Mercurial > repos > q2d2 > qiime2_core__tools__import
changeset 0:1370f8d6e95b draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
|---|---|
| date | Mon, 29 Aug 2022 20:36:58 +0000 |
| parents | |
| children | 5d9a36073ed6 |
| files | qiime2_core__tools__import.xml test-data/.gitkeep |
| diffstat | 1 files changed, 1635 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2_core__tools__import.xml Mon Aug 29 20:36:58 2022 +0000 @@ -0,0 +1,1635 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2022, QIIME 2 development team. + +Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) +--> +<!-- +This tool was automatically generated by: + q2galaxy (version: 2022.8.1) +for: + qiime2 (version: 2022.8.1) +--> +<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2022.8.1+dist.h91e3be72.2" profile="22.05" license="BSD-3-Clause"> + <description>Import data into a QIIME 2 artifact</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <command>q2galaxy run tools import '$inputs'</command> + <configfiles> + <configfile name="inputs"><% +# This is an exercise in cheating the Cheetah +import json + +def expand_collection(collection): + # All of this work is just to extract the + # element identifier AND the path + return [dict(name=d.element_identifier, data=stringify(d)) + for d in collection] + +def stringify(obj): + if type(obj) is dict: + new = {} + for key, value in obj.items(): + if (key.startswith('__') and key.endswith('__') + and not key.startswith('__q2galaxy__')): + continue + new[str(key)] = stringify(value) + + return new + elif type(obj) is list: + return [stringify(x) for x in obj] + elif type(obj.__str__) is not type(object().__str__): # noqa + # There is an associated __str__ which will be used for + # "normal" templating, it looks like a strange check because + # it really is, we're testing for method-wrapper as a sign + # of non-implementation + return str(obj) + elif obj.is_collection: + return expand_collection(obj) + else: + raise NotImplementedError("Unrecognized situation in q2galaxy") + +dataset = self.getVar('import_root') +inputs = stringify(dataset) +write(json.dumps(inputs)) + %></configfile> + </configfiles> + <inputs> + <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="Bowtie2Index">Bowtie2Index</option> + <option value="DeblurStats">DeblurStats</option> + <option value="DistanceMatrix">DistanceMatrix</option> + <option value="EMPPairedEndSequences">EMPPairedEndSequences</option> + <option value="EMPSingleEndSequences">EMPSingleEndSequences</option> + <option value="ErrorCorrectionDetails">ErrorCorrectionDetails</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> + <option value="FeatureData__ob__BLAST6__cb__">FeatureData[BLAST6]</option> + <option value="FeatureData__ob__Differential__cb__">FeatureData[Differential]</option> + <option value="FeatureData__ob__Importance__cb__">FeatureData[Importance]</option> + <option value="FeatureData__ob__PairedEndRNASequence__cb__">FeatureData[PairedEndRNASequence]</option> + <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__Sequence__cb__">FeatureData[Sequence]</option> + <option value="FeatureData__ob__Taxonomy__cb__">FeatureData[Taxonomy]</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> + <option value="FeatureTable__ob__Frequency__cb__">FeatureTable[Frequency]</option> + <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="Hierarchy">Hierarchy</option> + <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option> + <option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option> + <option value="PCoAResults">PCoAResults</option> + <option value="Phylogeny__ob__Rooted__cb__">Phylogeny[Rooted]</option> + <option value="Phylogeny__ob__Unrooted__cb__">Phylogeny[Unrooted]</option> + <option value="Placements">Placements</option> + <option value="ProcrustesStatistics">ProcrustesStatistics</option> + <option value="QualityFilterStats">QualityFilterStats</option> + <option value="RawSequences">RawSequences</option> + <option value="SampleData__ob__AlphaDiversity__cb__">SampleData[AlphaDiversity]</option> + <option value="SampleData__ob__ArtificialGrouping__cb__">SampleData[ArtificialGrouping]</option> + <option value="SampleData__ob__BooleanSeries__cb__">SampleData[BooleanSeries]</option> + <option value="SampleData__ob__ClassifierPredictions__cb__">SampleData[ClassifierPredictions]</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__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__TrueTargets__cb__">SampleData[TrueTargets]</option> + <option value="SampleEstimator__ob__Classifier__cb__">SampleEstimator[Classifier]</option> + <option value="SampleEstimator__ob__Regressor__cb__">SampleEstimator[Regressor]</option> + <option value="SeppReferenceDatabase">SeppReferenceDatabase</option> + <option value="TaxonomicClassifier">TaxonomicClassifier</option> + <option value="UchimeStats">UchimeStats</option> + </param> + <when value="None"/> + <when value="Bowtie2Index"> + <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="DeblurStats"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="DeblurStatsFmt" selected="true">Deblur Stats Format</option> + </param> + <when value="DeblurStatsFmt"> + <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 DeblurStatsFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="DistanceMatrix"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="LSMatFormat" selected="true">LS Mat Format</option> + </param> + <when value="LSMatFormat"> + <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 LSMatFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="EMPPairedEndSequences"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="EMPPairedEndCasavaDirFmt" selected="false">EMP Paired End Casava Directory Format</option> + <option value="EMPPairedEndDirFmt" selected="true">EMP Paired End Directory Format</option> + </param> + <when value="EMPPairedEndCasavaDirFmt"> + <section name="import_forward" expanded="true" title="Import forward"> + <param name="name" type="text" value="Undetermined_S0_L001_R1_001.