Mercurial > repos > q2d2 > qiime2_core__tools__export
changeset 1:d3b1853c4efd draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author | q2d2 |
---|---|
date | Fri, 13 Jan 2023 23:02:16 +0000 |
parents | 0214b9ae8a6e |
children | ddff0f6d5740 |
files | qiime2_core__tools__export.xml |
diffstat | 1 files changed, 79 insertions(+), 63 deletions(-) [+] |
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--- a/qiime2_core__tools__export.xml Mon Aug 29 20:37:34 2022 +0000 +++ b/qiime2_core__tools__export.xml Fri Jan 13 23:02:16 2023 +0000 @@ -1,21 +1,21 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2022, QIIME 2 development team. +Copyright (c) 2023, QIIME 2 development team. Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> <!-- This tool was automatically generated by: - q2galaxy (version: 2022.8.1) + q2galaxy (version: 2022.11.1) for: - qiime2 (version: 2022.8.1) + qiime2 (version: 2022.11.1) --> -<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2022.8.1+dist.h91e3be72.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2022.11.1+dist.h2bda5906.2" profile="22.05" license="BSD-3-Clause"> <description>Export data from a QIIME 2 artifact</description> <requirements> - <container type="docker">quay.io/qiime2/core:2022.8</container> + <container type="docker">quay.io/qiime2/core:2022.11</container> </requirements> - <command>q2galaxy run tools export '$inputs'</command> + <command detect_errors="exit_code">q2galaxy run tools export '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> @@ -44,6 +44,7 @@ <option value="FeatureData__ob__AlignedRNASequence__cb__">FeatureData[AlignedRNASequence]</option> <option value="FeatureData__ob__AlignedSequence__cb__">FeatureData[AlignedSequence]</option> <option value="FeatureData__ob__BLAST6__cb__">FeatureData[BLAST6]</option> + <option value="FeatureData__ob__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__PairedEndRNASequence__cb__">FeatureData[PairedEndRNASequence]</option> @@ -152,6 +153,12 @@ <option value="BLAST6Format">BLAST6 Format</option> </param> </when> + <when value="FeatureData__ob__DifferentialAbundance__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="DataLoafPackageDirFmt">Data Loaf Package Directory Format</option> + </param> + </when> <when value="FeatureData__ob__Differential__cb__"> <param name="output_format" type="select" label="QIIME 2 file format to convert to:"> <option value="None" selected="true">export as is (no conversion)</option> @@ -427,7 +434,7 @@ </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 {'NewickFormat', 'DADA2StatsFormat', 'AlignedProteinFASTAFormat', 'QualityFilterStatsDirFmt', 'ProbabilitiesFormat', 'OrdinationFormat', 'SingleLanePerSamplePairedEndFastqDirFmt', 'EMPPairedEndDirFmt', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'AlignedDNASequencesDirectoryFormat', 'TSVTaxonomyDirectoryFormat', 'AlignedRNAFASTAFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'BooleanSeriesFormat', 'QualityFilterStatsFmt', 'BIOMV210DirFmt', 'EMPSingleEndDirFmt', 'Bowtie2IndexDirFmt', 'PlacementsFormat', 'TrueTargetsDirectoryFormat', 'AlignedRNASequencesDirectoryFormat', 'ProbabilitiesDirectoryFormat', 'ArtificialGroupingDirectoryFormat', 'DifferentialDirectoryFormat', 'AlignedDNAFASTAFormat', 'LSMatFormat', 'FastqGzFormat', 'RNASequencesDirectoryFormat', 'ProteinSequencesDirectoryFormat', 'DADA2StatsDirFmt', 'SeppReferenceDirFmt', 'DNAFASTAFormat', 'QIIME1DemuxDirFmt', 'BooleanSeriesDirectoryFormat', 'PairedRNASequencesDirectoryFormat', 'AlphaDiversityFormat', 'PlacementsDirFmt', 'ProcrustesStatisticsDirFmt', 'ImportanceFormat', 'NewickDirectoryFormat', 'TSVTaxonomyFormat', 'DifferentialFormat', 'QIIME1DemuxFormat', 'CasavaOneEightSingleLanePerSampleDirFmt', 'BLAST6Format', 'UchimeStatsFmt', 'FirstDifferencesFormat', 'PredictionsDirectoryFormat', 'ProcrustesStatisticsFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'AlignedProteinSequencesDirectoryFormat', 