Mercurial > repos > q2d2 > qiime2_core__tools__export
changeset 4:e96704fc516d draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
| author | q2d2 |
|---|---|
| date | Thu, 25 Apr 2024 21:28:08 +0000 |
| parents | f47ed6c69f5d |
| children | |
| files | qiime2_core__tools__export.xml test-data/YY/YY_S49_R1_001.fastq.gz test-data/YY/YY_S49_R2_001.fastq.gz |
| diffstat | 3 files changed, 275 insertions(+), 73 deletions(-) [+] |
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--- a/qiime2_core__tools__export.xml Thu Feb 01 21:22:13 2024 +0000 +++ b/qiime2_core__tools__export.xml Thu Apr 25 21:28:08 2024 +0000 @@ -1,21 +1,21 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2023, QIIME 2 development team. +Copyright (c) 2024, QIIME 2 development team. Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> <!-- This tool was automatically generated by: - q2galaxy (version: 2023.5.0) + q2galaxy (version: 2024.2.1) for: - qiime2 (version: 2023.5.1) + qiime2 (version: 2024.2.0) --> -<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2023.5.0+dist.h193f7cc9.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2024.2.1+dist.he188c3c2" profile="22.05" license="BSD-3-Clause"> <description>Export data from a QIIME 2 artifact</description> <requirements> - <container type="docker">quay.io/qiime2/core:2023.5</container> + <container type="docker">quay.io/qiime2/amplicon:2024.2</container> </requirements> - <command detect_errors="exit_code">q2galaxy run tools export '$inputs'</command> + <command>q2galaxy run tools export '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> @@ -34,6 +34,7 @@ <conditional name="fmt_finder"> <param name="type" type="select" label="To change the format, select the type indicated above:"> <option value="None" selected="true">export as is (no conversion)</option> + <option value="BLASTDB">BLASTDB</option> <option value="Bowtie2Index">Bowtie2Index</option> <option value="DeblurStats">DeblurStats</option> <option value="DistanceMatrix">DistanceMatrix</option> @@ -52,8 +53,11 @@ <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__Sequence__cb__">FeatureData[Sequence]</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> <option value="FeatureTable__ob__Composition__cb__">FeatureTable[Composition]</option> <option value="FeatureTable__ob__Design__cb__">FeatureTable[Design]</option> @@ -61,6 +65,10 @@ <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__Genes__cb__">GenomeData[Genes]</option> + <option value="GenomeData__ob__Loci__cb__">GenomeData[Loci]</option> + <option value="GenomeData__ob__Proteins__cb__">GenomeData[Proteins]</option> <option value="Hierarchy">Hierarchy</option> <option value="ImmutableMetadata">ImmutableMetadata</option> <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option> @@ -72,18 +80,25 @@ <option value="ProcrustesStatistics">ProcrustesStatistics</option> <option value="QualityFilterStats">QualityFilterStats</option> <option value="RawSequences">RawSequences</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> + <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> <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__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__PairedEndSequencesWithQuality__cb__">SampleData[PairedEndSequencesWithQuality]</option> <option value="SampleData__ob__Probabilities__cb__">SampleData[Probabilities]</option> <option value="SampleData__ob__RegressorPredictions__cb__">SampleData[RegressorPredictions]</option> <option value="SampleData__ob__SequencesWithQuality__cb__">SampleData[SequencesWithQuality]</option> <option value="SampleData__ob__Sequences__cb__">SampleData[Sequences]</option> + <option value="SampleData__ob__SingleBowtie2Index__cb__">SampleData[SingleBowtie2Index]</option> <option value="SampleData__ob__TrueTargets__cb__">SampleData[TrueTargets]</option> <option value="SampleEstimator__ob__Classifier__cb__">SampleEstimator[Classifier]</option> <option value="SampleEstimator__ob__Regressor__cb__">SampleEstimator[Regressor]</option> @@ -96,6 +111,12 @@ <option value="None" selected="true">export as is (no conversion)</option> </param> </when> + <when