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Changeset 2:18c6b2b6740f (2023-06-08)

Previous changeset 1:5d9a36073ed6 (2023-01-13) Next changeset 3:10447a4b0cc3 (2024-02-01)

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

modified:
qiime2_core__tools__import.xml

diff -r 5d9a36073ed6 -r 18c6b2b6740f qiime2_core__tools__import.xml
--- a/qiime2_core__tools__import.xml Fri Jan 13 23:02:20 2023 +0000
+++ b/qiime2_core__tools__import.xml Thu Jun 08 19:53:28 2023 +0000

[

b'@@ -6,14 +6,14 @@\n -->\n \n-<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2022.11.1+dist.h2bda5906.2" profile="22.05" license="BSD-3-Clause">\n+<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.2" profile="22.05" license="BSD-3-Clause">\n <description>Import data into a QIIME 2 artifact</description>\n <requirements>\n- <container type="docker">quay.io/qiime2/core:2022.11</container>\n+ <container type="docker">quay.io/qiime2/core:2023.5</container>\n </requirements>\n <command detect_errors="exit_code">q2galaxy run tools import \'$inputs\'</command>\n <configfiles>\n@@ -69,6 +69,7 @@\n <option value="FeatureData__ob__AlignedRNASequence__cb__">FeatureData[AlignedRNASequence]</option>\n <option value="FeatureData__ob__AlignedSequence__cb__">FeatureData[AlignedSequence]</option>\n <option value="FeatureData__ob__BLAST6__cb__">FeatureData[BLAST6]</option>\n+ <option value="FeatureData__ob__DecontamScore__cb__">FeatureData[DecontamScore]</option>\n <option value="FeatureData__ob__DifferentialAbundance__cb__">FeatureData[DifferentialAbundance]</option>\n <option value="FeatureData__ob__Differential__cb__">FeatureData[Differential]</option>\n <option value="FeatureData__ob__Importance__cb__">FeatureData[Importance]</option>\n@@ -86,6 +87,7 @@\n <option value="FeatureTable__ob__PresenceAbsence__cb__">FeatureTable[PresenceAbsence]</option>\n <option value="FeatureTable__ob__RelativeFrequency__cb__">FeatureTable[RelativeFrequency]</option>\n <option value="Hierarchy">Hierarchy</option>\n+ <option value="ImmutableMetadata">ImmutableMetadata</option>\n <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option>\n <option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option>\n <option value="PCoAResults">PCoAResults</option>\n@@ -329,6 +331,19 @@\n </when>\n </conditional>\n </when>\n+ <when value="FeatureData__ob__DecontamScore__cb__">\n+ <conditional name="__q2galaxy__GUI__cond__format__">\n+ <param name="format" type="select" label="QIIME 2 file format to import from:">\n+ <option value="DecontamScoreFormat" selected="true">Decontam Score Format</option>\n+ </param>\n+ <when value="DecontamScoreFormat">\n+ <section name="import" expanded="true" title="Import">\n+ <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>\n+ <param name="data" type="data" format="data" help="This data should be formatted as a DecontamScoreFormat. See the documentation below for more information."/>\n+ </section>\n+ </when>\n+ </conditional>\n+ </when>\n <when value="FeatureData__ob__DifferentialAbundance__cb__">\n <conditional name="__q2galaxy__GUI__cond__format__">\n <param name="format" type="select" label="QIIME 2 file format to import from:">\n@@ -664,6 +679,19 @@\n </when>\n </conditional>\n </when>\n+ <when value="ImmutableMetadata">\n+ <conditional name="__q2galaxy__GUI__cond__format__">\n+ <param name="format" type="select" label="QIIME 2 file format to import from:">\n+ <option value="ImmutableMetadataFormat" selected="true">Immutable Metad'..b'ltiplexed FASTA format.\n@@ -1719,6 +1722,21 @@\n - Each sequence must be DNA and cannot be empty.\n \n \n+TSVTaxonomyFormat\n+*****************\n+Format for a 2+ column TSV file with an expected minimal header.\n+\n+The only header recognized by this format is:\n+\n+ Feature ID<tab>Taxon\n+\n+Optionally followed by other arbitrary columns.