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + <section name="import_reverse" expanded="true" title="Import reverse"> + <param name="name" type="text" value="Undetermined_S0_L001_R2_001.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + <section name="import_barcodes" expanded="true" title="Import barcodes"> + <param name="name" type="text" value="Undetermined_S0_L001_I1_001.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + </when> + <when value="EMPPairedEndDirFmt"> + <section name="import_forward" expanded="true" title="Import forward"> + <param name="name" type="text" value="forward.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + <section name="import_reverse" expanded="true" title="Import reverse"> + <param name="name" type="text" value="reverse.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + <section name="import_barcodes" expanded="true" title="Import barcodes"> + <param name="name" type="text" value="barcodes.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="EMPSingleEndSequences"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="EMPSingleEndCasavaDirFmt" selected="false">EMP Single End Casava Directory Format</option> + <option value="EMPSingleEndDirFmt" selected="true">EMP Single End Directory Format</option> + </param> + <when value="EMPSingleEndCasavaDirFmt"> + <section name="import_sequences" expanded="true" title="Import sequences"> + <param name="name" type="text" value="Undetermined_S0_L001_R1_001.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + <section name="import_barcodes" expanded="true" title="Import barcodes"> + <param name="name" type="text" value="Undetermined_S0_L001_I1_001.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + </when> + <when value="EMPSingleEndDirFmt"> + <section name="import_sequences" expanded="true" title="Import sequences"> + <param name="name" type="text" value="sequences.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + <section name="import_barcodes" expanded="true" title="Import barcodes"> + <param name="name" type="text" value="barcodes.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="ErrorCorrectionDetails"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="ErrorCorrectionDetailsFmt" selected="true">Error Correction Details Format</option> + </param> + <when value="ErrorCorrectionDetailsFmt"> + <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 ErrorCorrectionDetailsFmt. 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:"> + <option value="AlignedProteinFASTAFormat" selected="true">Aligned Protein FASTA Format</option> + </param> + <when value="AlignedProteinFASTAFormat"> + <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 AlignedProteinFASTAFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureData__ob__AlignedRNASequence__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="AlignedRNAFASTAFormat" selected="true">Aligned RNAFASTA Format</option> + </param> + <when value="AlignedRNAFASTAFormat"> + <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 AlignedRNAFASTAFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureData__ob__AlignedSequence__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="AlignedDNAFASTAFormat" selected="true">Aligned DNAFASTA Format</option> + </param> + <when value="AlignedDNAFASTAFormat"> + <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 AlignedDNAFASTAFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureData__ob__BLAST6__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="BLAST6Format" selected="true">BLAST6 Format</option> + </param> + <when value="BLAST6Format"> + <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 BLAST6Format. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureData__ob__Differential__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="DifferentialFormat" selected="true">Differential Format</option> + </param> + <when value="DifferentialFormat"> + <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 DifferentialFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureData__ob__Importance__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="ImportanceFormat" selected="true">Importance Format</option> + </param> + <when value="ImportanceFormat"> + <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 ImportanceFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureData__ob__PairedEndRNASequence__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="PairedRNASequencesDirectoryFormat" selected="true">Paired RNA Sequences Directory Format</option> + </param> + <when value="PairedRNASequencesDirectoryFormat"> + <section name="import_left_rna_sequences" expanded="true" title="Import left_rna_sequences"> + <param name="name" type="text" value="left-rna-sequences.fasta" 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 RNAFASTAFormat. See the documentation below for more information."/> + </section> + <section name="import_right_rna_sequences" expanded="true" title="Import right_rna_sequences"> + <param name="name" type="text" value="right-rna-sequences.fasta" 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 RNAFASTAFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureData__ob__PairedEndSequence__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="PairedDNASequencesDirectoryFormat" selected="true">Paired DNA Sequences Directory Format</option> + </param> + <when value="PairedDNASequencesDirectoryFormat"> + <section name="import_left_dna_sequences" expanded="true" title="Import left_dna_sequences"> + <param name="name" type="text" value="left-dna-sequences.fasta" 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 DNAFASTAFormat. See the documentation below for more information."