value="BLASTDB"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="BLASTDBDirFmtV5">BLASTDB Directory Format V5</option> + </param> + </when> <when value="Bowtie2Index"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> @@ -200,9 +221,22 @@ <when value="FeatureData__ob__RNASequence__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> + <option value="DNAFASTAFormat">DNAFASTA Format</option> <option value="RNAFASTAFormat">RNAFASTA Format</option> </param> </when> + <when value="FeatureData__ob__SILVATaxidMap__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="SILVATaxidMapFormat">SILVA Taxid Map Format</option> + </param> + </when> + <when value="FeatureData__ob__SILVATaxonomy__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="SILVATaxonomyFormat">SILVA Taxonomy Format</option> + </param> + </when> <when value="FeatureData__ob__Sequence__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> @@ -215,6 +249,12 @@ <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> </param> </when> + <when value="FeatureMap__ob__MAGtoContigs__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="MAGtoContigsFormat">MA Gto Contigs Format</option> + </param> + </when> <when value="FeatureTable__ob__Balance__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> @@ -264,6 +304,30 @@ <option value="TSVTaxonomyFormat">TSV Taxonomy Format</option> </param> </when> + <when value="GenomeData__ob__BLAST6__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="SeedOrthologDirFmt">Seed Ortholog Directory Format</option> + </param> + </when> + <when value="GenomeData__ob__Genes__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="GenesDirectoryFormat">Genes Directory Format</option> + </param> + </when> + <when value="GenomeData__ob__Loci__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="LociDirectoryFormat">Loci Directory Format</option> + </param> + </when> + <when value="GenomeData__ob__Proteins__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="ProteinsDirectoryFormat">Proteins Directory Format</option> + </param> + </when> <when value="Hierarchy"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> @@ -330,6 +394,12 @@ <option value="EMPSingleEndDirFmt">EMP Single End Directory Format</option> </param> </when> + <when value="SampleData__ob__AlignmentMap__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="BAMDirFmt">BAM Directory Format</option> + </param> + </when> <when value="SampleData__ob__AlphaDiversity__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> @@ -342,6 +412,12 @@ <option value="ArtificialGroupingFormat">Artificial Grouping Format</option> </param> </when> + <when value="SampleData__ob__BLAST6__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="SeedOrthologDirFmt">Seed Ortholog Directory Format</option> + </param> + </when> <when value="SampleData__ob__BooleanSeries__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> @@ -354,6 +430,12 @@ <option value="PredictionsFormat">Predictions Format</option> </param> </when> + <when value="SampleData__ob__Contigs__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="ContigSequencesDirFmt">Contig Sequences Directory Format</option> + </param> + </when> <when value="SampleData__ob__DADA2Stats__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> @@ -374,6 +456,24 @@ <option value="SingleLanePerSampleSingleEndFastqDirFmt">Single Lane Per Sample Single End Fastq Directory Format</option> </param> </when> + <when value="SampleData__ob__MAGs__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="MultiMAGSequencesDirFmt">Multi MAG Sequences Directory Format</option> + </param> + </when> + <when value="SampleData__ob__MultiAlignmentMap__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="MultiBAMDirFmt">Multi BAM Directory Format</option> + </param> + </when> + <when value="SampleData__ob__MultiBowtie2Index__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="MultiBowtie2IndexDirFmt">Multi Bowtie2 Index Directory Format</option> + </param> + </when> <when value="SampleData__ob__PairedEndSequencesWithQuality__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> @@ -408,6 +508,12 @@ <option value="QIIME1DemuxFormat">QIIME1 Demux Format</option> </param> </when> + <when