Mercurial > repos > q2d2 > qiime2_core__tools__import
changeset 5:f9e68fa06585 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit c7e80dcda727ce63b42aa8a946e9330310929797
| author | q2d2 |
|---|---|
| date | Mon, 03 Jun 2024 23:32:49 +0000 |
| parents | 9dbdf05beaa9 |
| children | |
| files | qiime2_core__tools__import.xml |
| diffstat | 1 files changed, 754 insertions(+), 79 deletions(-) [+] |
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--- a/qiime2_core__tools__import.xml Thu Apr 25 21:28:32 2024 +0000 +++ b/qiime2_core__tools__import.xml Mon Jun 03 23:32:49 2024 +0000 @@ -6,14 +6,14 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2024.2.1) + q2galaxy (version: 2024.5.0) for: - qiime2 (version: 2024.2.0) + qiime2 (version: 2024.5.0) --> -<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2024.2.1+dist.he188c3c2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2024.5.0+dist.he540b0b0" profile="22.05" license="BSD-3-Clause"> <description>Import data into a QIIME 2 artifact</description> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2024.2</container> + <container type="docker">quay.io/qiime2/amplicon:2024.5</container> </requirements> <command>q2galaxy run tools import '$inputs'</command> <configfiles> @@ -62,6 +62,7 @@ <option value="None">Select a QIIME 2 type to import.</option> <option value="BLASTDB">BLASTDB</option> <option value="Bowtie2Index">Bowtie2Index</option> + <option value="BrackenDB">BrackenDB</option> <option value="DeblurStats">DeblurStats</option> <option value="DistanceMatrix">DistanceMatrix</option> <option value="EMPPairedEndSequences">EMPPairedEndSequences</option> @@ -70,18 +71,28 @@ <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__AlignmentMap__cb__">FeatureData[AlignmentMap]</option> <option value="FeatureData__ob__BLAST6__cb__">FeatureData[BLAST6]</option> + <option value="FeatureData__ob__Contig__cb__">FeatureData[Contig]</option> <option value="FeatureData__ob__DecontamScore__cb__">FeatureData[DecontamScore]</option> <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> <option value="FeatureData__ob__RNASequence__cb__">FeatureData[RNASequence]</option> <option value="FeatureData__ob__SILVATaxidMap__cb__">FeatureData[SILVATaxidMap]</option> <option value="FeatureData__ob__SILVATaxonomy__cb__">FeatureData[SILVATaxonomy]</option> + <option value="FeatureData__ob__SequenceCharacteristics__cb__">FeatureData[SequenceCharacteristics]</option> <option value="FeatureData__ob__Sequence__cb__">FeatureData[Sequence]</option> + <option value="FeatureData__ob__SingleBowtie2Index__cb__">FeatureData[SingleBowtie2Index]</option> <option value="FeatureData__ob__Taxonomy__cb__">FeatureData[Taxonomy]</option> <option value="FeatureMap__ob__MAGtoContigs__cb__">FeatureMap[MAGtoContigs]</option> <option value="FeatureTable__ob__Balance__cb__">FeatureTable[Balance]</option> @@ -97,6 +108,9 @@ <option value="GenomeData__ob__Proteins__cb__">GenomeData[Proteins]</option> <option value="Hierarchy">Hierarchy</option> <option value="ImmutableMetadata">ImmutableMetadata</option> + <option value="KaijuDB">KaijuDB</option> + <option value="Kraken2DB">Kraken2DB</option> + <option value="Kraken2DBReport">Kraken2DBReport</option> <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option> <option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option> <option value="PCoAResults">PCoAResults</option> @@ -106,6 +120,10 @@ <option value="ProcrustesStatistics">ProcrustesStatistics</option> <option value="QualityFilterStats">QualityFilterStats</option> <option value="RawSequences">RawSequences</option> + <option value="ReferenceDB__ob__Diamond__cb__">ReferenceDB[Diamond]</option> + <option value="ReferenceDB__ob__EggnogProteinSequences__cb__">ReferenceDB[EggnogProteinSequences]</option> + <option value="ReferenceDB__ob__Eggnog__cb__">ReferenceDB[Eggnog]</option> + <option value="ReferenceDB__ob__NCBITaxonomy__cb__">ReferenceDB[NCBITaxonomy]</option> <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> @@ -116,6 +134,8 @@ <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__Kraken2Output__cb__">SampleData[Kraken2Output]</option> + <option value="SampleData__ob__Kraken2Report__cb__">SampleData[Kraken2Report]</option> <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> @@ -235,6 +255,44 @@ </when> </conditional> </when> + <when value="BrackenDB"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="BrackenDBDirectoryFormat" selected="true">Bracken DB Directory Format</option> + </param> + <when value="BrackenDBDirectoryFormat"> + <section name="import_kmers" expanded="true" title="Import kmers"> + <conditional name="__q2galaxy__GUI__cond__kmers__"> + <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 BrackenDBFormat. See the documentation below for more information. Elements must match regex: database(\d{2,})mers\.kmer_distrib$" 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: database(\d{2,})mers\.kmer_distrib$"> + <validator type="regex" message="This filename doesn't match the regex.">database(\d{2,})mers\.kmer_distrib$</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a BrackenDBFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> <when value="DeblurStats"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -391,6 +449,44 @@ </when> </conditional> </when> + <when value="FeatureData__ob__AlignmentMap__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="BAMDirFmt" selected="true">BAM Directory Format</option> + </param> + <when value="BAMDirFmt"> + <section name="import_bams" expanded="true" title="Import bams"> + <conditional name="__q2galaxy__GUI__cond__bams__"> + <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 BAMFormat. See the documentation below for more information. Elements must match regex: .