Mercurial > repos > q2d2 > qiime2_core__tools__import
changeset 4:9dbdf05beaa9 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 21:28:32 +0000 |
| parents | 10447a4b0cc3 |
| children | |
| files | qiime2_core__tools__import.xml test-data/YY/YY_S49_R1_001.fastq.gz test-data/YY/YY_S49_R2_001.fastq.gz |
| diffstat | 3 files changed, 694 insertions(+), 152 deletions(-) [+] |
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--- a/qiime2_core__tools__import.xml Thu Feb 01 21:22:08 2024 +0000 +++ b/qiime2_core__tools__import.xml Thu Apr 25 21:28:32 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 import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.3" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2024.2.1+dist.he188c3c2" profile="22.05" license="BSD-3-Clause"> <description>Import data into 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 import '$inputs'</command> + <command>q2galaxy run tools import '$inputs'</command> <configfiles> <configfile name="inputs"><% # This is an exercise in cheating the Cheetah @@ -60,6 +60,7 @@ <conditional name="import_root"> <param name="type" type="select" label="Type of data to import:"> <option value="None">Select a QIIME 2 type to import.</option> + <option value="BLASTDB">BLASTDB</option> <option value="Bowtie2Index">Bowtie2Index</option> <option value="DeblurStats">DeblurStats</option> <option value="DistanceMatrix">DistanceMatrix</option> @@ -78,8 +79,11 @@ <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> @@ -87,6 +91,10 @@ <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> @@ -98,18 +106,25 @@ <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> @@ -118,6 +133,63 @@ <option value="UchimeStats">UchimeStats</option> </param> <when value="None"/> + <when value="BLASTDB"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="BLASTDBDirFmtV5" selected="true">BLASTDB Directory Format V5</option> + </param> + <when value="BLASTDBDirFmtV5"> + <section name="import_idx1" expanded="true" title="Import idx1"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.ndb"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.ndb</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/> + </section> + <section name="import_idx2" expanded="true" title="Import idx2"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.nhr"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.nhr</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/> + </section> + <section name="import_idx3" expanded="true" title="Import idx3"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.nin"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.nin</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/> + </section> + <section name="import_idx4" expanded="true" title="Import idx4"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.not"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.not</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/> + </section> + <section name="import_idx5" expanded="true" title="Import idx5"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.nsq"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.nsq</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/> + </section> + <section name="import_idx6" expanded="true" title="Import idx6"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.ntf"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.ntf</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/> + </section> + <section name="import_idx7" expanded="true" title="Import idx7"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.nto"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.nto</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/> + </section> + <section name="import_idx8" expanded="true" title="Import idx8"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.njs"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.njs</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a BLASTDBFileFmtV5. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="Bowtie2Index"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -358,7 +430,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FrictionlessCSVFileFormat. See the documentation below for more information. Elements must match regex: .+\.csv"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FrictionlessCSVFileFormat. See the documentation below for more information. Elements must match regex: .+\.csv" 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> @@ -480,11 +552,38 @@ </when> </conditional> </when> + <when value="FeatureData__ob__SILVATaxidMap__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="SILVATaxidMapFormat" selected="true">SILVA Taxid Map Format</option> + </param> + <when value="SILVATaxidMapFormat"> + <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 SILVATaxidMapFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureData__ob__SILVATaxonomy__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="SILVATaxonomyFormat" selected="true">SILVA Taxonomy Format</option> + </param> + <when value="SILVATaxonomyFormat"> + <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 SILVATaxonomyFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="FeatureData__ob__Sequence__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> <option value="DNAFASTAFormat" selected="true">DNAFASTA Format</option> <option value="MixedCaseDNAFASTAFormat" selected="false">Mixed Case DNAFASTA Format</option> + <option value="RNAFASTAFormat" selected="false">RNAFASTA Format</option> </param> <when value="DNAFASTAFormat"> <section name="import" expanded="true" title="Import"> @@ -498,6 +597,12 @@ <param name="data" type="data" format="data" help="This data should be formatted as a MixedCaseDNAFASTAFormat. See the documentation below for more information."