value="SampleData__ob__SingleBowtie2Index__cb__"> + <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> + <option value="None" selected="true">export as is (no conversion)</option> + <option value="Bowtie2IndexDirFmt">Bowtie2 Index Directory Format</option> + </param> + </when> <when value="SampleData__ob__TrueTargets__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> @@ -448,7 +554,7 @@ </inputs> <outputs> <collection name="exported" type="list" label="${tool.name} on ${on_string} as ${fmt_peek}"> - <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'QIIME1DemuxFormat', 'DNAFASTAFormat', 'PlacementsDirFmt', 'ImmutableMetadataFormat', 'Bowtie2IndexDirFmt', 'QIIME1DemuxDirFmt', 'AlignedDNASequencesDirectoryFormat', 'DADA2StatsDirFmt', 'AlignedRNASequencesDirectoryFormat', 'OrdinationFormat', 'ProteinFASTAFormat', 'LSMatFormat', 'PairedRNASequencesDirectoryFormat', 'DifferentialFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'AlignedProteinFASTAFormat', 'ArtificialGroupingDirectoryFormat', 'RNAFASTAFormat', 'SeppReferenceDirFmt', 'FastqGzFormat', 'ProcrustesStatisticsDirFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'QualityFilterStatsFmt', 'PlacementsFormat', 'ProbabilitiesDirectoryFormat', 'ImportanceDirectoryFormat', 'FirstDifferencesFormat', 'TrueTargetsDirectoryFormat', 'ImmutableMetadataDirectoryFormat', 'UchimeStatsDirFmt', 'NewickDirectoryFormat', 'DADA2StatsFormat', 'AlignedDNAFASTAFormat', 'PredictionsDirectoryFormat', 'AlphaDiversityDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'DeblurStatsDirFmt', 'DNASequencesDirectoryFormat', 'SingleLanePerSamplePairedEndFastqDirFmt', 'UchimeStatsFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'ErrorCorrectionDetailsDirFmt', 'BLAST6DirectoryFormat', 'DecontamScoreDirFmt', 'SampleEstimatorDirFmt', 'FirstDifferencesDirectoryFormat', 'QualityFilterStatsDirFmt', 'DistanceMatrixDirectoryFormat', 'DecontamScoreFormat', 'EMPSingleEndDirFmt', 'EMPPairedEndDirFmt', 'DataLoafPackageDirFmt', 'PairedDNASequencesDirectoryFormat', 'BIOMV210DirFmt', 'AlignedRNAFASTAFormat', 'OrdinationDirectoryFormat', 'BIOMV210Format', 'AlphaDiversityFormat', 'ArtificialGroupingFormat', 'DeblurStatsFmt', 'TSVTaxonomyDirectoryFormat', 'PredictionsFormat', 'BooleanSeriesFormat', 'DifferentialDirectoryFormat', 'ProcrustesStatisticsFmt', 'BooleanSeriesDirectoryFormat', 'AlignedProteinSequencesDirectoryFormat', 'TSVTaxonomyFormat', 'NewickFormat', 'ProteinSequencesDirectoryFormat', 'BLAST6Format', 'ImportanceFormat', 'RNASequencesDirectoryFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'ProbabilitiesFormat'}</filter> + <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'PairedDNASequencesDirectoryFormat', 'DataLoafPackageDirFmt', 'BIOMV210Format', 'BLAST6DirectoryFormat', 'ProteinFASTAFormat', 'ProbabilitiesFormat', 'MultiBowtie2IndexDirFmt', 'MultiMAGSequencesDirFmt', 'ImmutableMetadataFormat', 'DecontamScoreFormat', 'SILVATaxidMapFormat', 'AlignedProteinFASTAFormat', 'NewickFormat', 'PredictionsFormat', 'AlignedProteinSequencesDirectoryFormat', 'SeppReferenceDirFmt', 'TaxonomicClassiferTemporaryPickleDirFmt', 'PlacementsDirFmt', 'ImmutableMetadataDirectoryFormat', 'CasavaOneEightSingleLanePerSampleDirFmt', 'EMPPairedEndDirFmt', 'RNAFASTAFormat', 'EMPSingleEndDirFmt', 'ProcrustesStatisticsDirFmt', 'DADA2StatsDirFmt', 'ErrorCorrectionDetailsDirFmt', 'ProbabilitiesDirectoryFormat', 'MultiBAMDirFmt', 'SeedOrthologDirFmt', 'AlignedRNASequencesDirectoryFormat', 'MAGtoContigsDirFmt', 'DifferentialDirectoryFormat', 'QualityFilterStatsDirFmt', 'SILVATaxonomyFormat', 'DADA2StatsFormat', 'UchimeStatsFmt', 'DecontamScoreDirFmt', 'SingleLanePerSamplePairedEndFastqDirFmt', 'RNASequencesDirectoryFormat', 'SingleLanePerSampleSingleEndFastqDirFmt', 'DNAFASTAFormat', 'BooleanSeriesDirectoryFormat', 'LociDirectoryFormat', 'NewickDirectoryFormat', 'ProteinSequencesDirectoryFormat', 'DeblurStatsFmt', 'BooleanSeriesFormat', 'OrdinationFormat', 'AlphaDiversityFormat', 'TSVTaxonomyFormat', 'SampleEstimatorDirFmt', 'MAGtoContigsFormat', 'SILVATaxonomyDirectoryFormat', 'QIIME1DemuxDirFmt', 'BLASTDBDirFmtV5', 'ProteinsDirectoryFormat', 'LSMatFormat', 'PredictionsDirectoryFormat', 