+\.bam" 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: .+\.bam"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.bam</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a BAMFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> <when value="FeatureData__ob__BLAST6__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -404,6 +500,44 @@ </when> </conditional> </when> + <when value="FeatureData__ob__Contig__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="ContigSequencesDirFmt" selected="true">Contig Sequences Directory Format</option> + </param> + <when value="ContigSequencesDirFmt"> + <section name="import_sequences" expanded="true" title="Import sequences"> + <conditional name="__q2galaxy__GUI__cond__sequences__"> + <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 DNAFASTAFormat. See the documentation below for more information. Elements must match regex: [^\.].+_contigs.(fasta|fa)$" collection_type="list"/> + <conditional name="__q2galaxy__GUI__cond__add_ext__"> + <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> + <option value="no">No, use element identifiers as is</option> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="individual"> + <repeat name="elements" min="1" title="Add Elements"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: [^\.].+_contigs.(fasta|fa)$"> + <validator type="regex" message="This filename doesn't match the regex.">[^\.].+_contigs.(fasta|fa)$</validator> + </param> + <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> + </section> + </when> + </conditional> + </when> <when value="FeatureData__ob__DecontamScore__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -485,6 +619,234 @@ </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:"> + <option value="Kraken2OutputDirectoryFormat" selected="true">Kraken2 Output Directory Format</option> + </param> + <when value="Kraken2OutputDirectoryFormat"> + <section name="import_reports" expanded="true" title="Import reports"> + <conditional name="__q2galaxy__GUI__cond__reports__"> + <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 Kraken2OutputFormat. See the documentation below for more information. Elements must match regex: .+output\.(txt|tsv)$" 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: .+output\.(txt|tsv)$"> + <validator type="regex" message="This filename doesn't match the regex.">.+output\.(txt|tsv)$</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2OutputFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> + <when value="FeatureData__ob__Kraken2Report__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="Kraken2ReportDirectoryFormat" selected="true">Kraken2 Report Directory Format</option> + </param> + <when value="Kraken2ReportDirectoryFormat"> + <section name="import_reports" expanded="true" title="Import reports"> + <conditional name="__q2galaxy__GUI__cond__reports__"> + <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 Kraken2ReportFormat. See the documentation below for more information. Elements must match regex: .+report\.(txt|tsv)$" collection_type="list"/> + <conditional name="__q2galaxy__GUI__cond__add_ext__"> + <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> + <option value="no">No, use element identifiers as is</option> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="individual"> + <repeat name="elements" min="1" title="Add Elements"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+report\.(txt|tsv)$"> + <validator type="regex" message="This filename doesn't match the regex.">.+report\.(txt|tsv)$</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2ReportFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> + <when value="FeatureData__ob__MAG__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="MAGSequencesDirFmt" selected="true">MAG Sequences Directory Format</option> + </param> + <when value="MAGSequencesDirFmt"> + <section name="import_sequences" expanded="true" title="Import sequences"> + <conditional name="__q2galaxy__GUI__cond__sequences__"> + <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> + <option value="collection" selected="true">Use collection to import</option> + <option value="individual">Associate individual files</option> + </param> + <when value="collection"> + <param name="elements" type="data_collection" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information. Elements must match regex: ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12}\.