/> + </section> + <section name="import_right_dna_sequences" expanded="true" title="Import right_dna_sequences"> + <param name="name" type="text" value="right-dna-sequences.fasta" 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 DNAFASTAFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureData__ob__ProteinSequence__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="ProteinFASTAFormat" selected="true">Protein FASTA Format</option> + </param> + <when value="ProteinFASTAFormat"> + <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 ProteinFASTAFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureData__ob__RNASequence__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="RNAFASTAFormat" selected="true">RNAFASTA Format</option> + </param> + <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__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> + </param> + <when value="DNAFASTAFormat"> + <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 DNAFASTAFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureData__ob__Taxonomy__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="BIOMV210Format" selected="false">BIOMV210 Format</option> + <option value="HeaderlessTSVTaxonomyFormat" selected="false">Headerless TSV Taxonomy Format</option> + <option value="TSVTaxonomyFormat" selected="true">TSV Taxonomy Format</option> + </param> + <when value="BIOMV210Format"> + <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 BIOMV210Format. See the documentation below for more information."/> + </section> + </when> + <when value="HeaderlessTSVTaxonomyFormat"> + <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 HeaderlessTSVTaxonomyFormat. See the documentation below for more information."/> + </section> + </when> + <when value="TSVTaxonomyFormat"> + <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 TSVTaxonomyFormat. 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:"> + <option value="BIOMV100Format" selected="false">BIOMV100 Format</option> + <option value="BIOMV210Format" selected="true">BIOMV210 Format</option> + </param> + <when value="BIOMV100Format"> + <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 BIOMV100Format. See the documentation below for more information."/> + </section> + </when> + <when value="BIOMV210Format"> + <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 BIOMV210Format. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureTable__ob__Composition__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="BIOMV100Format" selected="false">BIOMV100 Format</option> + <option value="BIOMV210Format" selected="true">BIOMV210 Format</option> + </param> + <when value="BIOMV100Format"> + <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 BIOMV100Format. See the documentation below for more information."/> + </section> + </when> + <when value="BIOMV210Format"> + <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 BIOMV210Format. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureTable__ob__Design__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="BIOMV100Format" selected="false">BIOMV100 Format</option> + <option value="BIOMV210Format" selected="true">BIOMV210 Format</option> + </param> + <when value="BIOMV100Format"> + <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 BIOMV100Format. See the documentation below for more information."/> + </section> + </when> + <when value="BIOMV210Format"> + <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 BIOMV210Format. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureTable__ob__Frequency__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="BIOMV100Format" selected="false">BIOMV100 Format</option> + <option value="BIOMV210Format" selected="true">BIOMV210 Format</option> + </param> + <when value="BIOMV100Format"> + <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 BIOMV100Format. See the documentation below for more information."/> + </section> + </when> + <when value="BIOMV210Format"> + <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 BIOMV210Format. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureTable__ob__PercentileNormalized__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="BIOMV100Format" selected="false">BIOMV100 Format</option> + <option value="BIOMV210Format" selected="true">BIOMV210 Format</option> + </param> + <when value="BIOMV100Format"> + <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 BIOMV100Format. See the documentation below for more information."/> + </section> + </when> + <when value="BIOMV210Format"> + <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 BIOMV210Format. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureTable__ob__PresenceAbsence__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="BIOMV100Format" selected="false">BIOMV100 Format</option> + <option value="BIOMV210Format" selected="true">BIOMV210 Format</option> + </param> + <when value="BIOMV100Format"> + <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 BIOMV100Format. See the documentation below for more information."/> + </section> + </when> + <when value="BIOMV210Format"> + <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 BIOMV210Format. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="FeatureTable__ob__RelativeFrequency__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="BIOMV100Format" selected="false">BIOMV100 Format</option> + <option value="BIOMV210Format" selected="true">BIOMV210 Format</option> + </param> + <when value="BIOMV100Format"> + <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 BIOMV100Format. See the documentation below for more information."/> + </section> + </when> + <when value="BIOMV210Format"> + <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 BIOMV210Format. See the documentation below for more information."