Mercurial > repos > q2d2 > qiime2_core__tools__import
changeset 7:65ea76686e11 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit b1fccfb38b4873cd4699743033449014a2978e7d
| author | q2d2 |
|---|---|
| date | Mon, 05 May 2025 19:06:07 +0000 |
| parents | 8a0db69428c7 |
| children | |
| files | qiime2_core__tools__import.xml |
| diffstat | 1 files changed, 188 insertions(+), 131 deletions(-) [+] |
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--- a/qiime2_core__tools__import.xml Wed Oct 30 20:00:15 2024 +0000 +++ b/qiime2_core__tools__import.xml Mon May 05 19:06:07 2025 +0000 @@ -1,22 +1,22 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2024, QIIME 2 development team. +Copyright (c) 2025, 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: 2024.10.0) + q2galaxy (version: 2025.4.0) for: - qiime2 (version: 2024.10.1) + qiime2 (version: 2025.4.0) --> -<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2024.10.0+dist.h3d8a7e27" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2025.4.0+dist.h1147124e" 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:2024.10</container> + <container type="docker">quay.io/qiime2/amplicon:2025.4</container> </requirements> <command>q2galaxy run tools import '$inputs'</command> <configfiles> @@ -81,6 +81,7 @@ <option value="EMPPairedEndSequences">EMPPairedEndSequences</option> <option value="EMPSingleEndSequences">EMPSingleEndSequences</option> <option value="ErrorCorrectionDetails">ErrorCorrectionDetails</option> + <option value="FeatureData__ob__ANCOMBC2Output__cb__">FeatureData[ANCOMBC2Output]</option> <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> @@ -550,6 +551,47 @@ </when> </conditional> </when> + <when value="FeatureData__ob__ANCOMBC2Output__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="ANCOMBC2OutputDirFmt" selected="true">ANCOMBC2 Output Directory Format</option> + </param> + <when value="ANCOMBC2OutputDirFmt"> + <section name="import_lfc" expanded="true" title="Import lfc"> + <param name="name" type="text" value="lfc.jsonl" 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 TableJSONLFileFormat. See the documentation below for more information."/> + </section> + <section name="import_se" expanded="true" title="Import se"> + <param name="name" type="text" value="se.jsonl" 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 TableJSONLFileFormat. See the documentation below for more information."/> + </section> + <section name="import_W" expanded="true" title="Import W"> + <param name="name" type="text" value="W.jsonl" 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 TableJSONLFileFormat. See the documentation below for more information."/> + </section> + <section name="import_p" expanded="true" title="Import p"> + <param name="name" type="text" value="p.jsonl" 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 TableJSONLFileFormat. See the documentation below for more information."/> + </section> + <section name="import_q" expanded="true" title="Import q"> + <param name="name" type="text" value="q.jsonl" 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 TableJSONLFileFormat. See the documentation below for more information."/> + </section> + <section name="import_diff" expanded="true" title="Import diff"> + <param name="name" type="text" value="diff.jsonl" 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 TableJSONLFileFormat. See the documentation below for more information."/> + </section> + <section name="import_passed_ss" expanded="true" title="Import passed_ss"> + <param name="name" type="text" value="passed_ss.jsonl" 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 TableJSONLFileFormat. See the documentation below for more information."/> + </section> + <section name="import_structural_zeros" expanded="true" title="Import structural_zeros"> + <param name="name" type="text" value="structural-zeros.jsonl" 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 TableJSONLFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="FeatureData__ob__AlignedProteinSequence__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -779,14 +821,14 @@ <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__"> + <section name="import_outputs" expanded="true" title="Import outputs"> + <conditional name="__q2galaxy__GUI__cond__outputs__"> <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"/> + <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)$" collection_type="list"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -800,8 +842,8 @@ </when> <when value="individual"> <repeat name="elements" min="1" title="Add Elements"> - <param name="name" type="text" help="Filename to import the data as. Must match regex: .+output\.(txt|tsv)$"> - <validator type="regex" message="This filename doesn't match the regex.">.+output\.(txt|tsv)$</validator> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.output\.