Mercurial > repos > q2d2 > qiime2_core__tools__import
changeset 9:52a1f79f0941 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b
| author | q2d2 |
|---|---|
| date | Sat, 01 Nov 2025 17:33:53 +0000 |
| parents | b2c99f2353b6 |
| children | |
| files | qiime2_core__tools__import.xml |
| diffstat | 1 files changed, 207 insertions(+), 127 deletions(-) [+] |
line wrap: on
line diff
--- a/qiime2_core__tools__import.xml Tue Jul 15 22:08:00 2025 +0000 +++ b/qiime2_core__tools__import.xml Sat Nov 01 17:33:53 2025 +0000 @@ -6,17 +6,17 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2025.7.0) + q2galaxy (version: 2025.10.0) for: - qiime2 (version: 2025.7.0) + qiime2 (version: 2025.10.0) --> -<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2025.7.0+dist.h44bd78f6" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2025.10.0+dist.hbfe50fe0" profile="22.05" license="BSD-3-Clause"> <description>Import data into a QIIME 2 artifact</description> <xrefs> <xref type="bio.tools">qiime2</xref> </xrefs> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2025.7</container> + <container type="docker">quay.io/qiime2/amplicon:2025.10</container> </requirements> <command>q2galaxy run tools import '$inputs'</command> <configfiles> @@ -66,6 +66,7 @@ <option value="BLASTDB">BLASTDB</option> <option value="Bowtie2Index">Bowtie2Index</option> <option value="BrackenDB">BrackenDB</option> + <option value="DADA2BaseTransitionStats">DADA2BaseTransitionStats</option> <option value="DeblurStats">DeblurStats</option> <option value="Dist1D__ob__Multi__comma__ Independent__cb__">Dist1D[Multi, Independent]</option> <option value="Dist1D__ob__Multi__comma__ Matched__cb__">Dist1D[Multi, Matched]</option> @@ -127,6 +128,7 @@ <option value="Kraken2DBReport">Kraken2DBReport</option> <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option> <option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option> + <option value="NCBIAccessionIDs">NCBIAccessionIDs</option> <option value="PCoAResults">PCoAResults</option> <option value="Phylogeny__ob__Rooted__cb__">Phylogeny[Rooted]</option> <option value="Phylogeny__ob__Unrooted__cb__">Phylogeny[Unrooted]</option> @@ -147,6 +149,8 @@ <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="SRAFailedIDs">SRAFailedIDs</option> + <option value="SRAMetadata">SRAMetadata</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> @@ -318,6 +322,19 @@ </when> </conditional> </when> + <when value="DADA2BaseTransitionStats"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="DADA2BaseTransitionStatsFormat" selected="true">DADA2 Base Transition Stats Format</option> + </param> + <when value="DADA2BaseTransitionStatsFormat"> + <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 DADA2BaseTransitionStatsFormat. See the documentation below for more information."/> + </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:"> @@ -1666,6 +1683,26 @@ </when> </conditional> </when> + <when value="NCBIAccessionIDs"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="NCBIAccessionIDsFormat" selected="true">NCBI Accession I Ds Format</option> + <option value="SRAMetadataFormat" selected="false">SRA Metadata Format</option> + </param> + <when value="NCBIAccessionIDsFormat"> + <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 NCBIAccessionIDsFormat. See the documentation below for more information."/> + </section> + </when> + <when value="SRAMetadataFormat"> + <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 SRAMetadataFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="PCoAResults"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -2050,6 +2087,32 @@ </when> </conditional> </when> + <when value="SRAFailedIDs"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="SRAFailedIDsFormat" selected="true">SRA Failed I Ds Format</option> + </param> + <when value="SRAFailedIDsFormat"> + <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 SRAFailedIDsFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="SRAMetadata"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="SRAMetadataFormat" selected="true">SRA Metadata Format</option> + </param> + <when value="SRAMetadataFormat"> + <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 SRAMetadataFormat. 