(fa|fasta)$" 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: ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12}\.(fa|fasta)$"> + <validator type="regex" message="This filename doesn't match the regex.">^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12}\.(fa|fasta)$</validator> + </param> + <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> + </section> + </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:"> @@ -578,13 +940,33 @@ </when> </conditional> </when> + <when value="FeatureData__ob__SequenceCharacteristics__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="SequenceCharacteristicsFormat" selected="true">Sequence Characteristics Format</option> + </param> + <when value="SequenceCharacteristicsFormat"> + <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 SequenceCharacteristicsFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="FeatureData__ob__Sequence__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="BIOMV210Format" selected="false">BIOMV210 Format</option> <option value="DNAFASTAFormat" selected="true">DNAFASTA Format</option> <option value="MixedCaseDNAFASTAFormat" selected="false">Mixed Case DNAFASTA Format</option> <option value="RNAFASTAFormat" selected="false">RNAFASTA Format</option> </param> + <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> <when value="DNAFASTAFormat"> <section name="import" expanded="true" title="Import"> <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> @@ -605,6 +987,51 @@ </when> </conditional> </when> + <when value="FeatureData__ob__SingleBowtie2Index__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="Bowtie2IndexDirFmt" selected="true">Bowtie2 Index Directory Format</option> + </param> + <when value="Bowtie2IndexDirFmt"> + <section name="import_idx1" expanded="true" title="Import idx1"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+(?‹!\.rev)\.1\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+(?<!\.rev)\.1\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_idx2" expanded="true" title="Import idx2"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+(?‹!\.rev)\.2\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+(?<!\.rev)\.2\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_ref3" expanded="true" title="Import ref3"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.3\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.3\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_ref4" expanded="true" title="Import ref4"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.4\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.4\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_rev1" expanded="true" title="Import rev1"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.rev\.1\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.rev\.1\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_rev2" expanded="true" title="Import rev2"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.rev\.2\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.rev\.2\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="FeatureData__ob__Taxonomy__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -836,7 +1263,7 @@ <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 DNAFASTAFormat. See the documentation below for more information. Elements must match regex: (.*\_)?genes[0-9]*\.(fa|fna|fasta)$" collection_type="list"/> + <param name="elements" type="data_collection" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information. Elements must match regex: .+\.(fa|fna|fasta)$" 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> @@ -850,8 +1277,8 @@ </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: (.*\_)?genes[0-9]*\.(fa|fna|fasta)$"> - <validator type="regex" message="This filename doesn't match the regex.">(.*\_)?genes[0-9]*\.(fa|fna|fasta)$</validator> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.(fa|fna|fasta)$"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.(fa|fna|fasta)$</validator> </param> <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/> </repeat> @@ -874,7 +1301,7 @@ <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 GFF3Format. See the documentation below for more information. Elements must match regex: (.*\_)?loci[0-9]*\.gff$" collection_type="list"/> + <param name="elements" type="data_collection" help="This data should be formatted as a GFF3Format. See the documentation below for more information. Elements must match regex: .+\.gff$" 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> @@ -888,8 +1315,8 @@ </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: (.*\_)?loci[0-9]*\.gff$"> - <validator type="regex" message="This filename doesn't match the regex.">(.*\_)?loci[0-9]*\.gff$</validator> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.gff$"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.gff$</validator> </param> <param name="data" type="data" format="data" help="This data should be formatted as a GFF3Format. See the documentation below for more information."