kraken2DBDirectoryFormat - MixedCaseAlignedDNAFASTAFormat + - MultiplexedFastaQualDirFmt + - BooleanSeriesFormat + - BLASTDBDirFmtV5 + - DADA2StatsFormat - BLAST6Format + - KaijuDBDirectoryFormat + - MultiFASTADirectoryFormat + - PairedEndFastqManifestPhred64 + - MAGtoContigsFormat + - DNASingleProfileHmmDirectoryFmt + - RNAFASTAFormat - ProbabilitiesFormat - - PairedEndFastqManifestPhred33 + - SampleEstimatorDirFmt + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - TableJSONLFileFormat + - LociDirectoryFormat + - PairedEndFastqManifestPhred33V2 + - UchimeStatsFmt + - ProcrustesStatisticsFmt + - AlphaDiversityFormat - MultiMAGSequencesDirFmt + - SeppReferenceDirFmt + - DNAMultipleProfileHmmDirectoryFmt + - PredictionsFormat + - PlacementsFormat + - NewickFormat + - BrackenDBDirectoryFormat + - GenomeSequencesDirectoryFormat + - EggnogRefDirFmt + - PairedEndFastqManifestPhred64V2 + - AlignedRNAFASTAFormat - EMPSingleEndDirFmt - - Bowtie2IndexDirFmt - TaxonomicClassiferTemporaryPickleDirFmt - - LociDirectoryFormat - - ArtificialGroupingFormat - - MAGtoContigsFormat - - BrackenDBDirectoryFormat - - ProteinFASTAFormat - - RNAFASTAFormat - - BIOMV100Format - - Kraken2DBReportFormat - - PairedEndFastqManifestPhred64 + - Kraken2ReportDirectoryFormat - MultiBowtie2IndexDirFmt - - EMPPairedEndDirFmt - - OrdinationFormat + - SILVATaxidMapFormat + - CasavaOneEightSingleLanePerSampleDirFmt + - RNASingleProfileHmmDirectoryFmt + - MixedCaseRNAFASTAFormat + - Bowtie2IndexDirFmt - SeedOrthologDirFmt - - SampleEstimatorDirFmt - - PlacementsFormat - - DNAFASTAFormat - - UchimeStatsFmt - - PairedEndFastqManifestPhred33V2 - - AlignedRNAFASTAFormat - - KaijuDBDirectoryFormat + - DiamondDatabaseFileFmt + - ProteinFASTAFormat + - EMPPairedEndDirFmt - ContigSequencesDirFmt + - Kraken2DBReportFormat + - RNAMultipleProfileHmmDirectoryFmt + - SILVATaxonomyFormat + - BIOMV100Format + - DataLoafPackageDirFmt + - MixedCaseAlignedRNAFASTAFormat - EMPSingleEndCasavaDirFmt - - FirstDifferencesFormat - - SeppReferenceDirFmt - - PredictionsFormat + - DNAFASTAFormat - ProteinsDirectoryFormat - - MixedCaseRNAFASTAFormat - - PairedEndFastqManifestPhred64V2 - - BLASTDBDirFmtV5 - - AlphaDiversityFormat - - CasavaOneEightSingleLanePerSampleDirFmt + - PairedDNASequencesDirectoryFormat + - NCBITaxonomyDirFmt + - BIOMV210Format + - AlignedProteinFASTAFormat + - SingleLanePerSampleSingleEndFastqDirFmt + - EMPPairedEndCasavaDirFmt + - BAMDirFmt + - PairedRNASequencesDirectoryFormat + - GenesDirectoryFormat + - SingleEndFastqManifestPhred33 </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>