/> + </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:"> + <option value="NewickFormat" selected="true">Newick Format</option> + </param> + <when value="NewickFormat"> + <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 NewickFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="MultiplexedPairedEndBarcodeInSequence"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="MultiplexedPairedEndBarcodeInSequenceDirFmt" selected="true">Multiplexed Paired End Barcode In Sequence Directory Format</option> + </param> + <when value="MultiplexedPairedEndBarcodeInSequenceDirFmt"> + <section name="import_forward_sequences" expanded="true" title="Import forward_sequences"> + <param name="name" type="text" value="forward.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + <section name="import_reverse_sequences" expanded="true" title="Import reverse_sequences"> + <param name="name" type="text" value="reverse.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="MultiplexedSingleEndBarcodeInSequence"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="FastqGzFormat" selected="true">Fastq Gz Format</option> + </param> + <when value="FastqGzFormat"> + <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 FastqGzFormat. 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:"> + <option value="OrdinationFormat" selected="true">Ordination Format</option> + </param> + <when value="OrdinationFormat"> + <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 OrdinationFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Phylogeny__ob__Rooted__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="NewickFormat" selected="true">Newick Format</option> + </param> + <when value="NewickFormat"> + <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 NewickFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Phylogeny__ob__Unrooted__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="NewickFormat" selected="true">Newick Format</option> + </param> + <when value="NewickFormat"> + <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 NewickFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="Placements"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="PlacementsFormat" selected="true">Placements Format</option> + </param> + <when value="PlacementsFormat"> + <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 PlacementsFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="ProcrustesStatistics"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="ProcrustesStatisticsFmt" selected="true">Procrustes Statistics Format</option> + </param> + <when value="ProcrustesStatisticsFmt"> + <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 ProcrustesStatisticsFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="QualityFilterStats"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="QualityFilterStatsFmt" selected="true">Quality Filter Stats Format</option> + </param> + <when value="QualityFilterStatsFmt"> + <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 QualityFilterStatsFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="RawSequences"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="EMPSingleEndCasavaDirFmt" selected="false">EMP Single End Casava Directory Format</option> + <option value="EMPSingleEndDirFmt" selected="true">EMP Single End Directory Format</option> + </param> + <when value="EMPSingleEndCasavaDirFmt"> + <section name="import_sequences" expanded="true" title="Import sequences"> + <param name="name" type="text" value="Undetermined_S0_L001_R1_001.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + <section name="import_barcodes" expanded="true" title="Import barcodes"> + <param name="name" type="text" value="Undetermined_S0_L001_I1_001.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + </when> + <when value="EMPSingleEndDirFmt"> + <section name="import_sequences" expanded="true" title="Import sequences"> + <param name="name" type="text" value="sequences.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </section> + <section name="import_barcodes" expanded="true" title="Import barcodes"> + <param name="name" type="text" value="barcodes.fastq.gz" 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 FastqGzFormat. See the documentation below for more information."/> + </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:"> + <option value="AlphaDiversityFormat" selected="true">Alpha Diversity Format</option> + </param> + <when value="AlphaDiversityFormat"> + <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 AlphaDiversityFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="SampleData__ob__ArtificialGrouping__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="ArtificialGroupingFormat" selected="true">Artificial Grouping Format</option> + </param> + <when value="ArtificialGroupingFormat"> + <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 ArtificialGroupingFormat. See the documentation below for more information."/> + </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:"> + <option value="BooleanSeriesFormat" selected="true">Boolean Series Format</option> + </param> + <when value="BooleanSeriesFormat"> + <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 BooleanSeriesFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="SampleData__ob__ClassifierPredictions__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="PredictionsFormat" selected="true">Predictions Format</option> + </param> + <when value="PredictionsFormat"> + <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 PredictionsFormat. See the documentation below for more information."