Galaxy |

Changeset 1:5d9a36073ed6 (2023-01-13)

Previous changeset 0:1370f8d6e95b (2022-08-29) Next changeset 2:18c6b2b6740f (2023-06-08)

Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 69da7976573cc07a363ac66bdacc9269d7cd3732

modified:
qiime2_core__tools__import.xml

diff -r 1370f8d6e95b -r 5d9a36073ed6 qiime2_core__tools__import.xml
--- a/qiime2_core__tools__import.xml Mon Aug 29 20:36:58 2022 +0000
+++ b/qiime2_core__tools__import.xml Fri Jan 13 23:02:20 2023 +0000

[

b'@@ -1,21 +1,21 @@\n <?xml version=\'1.0\' encoding=\'utf-8\'?>\n \n \n-<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2022.8.1+dist.h91e3be72.2" profile="22.05" license="BSD-3-Clause">\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 <description>Import data into a QIIME 2 artifact</description>\n <requirements>\n- <container type="docker">quay.io/qiime2/core:2022.8</container>\n+ <container type="docker">quay.io/qiime2/core:2022.11</container>\n </requirements>\n- <command>q2galaxy run tools import \'$inputs\'</command>\n+ <command detect_errors="exit_code">q2galaxy run tools import \'$inputs\'</command>\n <configfiles>\n <configfile name="inputs"><%\n # This is an exercise in cheating the Cheetah\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__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 <option value="FeatureData__ob__PairedEndRNASequence__cb__">FeatureData[PairedEndRNASequence]</option>\n@@ -279,6 +280,7 @@\n <conditional name="__q2galaxy__GUI__cond__format__">\n <param name="format" type="select" label="QIIME 2 file format to import from:">\n <option value="AlignedRNAFASTAFormat" selected="true">Aligned RNAFASTA Format</option>\n+ <option value="MixedCaseAlignedRNAFASTAFormat" selected="false">Mixed Case Aligned RNAFASTA Format</option>\n </param>\n <when value="AlignedRNAFASTAFormat">\n <section name="import" expanded="true" title="Import">\n@@ -286,12 +288,19 @@\n <param name="data" type="data" format="data" help="This data should be formatted as a AlignedRNAFASTAFormat. See the documentation below for more information."/>\n </section>\n </when>\n+ <when value="MixedCaseAlignedRNAFASTAFormat">\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 MixedCaseAlignedRNAFASTAFormat. See the documentation below for more information."/>\n+ </section>\n+ </when>\n </conditional>\n </when>\n <when value="FeatureData__ob__AlignedSequence__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="AlignedDNAFASTAFormat" selected="true">Aligned DNAFASTA Format</option>\n+ <option value="MixedCaseAlignedDNAFASTAFormat" selected="false">Mixed Case Aligned DNAFASTA Format</option>\n </param>\n <whe'..b'>\n@@ -1514,12 +1660,15 @@\n --------\n These formats have documentation available.\n \n-HeaderlessTSVTaxonomyFormat\n-***************************\n-Format for a 2+ column TSV file without a header.\n+SampleIdIndexedSingleEndPerSampleDirFmt\n+***************************************\n+Single-end reads in fastq.gz files where base filename is the sample id\n \n-This format supports comment lines starting with #, and blank lines.\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 TSVTaxonomyFormat\n *****************\n@@ -1570,6 +1719,13 @@\n - Each sequence must be DNA and cannot be empty.