'DifferentialFormat', 'BAMDirFmt', 'ArtificialGroupingFormat', 'ImportanceDirectoryFormat', 'DNASequencesDirectoryFormat', 'SILVATaxidMapDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'QIIME1DemuxFormat', 'OrdinationDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'QualityFilterStatsFmt', 'PairedRNASequencesDirectoryFormat', 'DeblurStatsDirFmt', 'ContigSequencesDirFmt', 'GenesDirectoryFormat', 'ImportanceFormat', 'ProcrustesStatisticsFmt', 'ArtificialGroupingDirectoryFormat', 'FirstDifferencesDirectoryFormat', 'BLAST6Format', 'TSVTaxonomyDirectoryFormat', 'AlphaDiversityDirectoryFormat', 'BIOMV210DirFmt', 'TrueTargetsDirectoryFormat', 'AlignedDNASequencesDirectoryFormat', 'FastqGzFormat', 'AlignedRNAFASTAFormat', 'AlignedDNAFASTAFormat', 'FirstDifferencesFormat', 'Bowtie2IndexDirFmt', 'UchimeStatsDirFmt', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'PlacementsFormat'}</filter> <discover_datasets pattern="__designation_and_ext__" visible="false"/> </collection> <data name="AlignedDNAFASTAFormat" label="${tool.name} on ${on_string} as AlignedDNAFASTAFormat"> @@ -491,6 +597,10 @@ <filter>fmt_finder['output_format'] == 'ArtificialGroupingFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ArtificialGroupingFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <collection name="BAMDirFmt_bams" type="list" label="${tool.name} on ${on_string} as BAMDirFmt (bams)"> + <filter>fmt_finder['output_format'] == 'BAMDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BAMDirFmt')</filter> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>bam)" visible="false"/> + </collection> <data name="BIOMV210DirFmt" label="${tool.name} on ${on_string} as BIOMV210DirFmt"> <filter>fmt_finder['output_format'] == 'BIOMV210DirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BIOMV210DirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>feature-table)\.(?P<ext>biom)" visible="true"/> @@ -507,6 +617,17 @@ <filter>fmt_finder['output_format'] == 'BLAST6Format' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BLAST6Format')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <data name="BLASTDBDirFmtV5" label="${tool.name} on ${on_string} as BLASTDBDirFmtV5"> + <filter>fmt_finder['output_format'] == 'BLASTDBDirFmtV5' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BLASTDBDirFmtV5')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>.+)\.(?P<ext>ndb)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>nhr)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>nin)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>not)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>nsq)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>ntf)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>nto)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>njs)" visible="true"/> + </data> <data name="BooleanSeriesDirectoryFormat" label="${tool.name} on ${on_string} as BooleanSeriesDirectoryFormat"> <filter>fmt_finder['output_format'] == 'BooleanSeriesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BooleanSeriesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>outliers)\.(?P<ext>tsv)" visible="true"/> @@ -528,6 +649,10 @@ <filter>fmt_finder['output_format'] == 'CasavaOneEightSingleLanePerSampleDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'CasavaOneEightSingleLanePerSampleDirFmt')</filter> <discover_datasets pattern="(?P<designation>.+_.+_L[0-9][0-9][0-9]_R[12]_001)\.(?P<ext>fastq\.gz)" visible="false"/> </collection> + <collection name="ContigSequencesDirFmt_sequences" type="list" label="${tool.name} on ${on_string} as ContigSequencesDirFmt (sequences)"> + <filter>fmt_finder['output_format'] == 'ContigSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ContigSequencesDirFmt')</filter> + <discover_datasets pattern="(?P<designation>[^)\.(?P<ext>].+_contigs.(fasta|fa)$)" visible="false"/> + </collection> <data name="DADA2StatsDirFmt" label="${tool.name} on ${on_string} as DADA2StatsDirFmt"> <filter>fmt_finder['output_format'] == 'DADA2StatsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DADA2StatsDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>stats)\.