/> </section> </when> + <when value="RNAFASTAFormat"> + <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 RNAFASTAFormat. See the documentation below for more information."/> + </section> + </when> </conditional> </when> <when value="FeatureData__ob__Taxonomy__cb__"> @@ -527,6 +632,19 @@ </when> </conditional> </when> + <when value="FeatureMap__ob__MAGtoContigs__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="MAGtoContigsFormat" selected="true">MA Gto Contigs Format</option> + </param> + <when value="MAGtoContigsFormat"> + <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 MAGtoContigsFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="FeatureTable__ob__Balance__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -667,6 +785,158 @@ </when> </conditional> </when> + <when value="GenomeData__ob__BLAST6__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="SeedOrthologDirFmt" selected="true">Seed Ortholog Directory Format</option> + </param> + <when value="SeedOrthologDirFmt"> + <section name="import_seed_orthologs" expanded="true" title="Import seed_orthologs"> + <conditional name="__q2galaxy__GUI__cond__seed_orthologs__"> + <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 OrthologFileFmt. See the documentation below for more information. Elements must match regex: .*\..*\.seed_orthologs" 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> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </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: .*\..*\.seed_orthologs"> + <validator type="regex" message="This filename doesn't match the regex.">.*\..*\.seed_orthologs</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> + <when value="GenomeData__ob__Genes__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="GenesDirectoryFormat" selected="true">Genes Directory Format</option> + </param> + <when value="GenesDirectoryFormat"> + <section name="import_genes" expanded="true" title="Import genes"> + <conditional name="__q2galaxy__GUI__cond__genes__"> + <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 DNAFASTAFormat. See the documentation below for more information. Elements must match regex: (.*\_)?genes[0-9]*\.(fa|fna|fasta)$" collection_type="list"/> + <conditional name="__q2galaxy__GUI__cond__add_ext__"> + <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> + <option value="no">No, use element identifiers as is</option> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="individual"> + <repeat name="elements" min="1" title="Add Elements"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: (.*\_)?genes[0-9]*\.(fa|fna|fasta)$"> + <validator type="regex" message="This filename doesn't match the regex.">(.*\_)?genes[0-9]*\.(fa|fna|fasta)$</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> + <when value="GenomeData__ob__Loci__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="LociDirectoryFormat" selected="true">Loci Directory Format</option> + </param> + <when value="LociDirectoryFormat"> + <section name="import_loci" expanded="true" title="Import loci"> + <conditional name="__q2galaxy__GUI__cond__loci__"> + <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> + <option value="collection" selected="true">Use collection to import</option> + <option value="individual">Associate individual files</option> + </param> + <when value="collection"> + <param name="elements" type="data_collection" help="This data should be formatted as a GFF3Format. See the documentation below for more information. Elements must match regex: (.*\_)?loci[0-9]*\.gff$" 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> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </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: (.*\_)?loci[0-9]*\.gff$"> + <validator type="regex" message="This filename doesn't match the regex.">(.*\_)?loci[0-9]*\.gff$</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a GFF3Format. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> + <when value="GenomeData__ob__Proteins__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="ProteinsDirectoryFormat" selected="true">Proteins Directory Format</option> + </param> + <when value="ProteinsDirectoryFormat"> + <section name="import_proteins" expanded="true" title="Import proteins"> + <conditional name="__q2galaxy__GUI__cond__proteins__"> + <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 ProteinFASTAFormat. See the documentation below for more information. Elements must match regex: (.*\_)?proteins[0-9]*\.(fa|faa|fasta)$" collection_type="list"/> + <conditional name="__q2galaxy__GUI__cond__add_ext__"> + <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> + <option value="no">No, use element identifiers as is</option> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="individual"> + <repeat name="elements" min="1" title="Add Elements"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: (.*\_)?proteins[0-9]*\.(fa|faa|fasta)$"> + <validator type="regex" message="This filename doesn't match the regex.">(.*\_)?proteins[0-9]*\.(fa|faa|fasta)$</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a ProteinFASTAFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> <when value="Hierarchy"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -840,6 +1110,44 @@ </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:"> + <option value="BAMDirFmt" selected="true">BAM Directory Format</option> + </param> + <when value="BAMDirFmt"> + <section name="import_bams" expanded="true" title="Import bams"> + <conditional name="__q2galaxy__GUI__cond__bams__"> + <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 BAMFormat. See the documentation below for more information. Elements must match regex: .+\.bam" 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> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </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: .