\n \n \n+HeaderlessTSVTaxonomyFormat\n+***************************\n+Format for a 2+ column TSV file without a header.\n+\n+This format supports comment lines starting with #, and blank lines.\n+\n+\n FastqGzFormat\n *************\n \n@@ -1578,56 +1734,62 @@\n \n Additional formats without documentation:\n *****************************************\n- - PairedEndFastqManifestPhred64\n- - SingleEndFastqManifestPhred64\n- - NewickFormat\n- - SeppReferenceDirFmt\n- - PairedRNASequencesDirectoryFormat\n- - EMPPairedEndDirFmt\n- - ArtificialGroupingFormat\n- - BLAST6Format\n- - CasavaOneEightLanelessPerSampleDirFmt\n- - ProbabilitiesFormat\n- - PlacementsFormat\n- - DADA2StatsFormat\n- - SampleEstimatorDirFmt\n- - ImportanceFormat\n- - AlignedProteinFASTAFormat\n- - SingleLanePerSampleSingleEndFastqDirFmt\n- - BIOMV210Format\n- - PairedEndFastqManifestPhred33V2\n- - CasavaOneEightSingleLanePerSampleDirFmt\n- - ProteinFASTAFormat\n- - SingleEndFastqManifestPhred64V2\n- - Bowtie2IndexDirFmt\n- - DifferentialFormat\n- - UchimeStatsFmt\n+ - MixedCaseAlignedDNAFASTAFormat\n - DeblurStatsFmt\n+ - DADA2StatsFormat\n+ - PairedEndFastqManifestPhred64\n+ - BIOMV210Format\n+ - AlignedDNAFASTAFormat\n+ - DataLoafPackageDirFmt\n+ - SingleEndFastqManifestPhred64\n+ - PairedDNASequencesDirectoryFormat\n+ - BLAST6Format\n+ - EMPPairedEndDirFmt\n+ - PlacementsFormat\n+ - AlignedProteinFASTAFormat\n+ - MixedCaseRNAFASTAFormat\n+ - FirstDifferencesFormat\n+ - CasavaOneEightLanelessPerSampleDirFmt\n+ - Bowtie2IndexDirFmt\n+ - EMPSingleEndCasavaDirFmt\n+ - ProcrustesStatisticsFmt\n+ - ProteinFASTAFormat\n+ - RNAFASTAFormat\n+ - SingleLanePerSampleSingleEndFastqDirFmt\n+ - PairedEndFastqManifestPhred33V2\n+ - OrdinationFormat\n+ - MixedCaseDNAFASTAFormat\n+ - TaxonomicClassiferTemporaryPickleDirFmt\n+ - ArtificialGroupingFormat\n+ - BIOMV100Format\n+ - CasavaOneEightSingleLanePerSampleDirFmt\n+ - ErrorCorrectionDetailsFmt\n+ - ImportanceFormat\n+ - SingleEndFastqManifestPhred33V2\n+ - DNAFASTAFormat\n+ - MultiplexedFastaQualDirFmt\n+ - PredictionsFormat\n+ - MultiplexedPairedEndBarcodeInSequenceDirFmt\n - PairedEndFastqManifestPhred33\n- - AlignedRNAFASTAFormat\n+ - AlphaDiversityFormat\n+ - ProbabilitiesFormat\n - EMPSingleEndDirFmt\n+ - PairedRNASequencesDirectoryFormat\n - SingleEndFastqManifestPhred33\n- - AlignedDNAFASTAFormat\n+ - UchimeStatsFmt\n - EMPPairedEndCasavaDirFmt\n- - ProcrustesStatisticsFmt\n- - FirstDifferencesFormat\n- - BIOMV100Format\n- - PairedDNASequencesDirectoryFormat\n- - MultiplexedPairedEndBarcodeInSequenceDirFmt\n- - AlphaDiversityFormat\n+ - NewickFormat\n+ - SampleEstimatorDirFmt\n+ - DifferentialFormat\n - LSMatFormat\n- - BooleanSeriesFormat\n- - OrdinationFormat\n - SingleLanePerSamplePairedEndFastqDirFmt\n+ - QualityFilterStatsFmt\n - PairedEndFastqManifestPhred64V2\n- - RNAFASTAFormat\n- - TaxonomicClassiferTemporaryPickleDirFmt\n- - PredictionsFormat\n- - DNAFASTAFormat\n- - QualityFilterStatsFmt\n- - ErrorCorrectionDetailsFmt\n- - EMPSingleEndCasavaDirFmt\n- - SingleEndFastqManifestPhred33V2\n+ - MixedCaseAlignedRNAFASTAFormat\n+ - SingleEndFastqManifestPhred64V2\n+ - AlignedRNAFASTAFormat\n+ - BooleanSeriesFormat\n+ - SeppReferenceDirFmt\n </help>\n <citations>\n <citation type="doi">10.1038/s41587-019-0209-9</citation>\n'