(?P<ext>tsv)" visible="true"/> @@ -607,6 +732,10 @@ <filter>fmt_finder['output_format'] == 'FirstDifferencesFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'FirstDifferencesFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <collection name="GenesDirectoryFormat_genes" type="list" label="${tool.name} on ${on_string} as GenesDirectoryFormat (genes)"> + <filter>fmt_finder['output_format'] == 'GenesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'GenesDirectoryFormat')</filter> + <discover_datasets pattern="(?P<designation>(.*\_)?genes[0-9]*)\.(?P<ext>(fa|fna|fasta)$)" visible="false"/> + </collection> <data name="ImmutableMetadataDirectoryFormat" label="${tool.name} on ${on_string} as ImmutableMetadataDirectoryFormat"> <filter>fmt_finder['output_format'] == 'ImmutableMetadataDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ImmutableMetadataDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>metadata)\.(?P<ext>tsv)" visible="true"/> @@ -627,6 +756,39 @@ <filter>fmt_finder['output_format'] == 'LSMatFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'LSMatFormat')</filter> <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> </data> + <collection name="LociDirectoryFormat_loci" type="list" label="${tool.name} on ${on_string} as LociDirectoryFormat (loci)"> + <filter>fmt_finder['output_format'] == 'LociDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'LociDirectoryFormat')</filter> + <discover_datasets pattern="(?P<designation>(.*\_)?loci[0-9]*)\.(?P<ext>gff$)" visible="false"/> + </collection> + <data name="MAGtoContigsDirFmt" label="${tool.name} on ${on_string} as MAGtoContigsDirFmt"> + <filter>fmt_finder['output_format'] == 'MAGtoContigsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MAGtoContigsDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>mag-to-contigs)\.(?P<ext>json)" visible="true"/> + </data> + <data name="MAGtoContigsFormat" label="${tool.name} on ${on_string} as MAGtoContigsFormat"> + <filter>fmt_finder['output_format'] == 'MAGtoContigsFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MAGtoContigsFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <collection name="MultiBAMDirFmt_bams" type="list" label="${tool.name} on ${on_string} as MultiBAMDirFmt (bams)"> + <filter>fmt_finder['output_format'] == 'MultiBAMDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiBAMDirFmt')</filter> + <discover_datasets pattern="(?P<designation>.+\/.+)\.(?P<ext>bam)" visible="false"/> + </collection> + <data name="MultiBowtie2IndexDirFmt" label="${tool.name} on ${on_string} as MultiBowtie2IndexDirFmt"> + <filter>fmt_finder['output_format'] == 'MultiBowtie2IndexDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiBowtie2IndexDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>.+(?<!\.rev)\.1)\.(?P<ext>bt2l?)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+(?<!\.rev)\.2)\.(?P<ext>bt2l?)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+\.3)\.(?P<ext>bt2l?)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+\.4)\.(?P<ext>bt2l?)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+\.rev\.1)\.(?P<ext>bt2l?)" visible="true"/> + <discover_datasets pattern="(?P<designation>.+\.rev\.2)\.(?P<ext>bt2l?)" visible="true"/> + </data> + <collection name="MultiMAGSequencesDirFmt_sequences" type="list" label="${tool.name} on ${on_string} as MultiMAGSequencesDirFmt (sequences)"> + <filter>fmt_finder['output_format'] == 'MultiMAGSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiMAGSequencesDirFmt')</filter> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>(fa|fasta)$)" visible="false"/> + </collection> + <data name="MultiMAGSequencesDirFmt" label="${tool.name} on ${on_string} as MultiMAGSequencesDirFmt"> + <filter>fmt_finder['output_format'] == 'MultiMAGSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiMAGSequencesDirFmt')</filter> + <discover_datasets assign_primary_output="true" ext="txt" pattern="(?P<designation>MANIFEST)" visible="true"/> + </data> <data name="MultiplexedPairedEndBarcodeInSequenceDirFmt" label="${tool.name} on ${on_string} as MultiplexedPairedEndBarcodeInSequenceDirFmt"> <filter>fmt_finder['output_format'] == 'MultiplexedPairedEndBarcodeInSequenceDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiplexedPairedEndBarcodeInSequenceDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>forward)\.