qiime2_core__tools__import: qiime2_core__tools_

comparison qiime2_coretoolsimport.xml @ 2:18c6b2b6740f draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 65e4952f33eb335528e8553150e9097e5ea8f556

author	q2d2
date	Thu, 08 Jun 2023 19:53:28 +0000
parents	5d9a36073ed6
children	10447a4b0cc3

comparison

equal deleted inserted replaced

-:5d9a36073ed6
+:18c6b2b6740f
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-q2galaxy (version: 2022.11.1)
+q2galaxy (version: 2023.5.0)
 for:
-qiime2 (version: 2022.11.1)
+qiime2 (version: 2023.5.1)
 -->
-<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2022.11.1+dist.h2bda5906.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.2" profile="22.05" license="BSD-3-Clause">
 <description>Import data into a QIIME 2 artifact</description>
 <requirements>
-<container type="docker">quay.io/qiime2/core:2022.11</container>
+<container type="docker">quay.io/qiime2/core:2023.5</container>
 </requirements>
 <command detect_errors="exit_code">q2galaxy run tools import '$inputs'</command>
 <configfiles>
 <configfile name="inputs">&lt;%
 # This is an exercise in cheating the Cheetah
 <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__DecontamScore__cb__">FeatureData[DecontamScore]</option>
 <option value="FeatureData__ob__DifferentialAbundance__cb__">FeatureData[DifferentialAbundance]</option>
 <option value="FeatureData__ob__Differential__cb__">FeatureData[Differential]</option>
 <option value="FeatureData__ob__Importance__cb__">FeatureData[Importance]</option>
 <option value="FeatureData__ob__PairedEndRNASequence__cb__">FeatureData[PairedEndRNASequence]</option>
 <option value="FeatureData__ob__PairedEndSequence__cb__">FeatureData[PairedEndSequence]</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="ImmutableMetadata">ImmutableMetadata</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>
 <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__DecontamScore__cb__">
+<conditional name="__q2galaxy__GUI__cond__format__">
+<param name="format" type="select" label="QIIME 2 file format to import from:">
+<option value="DecontamScoreFormat" selected="true">Decontam Score Format</option>
+</param>
+<when value="DecontamScoreFormat">
+<section name="import" expanded="true" title="Import">
+<param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+<param name="data" type="data" format="data" help="This data should be formatted as a DecontamScoreFormat. See the documentation below for more information."/>
+</section>
+</when>
+</conditional>
+</when>
 <when value="FeatureData__ob__DifferentialAbundance__cb__">
 <conditional name="__q2galaxy__GUI__cond__format__">
 <param name="format" type="select" label="QIIME 2 file format to import from:">
 <option value="DataLoafPackageDirFmt" selected="true">Data Loaf Package Directory Format</option>
 </param>
 <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="ImmutableMetadata">
+<conditional name="__q2galaxy__GUI__cond__format__">
+<param name="format" type="select" label="QIIME 2 file format to import from:">
+<option value="ImmutableMetadataFormat" selected="true">Immutable Metadata Format</option>
+</param>
+<when value="ImmutableMetadataFormat">
+<section name="import" expanded="true" title="Import">
+<param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+<param name="data" type="data" format="data" help="This data should be formatted as a ImmutableMetadataFormat. See the documentation below for more information."/>
+</section>
+</when>
+</conditional>
+</when>
 <when value="MultiplexedPairedEndBarcodeInSequence">
 <conditional name="__q2galaxy__GUI__cond__format__">
 <param name="format" type="select" label="QIIME 2 file format to import from:">
 <option value="MultiplexedPairedEndBarcodeInSequenceDirFmt" selected="true">Multiplexed Paired End Barcode In Sequence Directory Format</option>
 </param>
 Formats:
 --------
 These formats have documentation available.
-SampleIdIndexedSingleEndPerSampleDirFmt
-***************************************
-Single-end reads in fastq.gz files where base filename is the sample id
-The full file name, minus the extension (`.fastq.gz`) is the sample id.
-For example, the sample id for the file:
-* `sample-1.fastq.gz` is `sample-1`
-* `xyz.fastq.gz` is `xyz`
-* `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001`
-TSVTaxonomyFormat
-*****************