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:"> @@ -3342,6 +3405,35 @@ -------- These formats have documentation available. +SRAFailedIDsFormat +****************** + +This is a "fake" format only used to store a list of failed SRA IDs, +which can be converted to QIIME's metadata and input into any fondue +action. + +NCBIAccessionIDsFormat +********************** + +This is a format used to store a list of SRA accession IDs (run, +study, BioProject, sample and experiment IDs), which can be converted +to QIIME's metadata. Artifacts containing of run, study and BioProject +IDs can be input into any fondue action. + +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". + SampleIdIndexedSingleEndPerSampleDirFmt *************************************** Single-end reads in fastq.gz files where base filename is the sample id @@ -3352,6 +3444,37 @@ * `xyz.fastq.gz` is `xyz` * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001` +ANCOMBC2OutputDirFmt +******************** + +Stores the model statistics and optionally the structural zeros table= +output by the ANCOMBC2 method. + +The slices are: + - lfc: log-fold change + - se: standard error + - W: lfc / se (the test statistic) + - p: p-value + - q: adjusted p-value + - diff: differentially abundant boolean (i.e. q < alpha) + - passed_ss: whether sensitivity analysis was passed + +FastqGzFormat +************* + +A gzipped fastq file. + + +PressedProfileHmmsDirectoryFmt +****************************** + +The <hmmfile>.h3m file contains the profile HMMs +and their annotation in a binary format. The <hmmfile>.h3i file is an +SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains +precomputed data structures for the fast heuristic filter +(the MSV filter). The <hmmfile>.h3p file contains precomputed data +structures for the rest of each profile. + QIIME1DemuxFormat ***************** QIIME 1 demultiplexed FASTA format. @@ -3386,12 +3509,6 @@ - Each sequence must be DNA and cannot be empty. -FastqGzFormat -************* - -A gzipped fastq file. - - HeaderlessTSVTaxonomyFormat *************************** Format for a 2+ column TSV file without a header. @@ -3414,139 +3531,102 @@ of data. -ANCOMBC2OutputDirFmt -******************** - -Stores the model statistics and optionally the structural zeros table= -output by the ANCOMBC2 method. - -The slices are: - - lfc: log-fold change - - se: standard error - - W: lfc / se (the test statistic) - - p: p-value - - q: adjusted p-value - - diff: differentially abundant boolean (i.e. q < alpha) - - passed_ss: whether sensitivity analysis was passed - -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". - -PressedProfileHmmsDirectoryFmt -****************************** - -The <hmmfile>.h3m file contains the profile HMMs -and their annotation in a binary format. The <hmmfile>.h3i file is an -SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains -precomputed data structures for the fast heuristic filter -(the MSV filter). The <hmmfile>.h3p file contains precomputed data -structures for the rest of each profile. - Additional formats without documentation: ***************************************** - - PredictionsFormat + - ContigSequencesDirFmt + - BrackenDBDirectoryFormat + - MixedCaseAlignedDNAFASTAFormat + - SILVATaxidMapFormat + - EggnogRefDirFmt + - CasavaOneEightSingleLanePerSampleDirFmt + - RNAMultipleProfileHmmDirectoryFmt + - BLAST6Format + - LSMatFormat + - MultiplexedFastaQualDirFmt + - RNAFASTAFormat + - NewickFormat + - MAGSequencesDirFmt - DiamondDatabaseFileFmt - - Kraken2DBReportFormat - - MultiFASTADirectoryFormat - - CasavaOneEightLanelessPerSampleDirFmt - - Kraken2OutputDirectoryFormat - - MixedCaseAlignedRNAFASTAFormat - - PairedEndFastqManifestPhred33 - - SeedOrthologDirFmt - - DNAFASTAFormat - - Kraken2DBDirectoryFormat - - PlacementsFormat + - OrthologAnnotationDirFmt - DeblurStatsFmt - - PairedDNASequencesDirectoryFormat - - AlphaDiversityFormat - - OrdinationFormat + - BAMDirFmt - BIOMV100Format - - MultiMAGSequencesDirFmt - - AlignedProteinFASTAFormat - - EMPPairedEndDirFmt - - PairedEndFastqManifestPhred64 - - OrthologAnnotationDirFmt - - UchimeStatsFmt - - LSMatFormat - - PairedRNASequencesDirectoryFormat - - PairedEndFastqManifestPhred33V2 - - MultiBowtie2IndexDirFmt - - DifferentialFormat - - ImmutableMetadataFormat - - Bowtie2IndexDirFmt - - AlignedDNAFASTAFormat - - PairedEndFastqManifestPhred64V2 - - ContigSequencesDirFmt - - EMPPairedEndCasavaDirFmt - - EggnogProteinSequencesDirFmt - - CasavaOneEightSingleLanePerSampleDirFmt - - MixedCaseDNAFASTAFormat - - BooleanSeriesFormat + - AlignedRNAFASTAFormat + - ProteinsDirectoryFormat + - MAGtoContigsFormat + - DecontamScoreFormat + - SingleEndFastqManifestPhred33V2 - EMPSingleEndDirFmt - ProteinSingleProfileHmmDirectoryFmt - ProbabilitiesFormat - - DADA2StatsFormat + - MixedCaseRNAFASTAFormat + - ProteinFASTAFormat + - MultiBAMDirFmt + - BIOMV210Format + - Kraken2DBReportFormat - ImportanceFormat - - GenesDirectoryFormat - - SeppReferenceDirFmt + - SeedOrthologDirFmt - SingleEndFastqManifestPhred64V2 - - SILVATaxonomyFormat - - BrackenDBDirectoryFormat - - BIOMV210Format + - EMPPairedEndDirFmt + - ArtificialGroupingFormat - ProteinMultipleProfileHmmDirectoryFmt - - QualityFilterStatsFmt - - MixedCaseAlignedDNAFASTAFormat - - NCBITaxonomyDirFmt - - Kraken2ReportDirectoryFormat - - BAMDirFmt - - BLAST6Format - - ProteinsDirectoryFormat - - NewickFormat - - SingleLanePerSampleSingleEndFastqDirFmt - - DataLoafPackageDirFmt - - RNAFASTAFormat - - ProcrustesStatisticsFmt + - SampleEstimatorDirFmt + - SingleEndFastqManifestPhred33 + - Kraken2OutputDirectoryFormat + - EggnogProteinSequencesDirFmt + - MixedCaseAlignedRNAFASTAFormat + - DNAFASTAFormat + - EMPSingleEndCasavaDirFmt + - OrdinationFormat - DNASingleProfileHmmDirectoryFmt - SingleLanePerSamplePairedEndFastqDirFmt + - PairedDNASequencesDirectoryFormat + - ImmutableMetadataFormat + - AlphaDiversityFormat + - SingleEndFastqManifestPhred64 + - AlignedProteinFASTAFormat + - GenesDirectoryFormat + - DADA2BaseTransitionStatsFormat - TaxonomicClassiferTemporaryPickleDirFmt - - MAGtoContigsFormat - - ArtificialGroupingFormat - - MultiBAMDirFmt + - SILVATaxonomyFormat + - EMPPairedEndCasavaDirFmt + - DNAMultipleProfileHmmDirectoryFmt + - BLASTDBDirFmtV5 + - PlacementsFormat + - MultiFASTADirectoryFormat + - CasavaOneEightLanelessPerSampleDirFmt + - PairedRNASequencesDirectoryFormat + - BooleanSeriesFormat + - SRAMetadataFormat + - PairedEndFastqManifestPhred33 + - RNASingleProfileHmmDirectoryFmt + - DifferentialFormat + - GenomeSequencesDirectoryFormat + - ProcrustesStatisticsFmt + - MultiMAGSequencesDirFmt + - AlignedDNAFASTAFormat + - PairedEndFastqManifestPhred64 + - DADA2StatsFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - TableJSONLFileFormat + - MixedCaseDNAFASTAFormat + - PredictionsFormat + - Kraken2ReportDirectoryFormat + - SeppReferenceDirFmt + - PairedEndFastqManifestPhred33V2 + - LociDirectoryFormat + - Bowtie2IndexDirFmt + - UchimeStatsFmt + - MultiBowtie2IndexDirFmt + - ErrorCorrectionDetailsFmt + - NCBITaxonomyDirFmt + - QualityFilterStatsFmt + - Kraken2DBDirectoryFormat + - DataLoafPackageDirFmt + - SingleLanePerSampleSingleEndFastqDirFmt + - PairedEndFastqManifestPhred64V2 - FirstDifferencesFormat - KaijuDBDirectoryFormat - - DecontamScoreFormat - - LociDirectoryFormat - - DNAMultipleProfileHmmDirectoryFmt - - TableJSONLFileFormat - - AlignedRNAFASTAFormat - - SingleEndFastqManifestPhred33 - - BLASTDBDirFmtV5 - - MAGSequencesDirFmt - - MixedCaseRNAFASTAFormat - - GenomeSequencesDirectoryFormat - - SingleEndFastqManifestPhred33V2 - - SampleEstimatorDirFmt - - RNASingleProfileHmmDirectoryFmt - - ProteinFASTAFormat - - ErrorCorrectionDetailsFmt - - EMPSingleEndCasavaDirFmt - - MultiplexedFastaQualDirFmt - - SingleEndFastqManifestPhred64 - - EggnogRefDirFmt - - SILVATaxidMapFormat - - MultiplexedPairedEndBarcodeInSequenceDirFmt - - RNAMultipleProfileHmmDirectoryFmt </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>