(txt|tsv)$"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.output\.(txt|tsv)$</validator> </param> <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2OutputFormat. See the documentation below for more information."/> </repeat> @@ -824,7 +866,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" help="This data should be formatted as a Kraken2ReportFormat. See the documentation below for more information. Elements must match regex: .+report\.(txt|tsv)$" collection_type="list"/> + <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)$" collection_type="list"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -838,8 +880,8 @@ </when> <when value="individual"> <repeat name="elements" min="1" title="Add Elements"> - <param name="name" type="text" help="Filename to import the data as. Must match regex: .+report\.(txt|tsv)$"> - <validator type="regex" message="This filename doesn't match the regex.">.+report\.(txt|tsv)$</validator> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.report\.(txt|tsv)$"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.report\.(txt|tsv)$</validator> </param> <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2ReportFormat. See the documentation below for more information."/> </repeat> @@ -2378,14 +2420,14 @@ <option value="Kraken2OutputDirectoryFormat" selected="true">Kraken2 Output Directory Format</option> </param> <when value="Kraken2OutputDirectoryFormat"> - <section name="import_reports" expanded="true" title="Import reports"> - <conditional name="__q2galaxy__GUI__cond__reports__"> + <section name="import_outputs" expanded="true" title="Import outputs"> + <conditional name="__q2galaxy__GUI__cond__outputs__"> <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> <option value="collection" selected="true">Use collection to import</option> <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" help="This data should be formatted as a Kraken2OutputFormat. See the documentation below for more information. Elements must match regex: .+output\.(txt|tsv)$" collection_type="list"/> + <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)$" collection_type="list"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -2399,8 +2441,8 @@ </when> <when value="individual"> <repeat name="elements" min="1" title="Add Elements"> - <param name="name" type="text" help="Filename to import the data as. Must match regex: .+output\.(txt|tsv)$"> - <validator type="regex" message="This filename doesn't match the regex.">.+output\.(txt|tsv)$</validator> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.output\.(txt|tsv)$"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.output\.(txt|tsv)$</validator> </param> <param name="data" type="data" format="data" help="This data should be formatted as a Kraken2OutputFormat. See the documentation below for more information."/> </repeat> @@ -2423,7 +2465,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" help="This data should be formatted as a Kraken2ReportFormat. See the documentation below for more information. Elements must match regex: .+report\.(txt|tsv)$" collection_type="list"/> + <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)$" collection_type="list"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -2437,8 +2479,8 @@ </when> <when value="individual"> <repeat name="elements" min="1" title="Add Elements"> - <param name="name" type="text" help="Filename to import the data as. Must match regex: .+report\.(txt|tsv)$"> - <validator type="regex" message="This filename doesn't match the regex.">.+report\.(txt|tsv)$</validator> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.report\.(txt|tsv)$"> + <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> @@ -3300,23 +3342,6 @@ -------- These formats have documentation available. -HeaderlessTSVTaxonomyFormat -*************************** -Format for a 2+ column TSV file without a header. - -This format supports comment lines starting with #, and blank lines. - - -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. - TSVTaxonomyFormat ***************** Format for a 2+ column TSV file with an expected minimal header. @@ -3332,6 +3357,20 @@ of data. +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 @@ -3342,6 +3381,16 @@ * `xyz.fastq.gz` is `xyz` * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001` +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. @@ -3376,120 +3425,128 @@ - Each sequence must be DNA and cannot be empty. -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". - FastqGzFormat ************* A gzipped fastq file. +HeaderlessTSVTaxonomyFormat +*************************** +Format for a 2+ column TSV file without a header. + +This format supports comment lines starting with #, and blank lines. + + +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 + Additional formats without documentation: ***************************************** - - DifferentialFormat - - Kraken2OutputDirectoryFormat - - MultiBAMDirFmt - - FirstDifferencesFormat - - SingleEndFastqManifestPhred33V2 - - AlignedDNAFASTAFormat - - EggnogProteinSequencesDirFmt - - SingleEndFastqManifestPhred64 - - MAGSequencesDirFmt - - ProteinSingleProfileHmmDirectoryFmt - - MixedCaseDNAFASTAFormat - - ImportanceFormat - - ImmutableMetadataFormat - - ErrorCorrectionDetailsFmt - - ArtificialGroupingFormat - - OrthologAnnotationDirFmt - - DecontamScoreFormat - - SingleEndFastqManifestPhred64V2 - - QualityFilterStatsFmt - - DeblurStatsFmt - - OrdinationFormat - - PairedEndFastqManifestPhred33 - - LSMatFormat - - ProteinMultipleProfileHmmDirectoryFmt - - SingleLanePerSamplePairedEndFastqDirFmt - - CasavaOneEightLanelessPerSampleDirFmt - - Kraken2DBDirectoryFormat + - BooleanSeriesFormat - MixedCaseAlignedDNAFASTAFormat - - MultiplexedFastaQualDirFmt - - BooleanSeriesFormat - - BLASTDBDirFmtV5 - - DADA2StatsFormat + - ProcrustesStatisticsFmt + - BAMDirFmt - BLAST6Format - - KaijuDBDirectoryFormat - - MultiFASTADirectoryFormat - - PairedEndFastqManifestPhred64 - - MAGtoContigsFormat - - DNASingleProfileHmmDirectoryFmt + - PlacementsFormat + - SingleLanePerSampleSingleEndFastqDirFmt - RNAFASTAFormat - - ProbabilitiesFormat + - SILVATaxidMapFormat + - EMPPairedEndDirFmt + - EggnogProteinSequencesDirFmt + - SingleLanePerSamplePairedEndFastqDirFmt - SampleEstimatorDirFmt - - MultiplexedPairedEndBarcodeInSequenceDirFmt + - DeblurStatsFmt + - EggnogRefDirFmt + - BIOMV100Format + - MAGtoContigsFormat + - MultiBAMDirFmt + - QualityFilterStatsFmt + - NewickFormat + - EMPSingleEndCasavaDirFmt + - ImportanceFormat + - OrdinationFormat + - Kraken2ReportDirectoryFormat + - AlignedRNAFASTAFormat + - SingleEndFastqManifestPhred33 + - DiamondDatabaseFileFmt + - FirstDifferencesFormat + - LSMatFormat + - MixedCaseRNAFASTAFormat + - ArtificialGroupingFormat + - SingleEndFastqManifestPhred33V2 + - EMPPairedEndCasavaDirFmt + - TaxonomicClassiferTemporaryPickleDirFmt + - ProteinSingleProfileHmmDirectoryFmt + - MAGSequencesDirFmt - TableJSONLFileFormat + - ProteinFASTAFormat + - ProbabilitiesFormat + - SingleEndFastqManifestPhred64 - LociDirectoryFormat - - PairedEndFastqManifestPhred33V2 - - UchimeStatsFmt - - ProcrustesStatisticsFmt + - SingleEndFastqManifestPhred64V2 + - ProteinMultipleProfileHmmDirectoryFmt + - MultiFASTADirectoryFormat + - CasavaOneEightLanelessPerSampleDirFmt + - BLASTDBDirFmtV5 + - DecontamScoreFormat + - MixedCaseAlignedRNAFASTAFormat + - PairedEndFastqManifestPhred33 + - DNAFASTAFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - Kraken2OutputDirectoryFormat + - ProteinsDirectoryFormat + - Kraken2DBReportFormat + - GenomeSequencesDirectoryFormat + - PairedDNASequencesDirectoryFormat + - BIOMV210Format - AlphaDiversityFormat + - DNASingleProfileHmmDirectoryFmt - MultiMAGSequencesDirFmt - - SeppReferenceDirFmt - - DNAMultipleProfileHmmDirectoryFmt - - PredictionsFormat - - PlacementsFormat - - NewickFormat + - AlignedProteinFASTAFormat + - GenesDirectoryFormat + - PairedEndFastqManifestPhred64 + - PairedRNASequencesDirectoryFormat + - PairedEndFastqManifestPhred33V2 + - MultiBowtie2IndexDirFmt + - SILVATaxonomyFormat - BrackenDBDirectoryFormat - - GenomeSequencesDirectoryFormat - - EggnogRefDirFmt - - PairedEndFastqManifestPhred64V2 - - AlignedRNAFASTAFormat - - EMPSingleEndDirFmt - - TaxonomicClassiferTemporaryPickleDirFmt - - Kraken2ReportDirectoryFormat - - MultiBowtie2IndexDirFmt - - SILVATaxidMapFormat - - CasavaOneEightSingleLanePerSampleDirFmt - - RNASingleProfileHmmDirectoryFmt - - MixedCaseRNAFASTAFormat + - DifferentialFormat + - MultiplexedFastaQualDirFmt + - DADA2StatsFormat + - Kraken2DBDirectoryFormat - Bowtie2IndexDirFmt - SeedOrthologDirFmt - - DiamondDatabaseFileFmt - - ProteinFASTAFormat - - EMPPairedEndDirFmt + - AlignedDNAFASTAFormat + - PairedEndFastqManifestPhred64V2 + - RNASingleProfileHmmDirectoryFmt - ContigSequencesDirFmt - - Kraken2DBReportFormat - - RNAMultipleProfileHmmDirectoryFmt - - SILVATaxonomyFormat - - BIOMV100Format + - ImmutableMetadataFormat + - SeppReferenceDirFmt + - CasavaOneEightSingleLanePerSampleDirFmt + - NCBITaxonomyDirFmt + - MixedCaseDNAFASTAFormat + - ErrorCorrectionDetailsFmt - DataLoafPackageDirFmt - - MixedCaseAlignedRNAFASTAFormat - - EMPSingleEndCasavaDirFmt - - DNAFASTAFormat - - ProteinsDirectoryFormat - - PairedDNASequencesDirectoryFormat - - NCBITaxonomyDirFmt - - BIOMV210Format - - AlignedProteinFASTAFormat - - SingleLanePerSampleSingleEndFastqDirFmt - - EMPPairedEndCasavaDirFmt - - BAMDirFmt - - PairedRNASequencesDirectoryFormat - - GenesDirectoryFormat - - SingleEndFastqManifestPhred33 + - OrthologAnnotationDirFmt + - PredictionsFormat + - RNAMultipleProfileHmmDirectoryFmt + - DNAMultipleProfileHmmDirectoryFmt + - UchimeStatsFmt + - EMPSingleEndDirFmt + - KaijuDBDirectoryFormat </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>