/> </repeat> @@ -912,7 +1339,7 @@ <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 ProteinFASTAFormat. See the documentation below for more information. Elements must match regex: (.*\_)?proteins[0-9]*\.(fa|faa|fasta)$" collection_type="list"/> + <param name="elements" type="data_collection" help="This data should be formatted as a ProteinFASTAFormat. See the documentation below for more information. Elements must match regex: .+\.(fa|faa|fasta)$" 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> @@ -926,8 +1353,8 @@ </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: (.*\_)?proteins[0-9]*\.(fa|faa|fasta)$"> - <validator type="regex" message="This filename doesn't match the regex.">(.*\_)?proteins[0-9]*\.(fa|faa|fasta)$</validator> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.(fa|faa|fasta)$"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.(fa|faa|fasta)$</validator> </param> <param name="data" type="data" format="data" help="This data should be formatted as a ProteinFASTAFormat. See the documentation below for more information."/> </repeat> @@ -963,6 +1390,63 @@ </when> </conditional> </when> + <when value="KaijuDB"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="KaijuDBDirectoryFormat" selected="true">Kaiju DB Directory Format</option> + </param> + <when value="KaijuDBDirectoryFormat"> + <section name="import_nodes" expanded="true" title="Import nodes"> + <param name="name" type="text" value="nodes.dmp" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/> + <param name="data" type="data" format="data" help="This data should be formatted as a NCBITaxonomyNodesFormat. See the documentation below for more information."/> + </section> + <section name="import_names" expanded="true" title="Import names"> + <param name="name" type="text" value="names.dmp" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/> + <param name="data" type="data" format="data" help="This data should be formatted as a NCBITaxonomyNamesFormat. See the documentation below for more information."/> + </section> + <section name="import_index" expanded="true" title="Import index"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: kaiju_db.+\.fmi"> + <validator type="regex" message="This filename doesn't match the regex.">kaiju_db.+\.fmi</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a KaijuIndexFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Kraken2DB"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="Kraken2DBDirectoryFormat" selected="true">Kraken2DB Directory Format</option> + </param> + <when value="Kraken2DBDirectoryFormat"> + <section name="import_hash" expanded="true" title="Import hash"> + <param name="name" type="text" value="hash.k2d" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/> + <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2DBFormat. See the documentation below for more information."/> + </section> + <section name="import_opts" expanded="true" title="Import opts"> + <param name="name" type="text" value="opts.k2d" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/> + <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2DBFormat. See the documentation below for more information."/> + </section> + <section name="import_taxo" expanded="true" title="Import taxo"> + <param name="name" type="text" value="taxo.k2d" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/> + <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2DBFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Kraken2DBReport"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="Kraken2DBReportFormat" selected="true">Kraken2DB Report Format</option> + </param> + <when value="Kraken2DBReportFormat"> + <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 Kraken2DBReportFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="MultiplexedPairedEndBarcodeInSequence"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -1110,6 +1594,95 @@ </when> </conditional> </when> + <when value="ReferenceDB__ob__Diamond__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="DiamondDatabaseFileFmt" selected="true">Diamond Database File Format</option> + </param> + <when value="DiamondDatabaseFileFmt"> + <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 DiamondDatabaseFileFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="ReferenceDB__ob__EggnogProteinSequences__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="EggnogProteinSequencesDirFmt" selected="true">Eggnog Protein Sequences Directory Format</option> + </param> + <when value="EggnogProteinSequencesDirFmt"> + <section name="import_taxid_info" expanded="true" title="Import taxid_info"> + <param name="name" type="text" value="e5.taxid_info.tsv" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/> + <param name="data" type="data" format="data" help="This data should be formatted as a EggnogRefTextFileFmt. See the documentation below for more information."