/> + </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:"> + <option value="DADA2StatsFormat" selected="true">DADA2 Stats Format</option> + </param> + <when value="DADA2StatsFormat"> + <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 DADA2StatsFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="SampleData__ob__FirstDifferences__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="FirstDifferencesFormat" selected="true">First Differences Format</option> + </param> + <when value="FirstDifferencesFormat"> + <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 FirstDifferencesFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="SampleData__ob__JoinedSequencesWithQuality__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="CasavaOneEightLanelessPerSampleDirFmt" selected="false">Casava One Eight Laneless Per Sample Directory Format</option> + <option value="CasavaOneEightSingleLanePerSampleDirFmt" selected="false">Casava One Eight Single Lane Per Sample Directory Format</option> + <option value="SingleEndFastqManifestPhred33" selected="false">Single End Fastq Manifest Phred33</option> + <option value="SingleEndFastqManifestPhred33V2" selected="false">Single End Fastq Manifest Phred33V2</option> + <option value="SingleEndFastqManifestPhred64" selected="false">Single End Fastq Manifest Phred64</option> + <option value="SingleEndFastqManifestPhred64V2" selected="false">Single End Fastq Manifest Phred64V2</option> + <option value="SingleLanePerSamplePairedEndFastqDirFmt" selected="false">Single Lane Per Sample Paired End Fastq Directory Format</option> + <option value="SingleLanePerSampleSingleEndFastqDirFmt" selected="true">Single Lane Per Sample Single End Fastq Directory Format</option> + </param> + <when value="CasavaOneEightLanelessPerSampleDirFmt"> + <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 FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/> + <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: .+_.+_R[12]_001\.fastq\.gz"> + <validator type="regex" message="This filename doesn't match the regex.">.+_.+_R[12]_001\.fastq\.gz</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + <when value="CasavaOneEightSingleLanePerSampleDirFmt"> + <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 FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <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: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"> + <validator type="regex" message="This filename doesn't match the regex.">.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + <when value="SingleEndFastqManifestPhred33"> + <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 SingleEndFastqManifestPhred33. See the documentation below for more information."/> + </section> + </when> + <when value="SingleEndFastqManifestPhred33V2"> + <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 SingleEndFastqManifestPhred33V2. See the documentation below for more information."/> + </section> + </when> + <when value="SingleEndFastqManifestPhred64"> + <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 SingleEndFastqManifestPhred64. See the documentation below for more information."/> + </section> + </when> + <when value="SingleEndFastqManifestPhred64V2"> + <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 SingleEndFastqManifestPhred64V2. See the documentation below for more information."/> + </section> + </when> + <when value="SingleLanePerSamplePairedEndFastqDirFmt"> + <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 FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <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: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"> + <validator type="regex" message="This filename doesn't match the regex.">.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. 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 FastqManifestFormat. See the documentation below for more information."/> + </section> + <section name="import_metadata" expanded="true" title="Import metadata"> + <param name="name" type="text" value="metadata.yml" 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 YamlFormat. See the documentation below for more information."/> + </section> + </when> + <when value="SingleLanePerSampleSingleEndFastqDirFmt"> + <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 FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <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: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"> + <validator type="regex" message="This filename doesn't match the regex.">.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. 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 FastqManifestFormat. See the documentation below for more information."/> + </section> + <section name="import_metadata" expanded="true" title="Import metadata"> + <param name="name" type="text" value="metadata.yml" 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 YamlFormat. 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:"> + <option value="CasavaOneEightLanelessPerSampleDirFmt" selected="false">Casava One Eight Laneless Per Sample Directory Format</option> + <option value="CasavaOneEightSingleLanePerSampleDirFmt" selected="false">Casava One Eight Single Lane Per Sample Directory Format</option> + <option value="PairedEndFastqManifestPhred33" selected="false">Paired End Fastq Manifest Phred33</option> + <option value="PairedEndFastqManifestPhred33V2" selected="false">Paired End Fastq Manifest Phred33V2</option> + <option value="PairedEndFastqManifestPhred64" selected="false">Paired End Fastq Manifest Phred64</option> + <option value="PairedEndFastqManifestPhred64V2" selected="false">Paired End Fastq Manifest Phred64V2</option> + <option value="SingleLanePerSamplePairedEndFastqDirFmt" selected="true">Single Lane Per Sample Paired End Fastq Directory Format</option> + </param> + <when value="CasavaOneEightLanelessPerSampleDirFmt"> + <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 FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/> + <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: .