'SampleEstimatorDirFmt', 'RNAFASTAFormat', 'ProteinFASTAFormat', 'ArtificialGroupingFormat', 'AlphaDiversityDirectoryFormat', 'UchimeStatsDirFmt', 'TaxonomicClassiferTemporaryPickleDirFmt', 'PairedDNASequencesDirectoryFormat', 'DNASequencesDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'DeblurStatsFmt', 'DeblurStatsDirFmt', 'ErrorCorrectionDetailsDirFmt', 'OrdinationDirectoryFormat', 'BLAST6DirectoryFormat', 'BIOMV210Format', 'PredictionsFormat', 'ImportanceDirectoryFormat', 'FirstDifferencesDirectoryFormat'}</filter> + <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'TSVTaxonomyDirectoryFormat', 'EMPPairedEndDirFmt', 'AlignedRNASequencesDirectoryFormat', 'AlignedProteinFASTAFormat', 'QualityFilterStatsDirFmt', 'OrdinationFormat', 'DeblurStatsFmt', 'ImportanceDirectoryFormat', 'ArtificialGroupingDirectoryFormat', 'Bowtie2IndexDirFmt', 'BooleanSeriesDirectoryFormat', 'ArtificialGroupingFormat', 'SampleEstimatorDirFmt', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'TaxonomicClassiferTemporaryPickleDirFmt', 'AlphaDiversityFormat', 'TrueTargetsDirectoryFormat', 'PairedDNASequencesDirectoryFormat', 'UchimeStatsDirFmt', 'DifferentialFormat', 'AlignedDNASequencesDirectoryFormat', 'PredictionsDirectoryFormat', 'DADA2StatsDirFmt', 'SingleLanePerSamplePairedEndFastqDirFmt', 'DNAFASTAFormat', 'DADA2StatsFormat', 'RNAFASTAFormat', 'AlignedRNAFASTAFormat', 'UchimeStatsFmt', 'ErrorCorrectionDetailsDirFmt', 'FastqGzFormat', 'QIIME1DemuxDirFmt', 'PairedRNASequencesDirectoryFormat', 'ProcrustesStatisticsDirFmt', 'DeblurStatsDirFmt', 'ImportanceFormat', 'AlignedProteinSequencesDirectoryFormat', 'DifferentialDirectoryFormat', 'NewickDirectoryFormat', 'NewickFormat', 'OrdinationDirectoryFormat', 'LSMatFormat', 'BooleanSeriesFormat', 'ProteinFASTAFormat', 'EMPSingleEndDirFmt', 'QIIME1DemuxFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'PlacementsFormat', 'PredictionsFormat', 'ProteinSequencesDirectoryFormat', 'QualityFilterStatsFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'FirstDifferencesDirectoryFormat', 'FirstDifferencesFormat', 'PlacementsDirFmt', 'DNASequencesDirectoryFormat', 'SeppReferenceDirFmt', 'TSVTaxonomyFormat', 'ProcrustesStatisticsFmt', 'RNASequencesDirectoryFormat', 'BIOMV210DirFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'BIOMV210Format', 'AlphaDiversityDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'BLAST6Format', 'AlignedDNAFASTAFormat', 'ProbabilitiesFormat', 'ProbabilitiesDirectoryFormat', 'BLAST6DirectoryFormat', 'DataLoafPackageDirFmt'}</filter> <discover_datasets pattern="__designation_and_ext__" visible="false"/> </collection> <data name="AlignedDNAFASTAFormat" label="${tool.name} on ${on_string} as AlignedDNAFASTAFormat"> @@ -523,6 +530,14 @@ <filter>fmt_finder['output_format'] == 'DNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNASequencesDirectoryFormat')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>dna-sequences)\.(?P<ext>fasta)" visible="true"/> </data> + <collection name="DataLoafPackageDirFmt_data_slices" type="list" label="${tool.name} on ${on_string} as DataLoafPackageDirFmt (data_slices)"> + <filter>fmt_finder['output_format'] == 'DataLoafPackageDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DataLoafPackageDirFmt')</filter> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>csv)" visible="false"/> + </collection> + <data name="DataLoafPackageDirFmt" label="${tool.name} on ${on_string} as DataLoafPackageDirFmt"> + <filter>fmt_finder['output_format'] == 'DataLoafPackageDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DataLoafPackageDirFmt')</filter> + <discover_datasets assign_primary_output="true" pattern="(?P<designation>datapackage)\.