-Format for a 2+ column TSV file with an expected minimal header.
-The only header recognized by this format is:
-Feature ID&lt;tab&gt;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
 - Header IDs must be unique within the file.
 - Each sequence must be DNA and cannot be empty.
+TSVTaxonomyFormat
+*****************
+Format for a 2+ column TSV file with an expected minimal header.
+The only header recognized by this format is:
+Feature ID&lt;tab&gt;Taxon
+Optionally followed by other arbitrary columns.
+This format supports blank lines. The expected header must be the first
+non-blank line. In addition to the header, there must be at least one line
+of data.
 HeaderlessTSVTaxonomyFormat
 ***************************
 Format for a 2+ column TSV file without a header.
 This format supports comment lines starting with #, and blank lines.
 *************
 A gzipped fastq file.
+SampleIdIndexedSingleEndPerSampleDirFmt
+***************************************
+Single-end reads in fastq.gz files where base filename is the sample id
+The full file name, minus the extension (`.fastq.gz`) is the sample id.
+For example, the sample id for the file:
+* `sample-1.fastq.gz` is `sample-1`
+* `xyz.fastq.gz` is `xyz`
+* `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001`
 Additional formats without documentation:
 *****************************************
+- FirstDifferencesFormat
 - MixedCaseAlignedDNAFASTAFormat
-- DeblurStatsFmt
+- SingleLanePerSamplePairedEndFastqDirFmt
+- EMPPairedEndDirFmt
+- ImmutableMetadataFormat
+- PairedEndFastqManifestPhred64V2
+- DataLoafPackageDirFmt
+- AlignedDNAFASTAFormat
+- BIOMV100Format
+- UchimeStatsFmt
+- BLAST6Format
+- PairedDNASequencesDirectoryFormat
+- SingleEndFastqManifestPhred33V2
+- QualityFilterStatsFmt
 - DADA2StatsFormat
-- PairedEndFastqManifestPhred64
-- BIOMV210Format
-- AlignedDNAFASTAFormat
-- DataLoafPackageDirFmt
-- SingleEndFastqManifestPhred64
-- PairedDNASequencesDirectoryFormat
-- BLAST6Format
-- EMPPairedEndDirFmt
-- PlacementsFormat
 - AlignedProteinFASTAFormat
 - MixedCaseRNAFASTAFormat
-- FirstDifferencesFormat
+- PlacementsFormat
-- CasavaOneEightLanelessPerSampleDirFmt
+- NewickFormat
-- Bowtie2IndexDirFmt
+- PairedEndFastqManifestPhred64
-- EMPSingleEndCasavaDirFmt
-- ProcrustesStatisticsFmt
 - ProteinFASTAFormat
 - RNAFASTAFormat
-- SingleLanePerSampleSingleEndFastqDirFmt
+- BooleanSeriesFormat
-- PairedEndFastqManifestPhred33V2
+- SingleEndFastqManifestPhred64
-- OrdinationFormat
+- LSMatFormat
+- DeblurStatsFmt
+- ErrorCorrectionDetailsFmt
 - MixedCaseDNAFASTAFormat
 - TaxonomicClassiferTemporaryPickleDirFmt
-- ArtificialGroupingFormat
+- DNAFASTAFormat
-- BIOMV100Format
+- ProcrustesStatisticsFmt
+- CasavaOneEightLanelessPerSampleDirFmt
+- EMPSingleEndDirFmt
+- DecontamScoreFormat
+- OrdinationFormat
+- SingleLanePerSampleSingleEndFastqDirFmt
+- Bowtie2IndexDirFmt
+- BIOMV210Format
+- PairedEndFastqManifestPhred33V2
+- SampleEstimatorDirFmt
+- EMPSingleEndCasavaDirFmt
+- PairedRNASequencesDirectoryFormat
+- EMPPairedEndCasavaDirFmt
 - CasavaOneEightSingleLanePerSampleDirFmt
-- ErrorCorrectionDetailsFmt
+- SingleEndFastqManifestPhred64V2
-- ImportanceFormat
-- SingleEndFastqManifestPhred33V2
-- DNAFASTAFormat
 - MultiplexedFastaQualDirFmt
-- PredictionsFormat
+- DifferentialFormat
+- AlphaDiversityFormat
 - MultiplexedPairedEndBarcodeInSequenceDirFmt
 - PairedEndFastqManifestPhred33
-- AlphaDiversityFormat
+- ArtificialGroupingFormat
 - ProbabilitiesFormat
-- EMPSingleEndDirFmt
+- SeppReferenceDirFmt
-- PairedRNASequencesDirectoryFormat
+- MixedCaseAlignedRNAFASTAFormat
 - SingleEndFastqManifestPhred33
-- UchimeStatsFmt
+- ImportanceFormat
-- EMPPairedEndCasavaDirFmt
-- NewickFormat
-- SampleEstimatorDirFmt
-- DifferentialFormat
-- LSMatFormat
-- SingleLanePerSamplePairedEndFastqDirFmt
-- QualityFilterStatsFmt
-- PairedEndFastqManifestPhred64V2
-- MixedCaseAlignedRNAFASTAFormat
-- SingleEndFastqManifestPhred64V2
 - AlignedRNAFASTAFormat
-- BooleanSeriesFormat
+- PredictionsFormat
-- SeppReferenceDirFmt
 </help>
 <citations>
 <citation type="doi">10.1038/s41587-019-0209-9</citation>
 </citations>
 </tool>

Mercurial > repos > q2d2 > qiime2_core__tools__import

comparison qiime2_core__tools__import.xml @ 2:18c6b2b6740f draft

Mercurial > repos > q2d2 > qiime2_coretoolsimport

comparison qiime2_coretoolsimport.xml @ 2:18c6b2b6740f draft