+_.+_R[12]_001\.fastq\.gz"> + <validator type="regex" message="This filename doesn't match the regex.">.+_.+_R[12]_001\.fastq\.gz</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + <when value="CasavaOneEightSingleLanePerSampleDirFmt"> + <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 FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <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: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"> + <validator type="regex" message="This filename doesn't match the regex.">.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + <when value="PairedEndFastqManifestPhred33"> + <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 PairedEndFastqManifestPhred33. See the documentation below for more information."/> + </section> + </when> + <when value="PairedEndFastqManifestPhred33V2"> + <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 PairedEndFastqManifestPhred33V2. See the documentation below for more information."/> + </section> + </when> + <when value="PairedEndFastqManifestPhred64"> + <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 PairedEndFastqManifestPhred64. See the documentation below for more information."/> + </section> + </when> + <when value="PairedEndFastqManifestPhred64V2"> + <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 PairedEndFastqManifestPhred64V2. See the documentation below for more information."/> + </section> + </when> + <when value="SingleLanePerSamplePairedEndFastqDirFmt"> + <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 FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <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: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"> + <validator type="regex" message="This filename doesn't match the regex.">.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. 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 FastqManifestFormat. See the documentation below for more information."/> + </section> + <section name="import_metadata" expanded="true" title="Import metadata"> + <param name="name" type="text" value="metadata.yml" 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 YamlFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="SampleData__ob__Probabilities__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="ProbabilitiesFormat" selected="true">Probabilities Format</option> + </param> + <when value="ProbabilitiesFormat"> + <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 ProbabilitiesFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="SampleData__ob__RegressorPredictions__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="PredictionsFormat" selected="true">Predictions Format</option> + </param> + <when value="PredictionsFormat"> + <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 PredictionsFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="SampleData__ob__SequencesWithQuality__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="CasavaOneEightLanelessPerSampleDirFmt" selected="false">Casava One Eight Laneless Per Sample Directory Format</option> + <option value="CasavaOneEightSingleLanePerSampleDirFmt" selected="false">Casava One Eight Single Lane Per Sample Directory Format</option> + <option value="SingleEndFastqManifestPhred33" selected="false">Single End Fastq Manifest Phred33</option> + <option value="SingleEndFastqManifestPhred33V2" selected="false">Single End Fastq Manifest Phred33V2</option> + <option value="SingleEndFastqManifestPhred64" selected="false">Single End Fastq Manifest Phred64</option> + <option value="SingleEndFastqManifestPhred64V2" selected="false">Single End Fastq Manifest Phred64V2</option> + <option value="SingleLanePerSamplePairedEndFastqDirFmt" selected="false">Single Lane Per Sample Paired End Fastq Directory Format</option> + <option value="SingleLanePerSampleSingleEndFastqDirFmt" selected="true">Single Lane Per Sample Single End Fastq Directory Format</option> + </param> + <when value="CasavaOneEightLanelessPerSampleDirFmt"> + <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 FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/> + <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: .+_.+_R[12]_001\.fastq\.gz"> + <validator type="regex" message="This filename doesn't match the regex.">.+_.+_R[12]_001\.fastq\.gz</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + <when value="CasavaOneEightSingleLanePerSampleDirFmt"> + <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 FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <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: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"> + <validator type="regex" message="This filename doesn't match the regex.">.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information."/> + </repeat> + </when> + </conditional> + </section> + </when> + <when value="SingleEndFastqManifestPhred33"> + <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 SingleEndFastqManifestPhred33. See the documentation below for more information."/> + </section> + </when> + <when value="SingleEndFastqManifestPhred33V2"> + <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 SingleEndFastqManifestPhred33V2. See the documentation below for more information."/> + </section> + </when> + <when value="SingleEndFastqManifestPhred64"> + <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 SingleEndFastqManifestPhred64. See the documentation below for more information."/> + </section> + </when> + <when value="SingleEndFastqManifestPhred64V2"> + <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 SingleEndFastqManifestPhred64V2. See the documentation below for more information."