(?P<ext>fastq.gz)" visible="true"/> @@ -702,6 +864,10 @@ <filter>fmt_finder['output_format'] == 'ProteinSequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinSequencesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>protein-sequences)\.(?P<ext>fasta)" visible="true"/> </data> + <collection name="ProteinsDirectoryFormat_proteins" type="list" label="${tool.name} on ${on_string} as ProteinsDirectoryFormat (proteins)"> + <filter>fmt_finder['output_format'] == 'ProteinsDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinsDirectoryFormat')</filter> + <discover_datasets pattern="(?P<designation>(.*\_)?proteins[0-9]*)\.(?P<ext>(fa|faa|fasta)$)" visible="false"/> + </collection> <data name="QIIME1DemuxDirFmt" label="${tool.name} on ${on_string} as QIIME1DemuxDirFmt"> <filter>fmt_finder['output_format'] == 'QIIME1DemuxDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'QIIME1DemuxDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>seqs)\.(?P<ext>fna)" visible="true"/> @@ -726,11 +892,31 @@ <filter>fmt_finder['output_format'] == 'RNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNASequencesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>rna-sequences)\.(?P<ext>fasta)" visible="true"/> </data> + <data name="SILVATaxidMapDirectoryFormat" label="${tool.name} on ${on_string} as SILVATaxidMapDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'SILVATaxidMapDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SILVATaxidMapDirectoryFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>silva_taxmap)\.(?P<ext>tsv)" visible="true"/> + </data> + <data name="SILVATaxidMapFormat" label="${tool.name} on ${on_string} as SILVATaxidMapFormat"> + <filter>fmt_finder['output_format'] == 'SILVATaxidMapFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SILVATaxidMapFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> + <data name="SILVATaxonomyDirectoryFormat" label="${tool.name} on ${on_string} as SILVATaxonomyDirectoryFormat"> + <filter>fmt_finder['output_format'] == 'SILVATaxonomyDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SILVATaxonomyDirectoryFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>silva_taxonomy)\.(?P<ext>tsv)" visible="true"/> + </data> + <data name="SILVATaxonomyFormat" label="${tool.name} on ${on_string} as SILVATaxonomyFormat"> + <filter>fmt_finder['output_format'] == 'SILVATaxonomyFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SILVATaxonomyFormat')</filter> + <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/> + </data> <data name="SampleEstimatorDirFmt" label="${tool.name} on ${on_string} as SampleEstimatorDirFmt"> <filter>fmt_finder['output_format'] == 'SampleEstimatorDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SampleEstimatorDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>sklearn_version)\.(?P<ext>json)" visible="true"/> <discover_datasets pattern="(?P<designation>sklearn_pipeline)\.(?P<ext>tar)" visible="true"/> </data> + <collection name="SeedOrthologDirFmt_seed_orthologs" type="list" label="${tool.name} on ${on_string} as SeedOrthologDirFmt (seed_orthologs)"> + <filter>fmt_finder['output_format'] == 'SeedOrthologDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SeedOrthologDirFmt')</filter> + <discover_datasets pattern="(?P<designation>.*\..*)\.(?P<ext>seed_orthologs)" visible="false"/> + </collection> <data name="SeppReferenceDirFmt" label="${tool.name} on ${on_string} as SeppReferenceDirFmt"> <filter>fmt_finder['output_format'] == 'SeppReferenceDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SeppReferenceDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>aligned-dna-sequences)\.