+\.bam"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.bam</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a BAMFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> <when value="SampleData__ob__AlphaDiversity__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -866,6 +1174,44 @@ </when> </conditional> </when> + <when value="SampleData__ob__BLAST6__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="SeedOrthologDirFmt" selected="true">Seed Ortholog Directory Format</option> + </param> + <when value="SeedOrthologDirFmt"> + <section name="import_seed_orthologs" expanded="true" title="Import seed_orthologs"> + <conditional name="__q2galaxy__GUI__cond__seed_orthologs__"> + <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 OrthologFileFmt. See the documentation below for more information. Elements must match regex: .*\..*\.seed_orthologs" 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> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </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: .*\..*\.seed_orthologs"> + <validator type="regex" message="This filename doesn't match the regex.">.*\..*\.seed_orthologs</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a OrthologFileFmt. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> <when value="SampleData__ob__BooleanSeries__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -892,6 +1238,44 @@ </when> </conditional> </when> + <when value="SampleData__ob__Contigs__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="ContigSequencesDirFmt" selected="true">Contig Sequences Directory Format</option> + </param> + <when value="ContigSequencesDirFmt"> + <section name="import_sequences" expanded="true" title="Import sequences"> + <conditional name="__q2galaxy__GUI__cond__sequences__"> + <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 DNAFASTAFormat. See the documentation below for more information. Elements must match regex: [^\.].+_contigs.(fasta|fa)$" 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> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </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: [^\.].+_contigs.(fasta|fa)$"> + <validator type="regex" message="This filename doesn't match the regex.">[^\.].+_contigs.(fasta|fa)$</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> <when value="SampleData__ob__DADA2Stats__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -939,7 +1323,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz" 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> @@ -970,7 +1354,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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> @@ -1001,7 +1385,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+\.fastq\.gz" 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> @@ -1056,7 +1440,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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> @@ -1095,7 +1479,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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> @@ -1128,6 +1512,163 @@ </when> </conditional> </when> + <when value="SampleData__ob__MAGs__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="MultiFASTADirectoryFormat" selected="false">Multi FASTA Directory Format</option> + <option value="MultiMAGSequencesDirFmt" selected="true">Multi MAG Sequences Directory Format</option> + </param> + <when value="MultiFASTADirectoryFormat"> + <section name="import_sequences" expanded="true" title="Import sequences"> + <conditional name="__q2galaxy__GUI__cond__sequences__"> + <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 DNAFASTAFormat. See the documentation below for more information. Elements must match regex: .+\.(fa|fasta)$" collection_type="list"/> + <conditional name="__q2galaxy__GUI__cond__add_ext__"> + <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> + <option value="no">No, use element identifiers as is</option> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="individual"> + <repeat name="elements" min="1" title="Add Elements"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.(fa|fasta)$"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.(fa|fasta)$</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + <when value="MultiMAGSequencesDirFmt"> + <section name="import_sequences" expanded="true" title="Import sequences"> + <conditional name="__q2galaxy__GUI__cond__sequences__"> + <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism"> + <option value="collection" selected="true">Use collection to import</option> + <option value="individual">Associate individual files</option> + </param> + <when value="collection"> + <param name="elements" type="data_collection" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information. Elements must match regex: .+\.(fa|fasta)$" 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> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </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: .+\.(fa|fasta)$"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.(fa|fasta)$</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + <section name="import_manifest" expanded="true" title="Import manifest"> + <param name="name" type="text" value="MANIFEST" 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 MultiMAGManifestFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="SampleData__ob__MultiAlignmentMap__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="MultiBAMDirFmt" selected="true">Multi BAM Directory Format</option> + </param> + <when value="MultiBAMDirFmt"> + <section name="import_bams" expanded="true" title="Import bams"> + <conditional name="__q2galaxy__GUI__cond__bams__"> + <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 BAMFormat. See the documentation below for more information. Elements must match regex: .+\/.