\n+\n+This format supports blank lines. The expected header must be the first\n+non-blank line. In addition to the header, there must be at least one line\n+of data.\n+\n+\n HeaderlessTSVTaxonomyFormat\n ***************************\n Format for a 2+ column TSV file without a header.\n@@ -1732,64 +1750,76 @@\n A gzipped fastq file.\n \n \n+SampleIdIndexedSingleEndPerSampleDirFmt\n+***************************************\n+Single-end reads in fastq.gz files where base filename is the sample id\n+\n+ The full file name, minus the extension (`.fastq.gz`) is the sample id.\n+ For example, the sample id for the file:\n+ * `sample-1.fastq.gz` is `sample-1`\n+ * `xyz.fastq.gz` is `xyz`\n+ * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001`\n+\n Additional formats without documentation:\n *****************************************\n+ - FirstDifferencesFormat\n - MixedCaseAlignedDNAFASTAFormat\n- - DeblurStatsFmt\n- - DADA2StatsFormat\n- - PairedEndFastqManifestPhred64\n- - BIOMV210Format\n+ - SingleLanePerSamplePairedEndFastqDirFmt\n+ - EMPPairedEndDirFmt\n+ - ImmutableMetadataFormat\n+ - PairedEndFastqManifestPhred64V2\n+ - DataLoafPackageDirFmt\n - AlignedDNAFASTAFormat\n- - DataLoafPackageDirFmt\n- - SingleEndFastqManifestPhred64\n+ - BIOMV100Format\n+ - UchimeStatsFmt\n+ - BLAST6Format\n - PairedDNASequencesDirectoryFormat\n- - BLAST6Format\n- - EMPPairedEndDirFmt\n- - PlacementsFormat\n+ - SingleEndFastqManifestPhred33V2\n+ - QualityFilterStatsFmt\n+ - DADA2StatsFormat\n - AlignedProteinFASTAFormat\n - MixedCaseRNAFASTAFormat\n- - FirstDifferencesFormat\n- - CasavaOneEightLanelessPerSampleDirFmt\n- - Bowtie2IndexDirFmt\n- - EMPSingleEndCasavaDirFmt\n- - ProcrustesStatisticsFmt\n+ - PlacementsFormat\n+ - NewickFormat\n+ - PairedEndFastqManifestPhred64\n - ProteinFASTAFormat\n - RNAFASTAFormat\n- - SingleLanePerSampleSingleEndFastqDirFmt\n- - PairedEndFastqManifestPhred33V2\n- - OrdinationFormat\n+ - BooleanSeriesFormat\n+ - SingleEndFastqManifestPhred64\n+ - LSMatFormat\n+ - DeblurStatsFmt\n+ - ErrorCorrectionDetailsFmt\n - MixedCaseDNAFASTAFormat\n - TaxonomicClassiferTemporaryPickleDirFmt\n- - ArtificialGroupingFormat\n- - BIOMV100Format\n+ - DNAFASTAFormat\n+ - ProcrustesStatisticsFmt\n+ - CasavaOneEightLanelessPerSampleDirFmt\n+ - EMPSingleEndDirFmt\n+ - DecontamScoreFormat\n+ - OrdinationFormat\n+ - SingleLanePerSampleSingleEndFastqDirFmt\n+ - Bowtie2IndexDirFmt\n+ - BIOMV210Format\n+ - PairedEndFastqManifestPhred33V2\n+ - SampleEstimatorDirFmt\n+ - EMPSingleEndCasavaDirFmt\n+ - PairedRNASequencesDirectoryFormat\n+ - EMPPairedEndCasavaDirFmt\n - CasavaOneEightSingleLanePerSampleDirFmt\n- - ErrorCorrectionDetailsFmt\n- - ImportanceFormat\n- - SingleEndFastqManifestPhred33V2\n- - DNAFASTAFormat\n+ - SingleEndFastqManifestPhred64V2\n - MultiplexedFastaQualDirFmt\n- - PredictionsFormat\n+ - DifferentialFormat\n+ - AlphaDiversityFormat\n - MultiplexedPairedEndBarcodeInSequenceDirFmt\n - PairedEndFastqManifestPhred33\n- - AlphaDiversityFormat\n+ - ArtificialGroupingFormat\n - ProbabilitiesFormat\n- - EMPSingleEndDirFmt\n- - PairedRNASequencesDirectoryFormat\n+ - SeppReferenceDirFmt\n+ - MixedCaseAlignedRNAFASTAFormat\n - SingleEndFastqManifestPhred33\n- - UchimeStatsFmt\n- - EMPPairedEndCasavaDirFmt\n- - NewickFormat\n- - SampleEstimatorDirFmt\n- - DifferentialFormat\n- - LSMatFormat\n- - SingleLanePerSamplePairedEndFastqDirFmt\n- - QualityFilterStatsFmt\n- - PairedEndFastqManifestPhred64V2\n- - MixedCaseAlignedRNAFASTAFormat\n- - SingleEndFastqManifestPhred64V2\n+ - ImportanceFormat\n - AlignedRNAFASTAFormat\n- - BooleanSeriesFormat\n- - SeppReferenceDirFmt\n+ - PredictionsFormat\n </help>\n <citations>\n <citation type="doi">10.1038/s41587-019-0209-9</citation>\n'