(?P<ext>fasta)" visible="true"/> @@ -805,6 +991,12 @@ -------- These formats have documentation available. +FastqGzFormat +************* + +A gzipped fastq file. + + QIIME1DemuxFormat ***************** QIIME 1 demultiplexed FASTA format. @@ -854,86 +1046,96 @@ of data. -FastqGzFormat -************* - -A gzipped fastq file. - - Additional formats without documentation: ***************************************** - - FirstDifferencesFormat - - DecontamScoreDirFmt - - OrdinationDirectoryFormat - - EMPPairedEndDirFmt - - ImmutableMetadataFormat - - PredictionsDirectoryFormat - - AlphaDiversityDirectoryFormat - - DataLoafPackageDirFmt - - AlignedDNAFASTAFormat - - DADA2StatsDirFmt + - BAMDirFmt + - TaxonomicClassiferTemporaryPickleDirFmt + - ProbabilitiesDirectoryFormat + - BooleanSeriesFormat + - ErrorCorrectionDetailsDirFmt + - AlignedRNASequencesDirectoryFormat + - ProcrustesStatisticsDirFmt + - DifferentialDirectoryFormat + - SampleEstimatorDirFmt + - PlacementsDirFmt + - SILVATaxidMapDirectoryFormat + - BIOMV210DirFmt + - MultiBAMDirFmt + - QualityFilterStatsDirFmt - TrueTargetsDirectoryFormat - - UchimeStatsFmt - - BLAST6Format + - MAGtoContigsFormat + - ArtificialGroupingDirectoryFormat + - BooleanSeriesDirectoryFormat + - PlacementsFormat + - PredictionsFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - DeblurStatsDirFmt + - SingleLanePerSampleSingleEndFastqDirFmt + - AlignedProteinFASTAFormat - PairedDNASequencesDirectoryFormat - - QIIME1DemuxDirFmt + - UchimeStatsDirFmt + - DataLoafPackageDirFmt + - ArtificialGroupingFormat + - PredictionsDirectoryFormat + - SILVATaxonomyDirectoryFormat + - DNAFASTAFormat + - EMPSingleEndDirFmt + - SingleLanePerSamplePairedEndFastqDirFmt + - AlignedProteinSequencesDirectoryFormat + - PairedRNASequencesDirectoryFormat + - SeppReferenceDirFmt + - MAGtoContigsDirFmt + - DifferentialFormat + - UchimeStatsFmt + - SILVATaxonomyFormat + - FirstDifferencesDirectoryFormat + - DNASequencesDirectoryFormat + - GenesDirectoryFormat + - EMPPairedEndDirFmt + - AlignedDNAFASTAFormat + - SILVATaxidMapFormat + - ProteinsDirectoryFormat + - MultiMAGSequencesDirFmt - QualityFilterStatsFmt + - AlignedDNASequencesDirectoryFormat + - LSMatFormat + - ImmutableMetadataFormat + - DeblurStatsFmt + - AlphaDiversityFormat + - MultiBowtie2IndexDirFmt + - ImportanceFormat + - FirstDifferencesFormat - DADA2StatsFormat - - AlignedProteinFASTAFormat - - PlacementsFormat - - NewickFormat - - ProbabilitiesDirectoryFormat - - ErrorCorrectionDetailsDirFmt + - DistanceMatrixDirectoryFormat + - ImmutableMetadataDirectoryFormat + - OrdinationFormat + - DecontamScoreDirFmt + - CasavaOneEightSingleLanePerSampleDirFmt + - MultiplexedSingleEndBarcodeInSequenceDirFmt + - AlphaDiversityDirectoryFormat - ProteinFASTAFormat - RNAFASTAFormat - - MultiplexedSingleEndBarcodeInSequenceDirFmt - - BooleanSeriesFormat - - LSMatFormat + - ContigSequencesDirFmt - ImportanceDirectoryFormat - - DeblurStatsFmt - - AlignedRNASequencesDirectoryFormat - - QualityFilterStatsDirFmt - - TaxonomicClassiferTemporaryPickleDirFmt - - BooleanSeriesDirectoryFormat - - DifferentialDirectoryFormat - - DNAFASTAFormat - - ProcrustesStatisticsFmt - - PlacementsDirFmt - - EMPSingleEndDirFmt - - DecontamScoreFormat - - BIOMV210DirFmt - - ImmutableMetadataDirectoryFormat - - AlignedDNASequencesDirectoryFormat + - DADA2StatsDirFmt + - NewickFormat + - OrdinationDirectoryFormat - TSVTaxonomyDirectoryFormat - - OrdinationFormat - - FirstDifferencesDirectoryFormat - - Bowtie2IndexDirFmt - - BIOMV210Format - - SingleLanePerSampleSingleEndFastqDirFmt - - SampleEstimatorDirFmt - - PairedRNASequencesDirectoryFormat - - CasavaOneEightSingleLanePerSampleDirFmt - - AlignedProteinSequencesDirectoryFormat - - UchimeStatsDirFmt - - NewickDirectoryFormat - - SingleLanePerSamplePairedEndFastqDirFmt - - DifferentialFormat + - BLAST6Format + - LociDirectoryFormat - ProteinSequencesDirectoryFormat - RNASequencesDirectoryFormat - - MultiplexedPairedEndBarcodeInSequenceDirFmt - - AlphaDiversityFormat - - DistanceMatrixDirectoryFormat - - ArtificialGroupingFormat - - ArtificialGroupingDirectoryFormat + - BIOMV210Format - ProbabilitiesFormat - - DeblurStatsDirFmt - - SeppReferenceDirFmt - - ImportanceFormat + - BLASTDBDirFmtV5 + - DecontamScoreFormat + - AlignedRNAFASTAFormat + - NewickDirectoryFormat + - ProcrustesStatisticsFmt - BLAST6DirectoryFormat - - AlignedRNAFASTAFormat - - DNASequencesDirectoryFormat - - ProcrustesStatisticsDirFmt - - PredictionsFormat + - SeedOrthologDirFmt + - QIIME1DemuxDirFmt + - Bowtie2IndexDirFmt </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>