/> + </section> + </when> + <when value="SingleLanePerSamplePairedEndFastqDirFmt"> + <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 FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <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: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"> + <validator type="regex" message="This filename doesn't match the regex.">.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. 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 FastqManifestFormat. See the documentation below for more information."/> + </section> + <section name="import_metadata" expanded="true" title="Import metadata"> + <param name="name" type="text" value="metadata.yml" 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 YamlFormat. See the documentation below for more information."/> + </section> + </when> + <when value="SingleLanePerSampleSingleEndFastqDirFmt"> + <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 FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <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: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"> + <validator type="regex" message="This filename doesn't match the regex.">.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. 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 FastqManifestFormat. See the documentation below for more information."/> + </section> + <section name="import_metadata" expanded="true" title="Import metadata"> + <param name="name" type="text" value="metadata.yml" 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 YamlFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="SampleData__ob__Sequences__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="QIIME1DemuxFormat" selected="true">QIIME1 Demux Format</option> + <option value="SingleLanePerSampleSingleEndFastqDirFmt" selected="false">Single Lane Per Sample Single End Fastq Directory Format</option> + </param> + <when value="QIIME1DemuxFormat"> + <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 QIIME1DemuxFormat. See the documentation below for more information."/> + </section> + </when> + <when value="SingleLanePerSampleSingleEndFastqDirFmt"> + <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 FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/> + <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: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"> + <validator type="regex" message="This filename doesn't match the regex.">.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz</validator> + </param> + <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. 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 FastqManifestFormat. See the documentation below for more information."/> + </section> + <section name="import_metadata" expanded="true" title="Import metadata"> + <param name="name" type="text" value="metadata.yml" 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 YamlFormat. 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:"> + <option value="PredictionsFormat" selected="true">Predictions Format</option> + </param> + <when value="PredictionsFormat"> + <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 PredictionsFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="SampleEstimator__ob__Classifier__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="SampleEstimatorDirFmt" selected="true">Sample Estimator Directory Format</option> + </param> + <when value="SampleEstimatorDirFmt"> + <section name="import_version_info" expanded="true" title="Import version_info"> + <param name="name" type="text" value="sklearn_version.json" 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 JSONFormat. See the documentation below for more information."/> + </section> + <section name="import_sklearn_pipeline" expanded="true" title="Import sklearn_pipeline"> + <param name="name" type="text" value="sklearn_pipeline.tar" 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 PickleFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="SampleEstimator__ob__Regressor__cb__"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="SampleEstimatorDirFmt" selected="true">Sample Estimator Directory Format</option> + </param> + <when value="SampleEstimatorDirFmt"> + <section name="import_version_info" expanded="true" title="Import version_info"> + <param name="name" type="text" value="sklearn_version.json" 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 JSONFormat. See the documentation below for more information."/> + </section> + <section name="import_sklearn_pipeline" expanded="true" title="Import sklearn_pipeline"> + <param name="name" type="text" value="sklearn_pipeline.tar" 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 PickleFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="SeppReferenceDatabase"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="SeppReferenceDirFmt" selected="true">Sepp Reference Directory Format</option> + </param> + <when value="SeppReferenceDirFmt"> + <section name="import_alignment" expanded="true" title="Import alignment"> + <param name="name" type="text" value="aligned-dna-sequences.fasta" 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 AlignedDNAFASTAFormat. See the documentation below for more information."/> + </section> + <section name="import_phylogeny" expanded="true" title="Import phylogeny"> + <param name="name" type="text" value="tree.nwk" 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 NewickFormat. See the documentation below for more information."