(?P<ext>json)" visible="true"/> + </data> <data name="DeblurStatsDirFmt" label="${tool.name} on ${on_string} as DeblurStatsDirFmt"> <filter>fmt_finder['output_format'] == 'DeblurStatsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DeblurStatsDirFmt')</filter> <discover_datasets assign_primary_output="true" pattern="(?P<designation>stats)\.(?P<ext>csv)" visible="true"/> @@ -817,73 +832,74 @@ Additional formats without documentation: ***************************************** - - AlignedRNASequencesDirectoryFormat + - QIIME1DemuxDirFmt + - ArtificialGroupingDirectoryFormat + - DeblurStatsFmt + - DADA2StatsFormat + - ImportanceDirectoryFormat + - BIOMV210Format + - AlphaDiversityDirectoryFormat + - AlignedDNAFASTAFormat + - DataLoafPackageDirFmt - MultiplexedSingleEndBarcodeInSequenceDirFmt - - AlignedDNASequencesDirectoryFormat - - NewickFormat - - SeppReferenceDirFmt - - ProcrustesStatisticsDirFmt - - PairedRNASequencesDirectoryFormat - - BIOMV210DirFmt + - QualityFilterStatsDirFmt + - BLAST6Format + - PairedDNASequencesDirectoryFormat - EMPPairedEndDirFmt - - DistanceMatrixDirectoryFormat - - AlphaDiversityDirectoryFormat - - OrdinationDirectoryFormat - - ArtificialGroupingFormat - - BLAST6Format - - RNASequencesDirectoryFormat - - ProbabilitiesFormat + - NewickDirectoryFormat - PlacementsFormat - - DADA2StatsFormat - - SampleEstimatorDirFmt - - ImportanceFormat + - FirstDifferencesDirectoryFormat - AlignedProteinFASTAFormat - - DNASequencesDirectoryFormat - - BIOMV210Format + - BIOMV210DirFmt + - DistanceMatrixDirectoryFormat - TSVTaxonomyDirectoryFormat - - QualityFilterStatsDirFmt - - SingleLanePerSampleSingleEndFastqDirFmt - - CasavaOneEightSingleLanePerSampleDirFmt + - FirstDifferencesFormat + - TrueTargetsDirectoryFormat + - Bowtie2IndexDirFmt + - ProcrustesStatisticsFmt - ProteinFASTAFormat + - RNAFASTAFormat - ProbabilitiesDirectoryFormat + - SingleLanePerSampleSingleEndFastqDirFmt + - OrdinationFormat + - AlignedRNASequencesDirectoryFormat + - PlacementsDirFmt + - TaxonomicClassiferTemporaryPickleDirFmt + - ArtificialGroupingFormat + - CasavaOneEightSingleLanePerSampleDirFmt + - ImportanceFormat + - DifferentialDirectoryFormat + - DNAFASTAFormat - DADA2StatsDirFmt - - Bowtie2IndexDirFmt - - DifferentialFormat - - QIIME1DemuxDirFmt + - BooleanSeriesDirectoryFormat + - AlignedDNASequencesDirectoryFormat + - PredictionsFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - AlphaDiversityFormat + - ProbabilitiesFormat + - EMPSingleEndDirFmt + - BLAST6DirectoryFormat + - PairedRNASequencesDirectoryFormat + - PredictionsDirectoryFormat - UchimeStatsFmt - - DeblurStatsFmt - - DeblurStatsDirFmt - - AlignedRNAFASTAFormat - - NewickDirectoryFormat - - EMPSingleEndDirFmt - - PredictionsDirectoryFormat - - AlignedDNAFASTAFormat - - ArtificialGroupingDirectoryFormat - - FirstDifferencesDirectoryFormat - - ProcrustesStatisticsFmt - - FirstDifferencesFormat - - BLAST6DirectoryFormat - - PairedDNASequencesDirectoryFormat - - ErrorCorrectionDetailsDirFmt - - MultiplexedPairedEndBarcodeInSequenceDirFmt + - AlignedProteinSequencesDirectoryFormat + - NewickFormat + - UchimeStatsDirFmt + - SampleEstimatorDirFmt + - ProcrustesStatisticsDirFmt + - DifferentialFormat + - ProteinSequencesDirectoryFormat + - RNASequencesDirectoryFormat - LSMatFormat - - AlphaDiversityFormat - - PlacementsDirFmt - - OrdinationFormat + - SingleLanePerSamplePairedEndFastqDirFmt + - QualityFilterStatsFmt + - OrdinationDirectoryFormat + - ErrorCorrectionDetailsDirFmt + - AlignedRNAFASTAFormat + - DNASequencesDirectoryFormat - BooleanSeriesFormat - - ImportanceDirectoryFormat - - AlignedProteinSequencesDirectoryFormat - - RNAFASTAFormat - - SingleLanePerSamplePairedEndFastqDirFmt - - TaxonomicClassiferTemporaryPickleDirFmt - - PredictionsFormat - - TrueTargetsDirectoryFormat - - ProteinSequencesDirectoryFormat - - DNAFASTAFormat - - QualityFilterStatsFmt - - BooleanSeriesDirectoryFormat - - DifferentialDirectoryFormat - - UchimeStatsDirFmt + - SeppReferenceDirFmt + - DeblurStatsDirFmt </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>