/> + </section> + <section name="import_proteins" expanded="true" title="Import proteins"> + <param name="name" type="text" value="e5.proteomes.faa" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/> + <param name="data" type="data" format="data" help="This data should be formatted as a MixedCaseProteinFASTAFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="ReferenceDB__ob__Eggnog__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="EggnogRefDirFmt" selected="true">Eggnog Ref Directory Format</option> + </param> + <when value="EggnogRefDirFmt"> + <section name="import_eggnog" expanded="true" title="Import eggnog"> + <conditional name="__q2galaxy__GUI__cond__eggnog__"> + <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 EggnogRefBinFileFmt. See the documentation below for more information. Elements must match regex: eggnog.*db.*" 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: eggnog.*db.*"> + <validator type="regex" message="This filename doesn't match the regex.">eggnog.*db.*</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a EggnogRefBinFileFmt. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> + <when value="ReferenceDB__ob__NCBITaxonomy__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="NCBITaxonomyDirFmt" selected="true">NCBI Taxonomy Directory Format</option> + </param> + <when value="NCBITaxonomyDirFmt"> + <section name="import_node" expanded="true" title="Import node"> + <param name="name" type="text" value="nodes.dmp" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/> + <param name="data" type="data" format="data" help="This data should be formatted as a NCBITaxonomyNodesFormat. See the documentation below for more information."/> + </section> + <section name="import_names" expanded="true" title="Import names"> + <param name="name" type="text" value="names.dmp" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/> + <param name="data" type="data" format="data" help="This data should be formatted as a NCBITaxonomyNamesFormat. See the documentation below for more information."/> + </section> + <section name="import_tax_map" expanded="true" title="Import tax_map"> + <param name="name" type="text" value="prot.accession2taxid.gz" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/> + <param name="data" type="data" format="data" help="This data should be formatted as a NCBITaxonomyBinaryFileFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="SampleData__ob__AlignmentMap__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -1512,6 +2085,82 @@ </when> </conditional> </when> + <when value="SampleData__ob__Kraken2Output__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="Kraken2OutputDirectoryFormat" selected="true">Kraken2 Output Directory Format</option> + </param> + <when value="Kraken2OutputDirectoryFormat"> + <section name="import_reports" expanded="true" title="Import reports"> + <conditional name="__q2galaxy__GUI__cond__reports__"> + <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 Kraken2OutputFormat. See the documentation below for more information. Elements must match regex: .+output\.(txt|tsv)$" collection_type="list"/> + <conditional name="__q2galaxy__GUI__cond__add_ext__"> + <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> + <option value="no">No, use element identifiers as is</option> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="individual"> + <repeat name="elements" min="1" title="Add Elements"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+output\.(txt|tsv)$"> + <validator type="regex" message="This filename doesn't match the regex.">.+output\.(txt|tsv)$</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2OutputFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> + <when value="SampleData__ob__Kraken2Report__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="Kraken2ReportDirectoryFormat" selected="true">Kraken2 Report Directory Format</option> + </param> + <when value="Kraken2ReportDirectoryFormat"> + <section name="import_reports" expanded="true" title="Import reports"> + <conditional name="__q2galaxy__GUI__cond__reports__"> + <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> + <option value="collection" selected="true">Use collection to import</option> + <option value="individual">Associate individual files</option> + </param> + <when value="collection"> + <param name="elements" type="data_collection" help="This data should be formatted as a Kraken2ReportFormat. See the documentation below for more information. Elements must match regex: .+report\.(txt|tsv)$" 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: .+report\.(txt|tsv)$"> + <validator type="regex" message="This filename doesn't match the regex.">.+report\.