Mercurial > repos > q2d2 > qiime2_core__tools__import
changeset 2:18c6b2b6740f draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 65e4952f33eb335528e8553150e9097e5ea8f556
author | q2d2 |
---|---|
date | Thu, 08 Jun 2023 19:53:28 +0000 |
parents | 5d9a36073ed6 |
children | 10447a4b0cc3 |
files | qiime2_core__tools__import.xml |
diffstat | 1 files changed, 99 insertions(+), 69 deletions(-) [+] |
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--- a/qiime2_core__tools__import.xml Fri Jan 13 23:02:20 2023 +0000 +++ b/qiime2_core__tools__import.xml Thu Jun 08 19:53:28 2023 +0000 @@ -6,14 +6,14 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2022.11.1) + q2galaxy (version: 2023.5.0) for: - qiime2 (version: 2022.11.1) + qiime2 (version: 2023.5.1) --> -<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2022.11.1+dist.h2bda5906.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.2" profile="22.05" license="BSD-3-Clause"> <description>Import data into a QIIME 2 artifact</description> <requirements> - <container type="docker">quay.io/qiime2/core:2022.11</container> + <container type="docker">quay.io/qiime2/core:2023.5</container> </requirements> <command detect_errors="exit_code">q2galaxy run tools import '$inputs'</command> <configfiles> @@ -69,6 +69,7 @@ <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__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> @@ -86,6 +87,7 @@ <option value="FeatureTable__ob__PresenceAbsence__cb__">FeatureTable[PresenceAbsence]</option> <option value="FeatureTable__ob__RelativeFrequency__cb__">FeatureTable[RelativeFrequency]</option> <option value="Hierarchy">Hierarchy</option> + <option value="ImmutableMetadata">ImmutableMetadata</option> <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option> <option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option> <option value="PCoAResults">PCoAResults</option> @@ -329,6 +331,19 @@ </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:"> + <option value="DecontamScoreFormat" selected="true">Decontam Score Format</option> + </param> + <when value="DecontamScoreFormat"> + <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 DecontamScoreFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="FeatureData__ob__DifferentialAbundance__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -664,6 +679,19 @@ </when> </conditional> </when> + <when value="ImmutableMetadata"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="ImmutableMetadataFormat" selected="true">Immutable Metadata Format</option> + </param> + <when value="ImmutableMetadataFormat"> + <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 ImmutableMetadataFormat. 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:"> @@ -1660,31 +1688,6 @@ -------- These formats have documentation available. -SampleIdIndexedSingleEndPerSampleDirFmt -*************************************** -Single-end reads in fastq.gz files where base filename is the sample id - - The full file name, minus the extension (`.fastq.gz`) is the sample id. - For example, the sample id for the file: - * `sample-1.fastq.gz` is `sample-1` - * `xyz.fastq.gz` is `xyz` - * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001` - -TSVTaxonomyFormat -***************** -Format for a 2+ column TSV file with an expected minimal header. - -The only header recognized by this format is: - - Feature ID<tab>Taxon - -Optionally followed by other arbitrary columns. - -This format supports blank lines. The expected header must be the first -non-blank line. In addition to the header, there must be at least one line -of data. - - QIIME1DemuxFormat ***************** QIIME 1 demultiplexed FASTA format. @@ -1719,6 +1722,21 @@ - Each sequence must be DNA and cannot be empty. +TSVTaxonomyFormat +***************** +Format for a 2+ column TSV file with an expected minimal header. + +The only header recognized by this format is: + + Feature ID<tab>Taxon + +Optionally followed by other arbitrary columns. + +This format supports blank lines. The expected header must be the first +non-blank line. In addition to the header, there must be at least one line +of data. + + HeaderlessTSVTaxonomyFormat *************************** Format for a 2+ column TSV file without a header. @@ -1732,64 +1750,76 @@ A gzipped fastq file. +SampleIdIndexedSingleEndPerSampleDirFmt +*************************************** +Single-end reads in fastq.gz files where base filename is the sample id + + The full file name, minus the extension (`.fastq.gz`) is the sample id. + For example, the sample id for the file: + * `sample-1.fastq.gz` is `sample-1` + * `xyz.fastq.gz` is `xyz` + * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001` + Additional formats without documentation: ***************************************** + - FirstDifferencesFormat - MixedCaseAlignedDNAFASTAFormat - - DeblurStatsFmt - - DADA2StatsFormat - - PairedEndFastqManifestPhred64 - - BIOMV210Format + - SingleLanePerSamplePairedEndFastqDirFmt + - EMPPairedEndDirFmt + - ImmutableMetadataFormat + - PairedEndFastqManifestPhred64V2 + - DataLoafPackageDirFmt - AlignedDNAFASTAFormat - - DataLoafPackageDirFmt - - SingleEndFastqManifestPhred64 + - BIOMV100Format + - UchimeStatsFmt + - BLAST6Format - PairedDNASequencesDirectoryFormat - - BLAST6Format - - EMPPairedEndDirFmt - - PlacementsFormat + - SingleEndFastqManifestPhred33V2 + - QualityFilterStatsFmt + - DADA2StatsFormat - AlignedProteinFASTAFormat - MixedCaseRNAFASTAFormat - - FirstDifferencesFormat - - CasavaOneEightLanelessPerSampleDirFmt - - Bowtie2IndexDirFmt - - EMPSingleEndCasavaDirFmt - - ProcrustesStatisticsFmt + - PlacementsFormat + - NewickFormat + - PairedEndFastqManifestPhred64 - ProteinFASTAFormat - RNAFASTAFormat - - SingleLanePerSampleSingleEndFastqDirFmt - - PairedEndFastqManifestPhred33V2 - - OrdinationFormat + - BooleanSeriesFormat + - SingleEndFastqManifestPhred64 + - LSMatFormat + - DeblurStatsFmt + - ErrorCorrectionDetailsFmt - MixedCaseDNAFASTAFormat - TaxonomicClassiferTemporaryPickleDirFmt - - ArtificialGroupingFormat - - BIOMV100Format + - DNAFASTAFormat + - ProcrustesStatisticsFmt + - CasavaOneEightLanelessPerSampleDirFmt + - EMPSingleEndDirFmt + - DecontamScoreFormat + - OrdinationFormat + - SingleLanePerSampleSingleEndFastqDirFmt + - Bowtie2IndexDirFmt + - BIOMV210Format + - PairedEndFastqManifestPhred33V2 + - SampleEstimatorDirFmt + - EMPSingleEndCasavaDirFmt + - PairedRNASequencesDirectoryFormat + - EMPPairedEndCasavaDirFmt - CasavaOneEightSingleLanePerSampleDirFmt - - ErrorCorrectionDetailsFmt - - ImportanceFormat - - SingleEndFastqManifestPhred33V2 - - DNAFASTAFormat + - SingleEndFastqManifestPhred64V2 - MultiplexedFastaQualDirFmt - - PredictionsFormat + - DifferentialFormat + - AlphaDiversityFormat - MultiplexedPairedEndBarcodeInSequenceDirFmt - PairedEndFastqManifestPhred33 - - AlphaDiversityFormat + - ArtificialGroupingFormat - ProbabilitiesFormat - - EMPSingleEndDirFmt - - PairedRNASequencesDirectoryFormat + - SeppReferenceDirFmt + - MixedCaseAlignedRNAFASTAFormat - SingleEndFastqManifestPhred33 - - UchimeStatsFmt - - EMPPairedEndCasavaDirFmt - - NewickFormat - - SampleEstimatorDirFmt - - DifferentialFormat - - LSMatFormat - - SingleLanePerSamplePairedEndFastqDirFmt - - QualityFilterStatsFmt - - PairedEndFastqManifestPhred64V2 - - MixedCaseAlignedRNAFASTAFormat - - SingleEndFastqManifestPhred64V2 + - ImportanceFormat - AlignedRNAFASTAFormat - - BooleanSeriesFormat - - SeppReferenceDirFmt + - PredictionsFormat </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>