/> + </section> + <section name="import_raxml_info" expanded="true" title="Import raxml_info"> + <param name="name" type="text" value="raxml-info.txt" 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 RAxMLinfoFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="TaxonomicClassifier"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="TaxonomicClassiferTemporaryPickleDirFmt" selected="true">Taxonomic Classifer Temporary Pickle Directory Format</option> + </param> + <when value="TaxonomicClassiferTemporaryPickleDirFmt"> + <section name="import_version_info" expanded="true" title="Import version_info"> + <param name="name" type="text" value="sklearn_version.json" 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 JSONFormat. See the documentation below for more information."/> + </section> + <section name="import_sklearn_pipeline" expanded="true" title="Import sklearn_pipeline"> + <param name="name" type="text" value="sklearn_pipeline.tar" 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 PickleFormat. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + <when value="UchimeStats"> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" type="select" label="QIIME 2 file format to import from:"> + <option value="UchimeStatsFmt" selected="true">Uchime Stats Format</option> + </param> + <when value="UchimeStatsFmt"> + <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 UchimeStatsFmt. See the documentation below for more information."/> + </section> + </when> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <data name="imported_data" format="qza" from_work_dir="imported_data.qza"/> + </outputs> + <help> +QIIME 2: tools import +===================== +Import data as a QIIME 2 artifact + +Instructions +------------ + + 1. Select the type you wish to import. If you are uncertain, consider what + your next action would be and identify what type it requires. + + 2. Identify which format will best suite the data you have available. Many + types will have only a single format available. There is some documentation + available below on the different formats, however there may not be + very much documentation available for your format. + + 3. For each part of the format, you will need to associate some data. + + a. If it is a simple format, you may just select the history dataset. + b. If it is a more complex format, you will need to provide either a + filename and history dataset, or a collection. + c. For collections, they can be constructed via matching a regex against + the names of the items in that collection. (You may need to append an + extension if your collection's element IDs lack one.) Or you can + provide individual history datasets with a filename as in the simpler + cases. + +Formats: +-------- +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. + + +TSVTaxonomyFormat +***************** +Format for a 2+ column TSV file with an expected minimal header. + +The only header recognized by this format is: + + Feature ID<tab>Taxon + +Optionally followed by other arbitrary columns. + +This format supports blank lines. The expected header must be the first +non-blank line. In addition to the header, there must be at least one line +of data. + + +QIIME1DemuxFormat +***************** +QIIME 1 demultiplexed FASTA format. + +The QIIME 1 demultiplexed FASTA format is the default output format of +``split_libraries.py`` and ``split_libraries_fastq.py``. The file output by +QIIME 1 is named ``seqs.fna``; this filename is sometimes associated with +the file format itself due to its widespread usage in QIIME 1. + +The format is documented here: +http://qiime.org/documentation/file_formats.html#demultiplexed-sequences + +Format details: + +- FASTA file with exactly two lines per record: header and sequence. Each + sequence must span exactly one line and cannot be split across multiple + lines. + +- The ID in each header must follow the format ``<sample-id>_<seq-id>``. + ``<sample-id>`` is the identifier of the sample the sequence belongs to, + and ``<seq-id>`` is an identifier for the sequence *within* its sample. + In QIIME 1, ``<seq-id>`` is typically an incrementing integer starting + from zero, but any non-empty value can be used here, as long as the + header IDs remain unique throughout the file. Note: ``<sample-id>`` may + contain sample IDs that contain underscores; the rightmost underscore + will used to delimit sample and sequence IDs. + +- Descriptions in headers are permitted and ignored. + +- Header IDs must be unique within the file. + +- Each sequence must be DNA and cannot be empty. + + +FastqGzFormat +************* + +A gzipped fastq file. + + +Additional formats without documentation: +***************************************** + - PairedEndFastqManifestPhred64 + - SingleEndFastqManifestPhred64 + - NewickFormat + - SeppReferenceDirFmt + - PairedRNASequencesDirectoryFormat + - EMPPairedEndDirFmt + - ArtificialGroupingFormat + - BLAST6Format + - CasavaOneEightLanelessPerSampleDirFmt + - ProbabilitiesFormat + - PlacementsFormat + - DADA2StatsFormat + - SampleEstimatorDirFmt + - ImportanceFormat + - AlignedProteinFASTAFormat + - SingleLanePerSampleSingleEndFastqDirFmt + - BIOMV210Format + - PairedEndFastqManifestPhred33V2 + - CasavaOneEightSingleLanePerSampleDirFmt + - ProteinFASTAFormat + - SingleEndFastqManifestPhred64V2 + - Bowtie2IndexDirFmt + - DifferentialFormat + - UchimeStatsFmt + - DeblurStatsFmt + - PairedEndFastqManifestPhred33 + - AlignedRNAFASTAFormat + - EMPSingleEndDirFmt + - SingleEndFastqManifestPhred33 + - AlignedDNAFASTAFormat + - EMPPairedEndCasavaDirFmt + - ProcrustesStatisticsFmt + - FirstDifferencesFormat + - BIOMV100Format + - PairedDNASequencesDirectoryFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - AlphaDiversityFormat + - LSMatFormat + - BooleanSeriesFormat + - OrdinationFormat + - SingleLanePerSamplePairedEndFastqDirFmt + - PairedEndFastqManifestPhred64V2 + - RNAFASTAFormat + - TaxonomicClassiferTemporaryPickleDirFmt + - PredictionsFormat + - DNAFASTAFormat + - QualityFilterStatsFmt + - ErrorCorrectionDetailsFmt + - EMPSingleEndCasavaDirFmt + - SingleEndFastqManifestPhred33V2 +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>