(txt|tsv)$</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2ReportFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> <when value="SampleData__ob__MAGs__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -2275,11 +2924,10 @@ -------- These formats have documentation available. -HeaderlessTSVTaxonomyFormat -*************************** -Format for a 2+ column TSV file without a header. +FastqGzFormat +************* -This format supports comment lines starting with #, and blank lines. +A gzipped fastq file. SampleIdIndexedSingleEndPerSampleDirFmt @@ -2292,12 +2940,6 @@ * `xyz.fastq.gz` is `xyz` * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001` -FastqGzFormat -************* - -A gzipped fastq file. - - QIIME1DemuxFormat ***************** QIIME 1 demultiplexed FASTA format. @@ -2332,6 +2974,27 @@ - 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 +***************************** + +Format for a TSV file with information about sequences like length of a +feature. The first column contains feature identifiers and is followed by +other optional columns. + +The file cannot be empty and must have at least two columns. + +Validation for additional columns can be added with a semantic validator +tied to a property. For example the "validate_seq_char_len" validator for +"FeatureData[SequenceCharacteristics % Properties("length")]" +adds validation for a numerical column called "length". + TSVTaxonomyFormat ***************** Format for a 2+ column TSV file with an expected minimal header. @@ -2349,78 +3012,90 @@ Additional formats without documentation: ***************************************** + - DataLoafPackageDirFmt + - EggnogRefDirFmt + - NCBITaxonomyDirFmt + - SILVATaxonomyFormat + - MixedCaseAlignedRNAFASTAFormat + - MAGSequencesDirFmt + - Kraken2OutputDirectoryFormat - BAMDirFmt - - TaxonomicClassiferTemporaryPickleDirFmt - - BooleanSeriesFormat - - SingleEndFastqManifestPhred33 - - SampleEstimatorDirFmt - - MultiBAMDirFmt - - MAGtoContigsFormat - - MixedCaseAlignedRNAFASTAFormat - - PlacementsFormat - - PredictionsFormat - - SingleEndFastqManifestPhred64 - - MultiplexedPairedEndBarcodeInSequenceDirFmt + - EggnogProteinSequencesDirFmt + - ImmutableMetadataFormat + - EMPPairedEndCasavaDirFmt + - LSMatFormat - SingleLanePerSampleSingleEndFastqDirFmt - AlignedProteinFASTAFormat - PairedDNASequencesDirectoryFormat - - DataLoafPackageDirFmt - - ArtificialGroupingFormat - - PairedEndFastqManifestPhred33 - - DNAFASTAFormat - - EMPSingleEndDirFmt - - SingleLanePerSamplePairedEndFastqDirFmt + - BooleanSeriesFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - DecontamScoreFormat + - OrthologAnnotationDirFmt + - GenesDirectoryFormat + - MultiBAMDirFmt + - BIOMV210Format + - ErrorCorrectionDetailsFmt + - DiamondDatabaseFileFmt - PairedRNASequencesDirectoryFormat - - SeppReferenceDirFmt - DifferentialFormat - - UchimeStatsFmt - - SILVATaxonomyFormat - - PairedEndFastqManifestPhred64 - - GenesDirectoryFormat - - MultiFASTADirectoryFormat - - EMPPairedEndDirFmt - - CasavaOneEightLanelessPerSampleDirFmt + - Kraken2DBDirectoryFormat + - DADA2StatsFormat - AlignedDNAFASTAFormat - - SILVATaxidMapFormat - - PairedEndFastqManifestPhred33V2 + - ImportanceFormat + - SingleEndFastqManifestPhred33 + - NewickFormat + - MultiplexedFastaQualDirFmt + - SingleLanePerSamplePairedEndFastqDirFmt + - DeblurStatsFmt + - MixedCaseDNAFASTAFormat - SingleEndFastqManifestPhred33V2 - - MixedCaseDNAFASTAFormat - - ProteinsDirectoryFormat - - MultiMAGSequencesDirFmt - - EMPSingleEndCasavaDirFmt - QualityFilterStatsFmt - - LSMatFormat - - ImmutableMetadataFormat - - DeblurStatsFmt - - PairedEndFastqManifestPhred64V2 + - SingleEndFastqManifestPhred64 + - MultiFASTADirectoryFormat + - ProcrustesStatisticsFmt + - CasavaOneEightLanelessPerSampleDirFmt + - SILVATaxidMapFormat - SingleEndFastqManifestPhred64V2 - - AlphaDiversityFormat - - MultiBowtie2IndexDirFmt - - EMPPairedEndCasavaDirFmt - - ImportanceFormat - - FirstDifferencesFormat + - Kraken2ReportDirectoryFormat - MixedCaseAlignedDNAFASTAFormat - - MultiplexedFastaQualDirFmt - - DADA2StatsFormat - - OrdinationFormat - - CasavaOneEightSingleLanePerSampleDirFmt + - BLAST6Format + - ProbabilitiesFormat + - PairedEndFastqManifestPhred33 + - MultiMAGSequencesDirFmt + - EMPSingleEndDirFmt + - Bowtie2IndexDirFmt + - TaxonomicClassiferTemporaryPickleDirFmt + - LociDirectoryFormat + - ArtificialGroupingFormat + - MAGtoContigsFormat + - BrackenDBDirectoryFormat - ProteinFASTAFormat - RNAFASTAFormat - BIOMV100Format + - Kraken2DBReportFormat + - PairedEndFastqManifestPhred64 + - MultiBowtie2IndexDirFmt + - EMPPairedEndDirFmt + - OrdinationFormat + - SeedOrthologDirFmt + - SampleEstimatorDirFmt + - PlacementsFormat + - DNAFASTAFormat + - UchimeStatsFmt + - PairedEndFastqManifestPhred33V2 + - AlignedRNAFASTAFormat + - KaijuDBDirectoryFormat - ContigSequencesDirFmt - - NewickFormat - - BLAST6Format - - LociDirectoryFormat - - BIOMV210Format - - ProbabilitiesFormat - - ErrorCorrectionDetailsFmt + - EMPSingleEndCasavaDirFmt + - FirstDifferencesFormat + - SeppReferenceDirFmt + - PredictionsFormat + - ProteinsDirectoryFormat + - MixedCaseRNAFASTAFormat + - PairedEndFastqManifestPhred64V2 - BLASTDBDirFmtV5 - - DecontamScoreFormat - - AlignedRNAFASTAFormat - - ProcrustesStatisticsFmt - - SeedOrthologDirFmt - - Bowtie2IndexDirFmt - - MixedCaseRNAFASTAFormat + - AlphaDiversityFormat + - CasavaOneEightSingleLanePerSampleDirFmt </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>