+\.bam" 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> + <option value="yes">Yes, append an extension</option> + </param> + <when value="yes"> + <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/> + </when> + <when value="no"/> + </conditional> + </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: .+\/.+\.bam"> + <validator type="regex" message="This filename doesn't match the regex.">.+\/.+\.bam</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a BAMFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + </conditional> + </when> + <when value="SampleData__ob__MultiBowtie2Index__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="MultiBowtie2IndexDirFmt" selected="true">Multi Bowtie2 Index Directory Format</option> + </param> + <when value="MultiBowtie2IndexDirFmt"> + <section name="import_idx1" expanded="true" title="Import idx1"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+(?‹!\.rev)\.1\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+(?<!\.rev)\.1\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_idx2" expanded="true" title="Import idx2"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+(?‹!\.rev)\.2\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+(?<!\.rev)\.2\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_ref3" expanded="true" title="Import ref3"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.3\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.3\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_ref4" expanded="true" title="Import ref4"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.4\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.4\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_rev1" expanded="true" title="Import rev1"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.rev\.1\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.rev\.1\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_rev2" expanded="true" title="Import rev2"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.rev\.2\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.rev\.2\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="SampleData__ob__PairedEndSequencesWithQuality__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -1147,7 +1688,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz" 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> @@ -1178,7 +1719,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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> @@ -1233,7 +1774,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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> @@ -1313,7 +1854,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz" 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> @@ -1344,7 +1885,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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> @@ -1375,7 +1916,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+\.fastq\.gz" 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> @@ -1430,7 +1971,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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> @@ -1469,7 +2010,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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> @@ -1522,7 +2063,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz" 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> @@ -1555,6 +2096,51 @@ </when> </conditional> </when> + <when value="SampleData__ob__SingleBowtie2Index__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="Bowtie2IndexDirFmt" selected="true">Bowtie2 Index Directory Format</option> + </param> + <when value="Bowtie2IndexDirFmt"> + <section name="import_idx1" expanded="true" title="Import idx1"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+(?‹!\.rev)\.1\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+(?<!\.rev)\.1\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_idx2" expanded="true" title="Import idx2"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+(?‹!\.rev)\.2\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+(?<!\.rev)\.2\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_ref3" expanded="true" title="Import ref3"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.3\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.3\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_ref4" expanded="true" title="Import ref4"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.4\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.4\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_rev1" expanded="true" title="Import rev1"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.rev\.1\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.rev\.1\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + <section name="import_rev2" expanded="true" title="Import rev2"> + <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.rev\.2\.bt2l?"> + <validator type="regex" message="This filename doesn't match the regex.">.+\.rev\.2\.bt2l?</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a Bowtie2IndexFileFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> <when value="SampleData__ob__TrueTargets__cb__"> <conditional name="__q2galaxy__GUI__cond__format__"> <param name="format" type="select" label="QIIME 2 file format to import from:"> @@ -1658,64 +2244,6 @@ <outputs> <data name="imported_data" format="qza" from_work_dir="imported_data.qza"/> </outputs> - <tests> - <test> - <conditional name="import_root"> - <param name="type" value="SampleData__ob__PairedEndSequencesWithQuality__cb__"/> - <conditional name="__q2galaxy__GUI__cond__format__"> - <param name="format" value="CasavaOneEightLanelessPerSampleDirFmt"/> - <section name="import_sequences"> - <conditional name="__q2galaxy__GUI__cond__sequences__"> - <param name="__q2galaxy__GUI__select__picker__" value="collection"/> - <param name="elements"> - <collection type="list"> - <element name="YY_S49_R1_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R1_001.fastq.gz" /> - <element name="YY_S49_R2_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R2_001.fastq.gz" /> - </collection> - </param> - <conditional name="__q2galaxy__GUI__cond__add_ext__"> - <param name="__q2galaxy__GUI__select__ext_pick__" value="yes"/> - <param name="ext" label="fastq.gz"/> - </conditional> - </conditional> - </section> - </conditional> - </conditional> - <output name="imported_data"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </output> - </test> - <test> - <conditional name="import_root"> - <param name="type" value="SampleData__ob__PairedEndSequencesWithQuality__cb__"/> - <conditional name="__q2galaxy__GUI__cond__format__"> - <param name="format" value="CasavaOneEightSingleLanePerSampleDirFmt"/> - <section name="import_sequences"> - <conditional name="__q2galaxy__GUI__cond__sequences__"> - <param name="__q2galaxy__GUI__select__picker__" value="collection"/> - <param name="elements"> - <collection type="list"> - <element name="YY_S49_L001_R1_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R1_001.fastq.gz" /> - <element name="YY_S49_L001_R2_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R2_001.fastq.gz" /> - </collection> - </param> - <conditional name="__q2galaxy__GUI__cond__add_ext__"> - <param name="__q2galaxy__GUI__select__ext_pick__" value="yes"/> - <param name="ext" label="fastq.gz"/> - </conditional> - </conditional> - </section> - </conditional> - </conditional> - <output name="imported_data"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </output> - </test> - </tests> <help> QIIME 2: tools import ===================== @@ -1747,6 +2275,29 @@ -------- 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. + + +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` + +FastqGzFormat +************* + +A gzipped fastq file. + + QIIME1DemuxFormat ***************** QIIME 1 demultiplexed FASTA format. @@ -1796,89 +2347,80 @@ of data. -HeaderlessTSVTaxonomyFormat -*************************** -Format for a 2+ column TSV file without a header. - -This format supports comment lines starting with #, and blank lines. - - -FastqGzFormat -************* - -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: ***************************************** + - BAMDirFmt + - TaxonomicClassiferTemporaryPickleDirFmt + - BooleanSeriesFormat + - SingleEndFastqManifestPhred33 + - SampleEstimatorDirFmt + - MultiBAMDirFmt + - MAGtoContigsFormat + - MixedCaseAlignedRNAFASTAFormat + - PlacementsFormat + - PredictionsFormat + - SingleEndFastqManifestPhred64 + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - SingleLanePerSampleSingleEndFastqDirFmt + - AlignedProteinFASTAFormat + - PairedDNASequencesDirectoryFormat + - DataLoafPackageDirFmt + - ArtificialGroupingFormat + - PairedEndFastqManifestPhred33 + - DNAFASTAFormat + - EMPSingleEndDirFmt + - SingleLanePerSamplePairedEndFastqDirFmt + - PairedRNASequencesDirectoryFormat + - SeppReferenceDirFmt + - DifferentialFormat + - UchimeStatsFmt + - SILVATaxonomyFormat + - PairedEndFastqManifestPhred64 + - GenesDirectoryFormat + - MultiFASTADirectoryFormat + - EMPPairedEndDirFmt + - CasavaOneEightLanelessPerSampleDirFmt + - AlignedDNAFASTAFormat + - SILVATaxidMapFormat + - PairedEndFastqManifestPhred33V2 + - SingleEndFastqManifestPhred33V2 + - MixedCaseDNAFASTAFormat + - ProteinsDirectoryFormat + - MultiMAGSequencesDirFmt + - EMPSingleEndCasavaDirFmt + - QualityFilterStatsFmt + - LSMatFormat + - ImmutableMetadataFormat + - DeblurStatsFmt + - PairedEndFastqManifestPhred64V2 + - SingleEndFastqManifestPhred64V2 + - AlphaDiversityFormat + - MultiBowtie2IndexDirFmt + - EMPPairedEndCasavaDirFmt + - ImportanceFormat - FirstDifferencesFormat - MixedCaseAlignedDNAFASTAFormat - - SingleLanePerSamplePairedEndFastqDirFmt - - EMPPairedEndDirFmt - - ImmutableMetadataFormat - - PairedEndFastqManifestPhred64V2 - - DataLoafPackageDirFmt - - AlignedDNAFASTAFormat - - BIOMV100Format - - UchimeStatsFmt - - BLAST6Format - - PairedDNASequencesDirectoryFormat - - SingleEndFastqManifestPhred33V2 - - QualityFilterStatsFmt + - MultiplexedFastaQualDirFmt - DADA2StatsFormat - - AlignedProteinFASTAFormat - - MixedCaseRNAFASTAFormat - - PlacementsFormat - - NewickFormat - - PairedEndFastqManifestPhred64 + - OrdinationFormat + - CasavaOneEightSingleLanePerSampleDirFmt - ProteinFASTAFormat - RNAFASTAFormat - - BooleanSeriesFormat - - SingleEndFastqManifestPhred64 - - LSMatFormat - - DeblurStatsFmt - - ErrorCorrectionDetailsFmt - - MixedCaseDNAFASTAFormat - - TaxonomicClassiferTemporaryPickleDirFmt - - DNAFASTAFormat - - ProcrustesStatisticsFmt - - CasavaOneEightLanelessPerSampleDirFmt - - EMPSingleEndDirFmt - - DecontamScoreFormat - - OrdinationFormat - - SingleLanePerSampleSingleEndFastqDirFmt - - Bowtie2IndexDirFmt + - BIOMV100Format + - ContigSequencesDirFmt + - NewickFormat + - BLAST6Format + - LociDirectoryFormat - BIOMV210Format - - PairedEndFastqManifestPhred33V2 - - SampleEstimatorDirFmt - - EMPSingleEndCasavaDirFmt - - PairedRNASequencesDirectoryFormat - - EMPPairedEndCasavaDirFmt - - CasavaOneEightSingleLanePerSampleDirFmt - - SingleEndFastqManifestPhred64V2 - - MultiplexedFastaQualDirFmt - - DifferentialFormat - - AlphaDiversityFormat - - MultiplexedPairedEndBarcodeInSequenceDirFmt - - PairedEndFastqManifestPhred33 - - ArtificialGroupingFormat - ProbabilitiesFormat - - SeppReferenceDirFmt - - MixedCaseAlignedRNAFASTAFormat - - SingleEndFastqManifestPhred33 - - ImportanceFormat + - ErrorCorrectionDetailsFmt + - BLASTDBDirFmtV5 + - DecontamScoreFormat - AlignedRNAFASTAFormat - - PredictionsFormat + - ProcrustesStatisticsFmt + - SeedOrthologDirFmt + - Bowtie2IndexDirFmt + - MixedCaseRNAFASTAFormat </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation>