Mercurial > repos > q2d2 > qiime2_core__tools__import

changeset 2:18c6b2b6740f draft

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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
files qiime2_core__tools__import.xml
diffstat 1 files changed, 99 insertions(+), 69 deletions(-) [+]
line wrap: on
line diff
--- 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
@@ -6,14 +6,14 @@
 -->
 <!--
 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>
@@ -69,6 +69,7 @@
                 <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>
@@ -86,6 +87,7 @@
                 <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>
@@ -329,6 +331,19 @@
                     </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:">
@@ -664,6 +679,19 @@
                     </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:">
@@ -1660,31 +1688,6 @@
 --------
 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.
@@ -1719,6 +1722,21 @@
 - 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.
@@ -1732,64 +1750,76 @@
 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
- - DADA2StatsFormat
- - PairedEndFastqManifestPhred64
- - BIOMV210Format
+ - SingleLanePerSamplePairedEndFastqDirFmt
+ - EMPPairedEndDirFmt
+ - ImmutableMetadataFormat
+ - PairedEndFastqManifestPhred64V2
+ - DataLoafPackageDirFmt
  - AlignedDNAFASTAFormat
- - DataLoafPackageDirFmt
- - SingleEndFastqManifestPhred64
+ - BIOMV100Format
+ - UchimeStatsFmt
+ - BLAST6Format
  - PairedDNASequencesDirectoryFormat
- - BLAST6Format
- - EMPPairedEndDirFmt
- - PlacementsFormat
+ - SingleEndFastqManifestPhred33V2
+ - QualityFilterStatsFmt
+ - DADA2StatsFormat
  - AlignedProteinFASTAFormat
  - MixedCaseRNAFASTAFormat
- - FirstDifferencesFormat
- - CasavaOneEightLanelessPerSampleDirFmt
- - Bowtie2IndexDirFmt
- - EMPSingleEndCasavaDirFmt
- - ProcrustesStatisticsFmt
+ - PlacementsFormat
+ - NewickFormat
+ - PairedEndFastqManifestPhred64
  - ProteinFASTAFormat
  - RNAFASTAFormat
- - SingleLanePerSampleSingleEndFastqDirFmt
- - PairedEndFastqManifestPhred33V2
- - OrdinationFormat
+ - BooleanSeriesFormat
+ - SingleEndFastqManifestPhred64
+ - LSMatFormat
+ - DeblurStatsFmt
+ - ErrorCorrectionDetailsFmt
  - MixedCaseDNAFASTAFormat
  - TaxonomicClassiferTemporaryPickleDirFmt
- - ArtificialGroupingFormat
- - BIOMV100Format
+ - DNAFASTAFormat
+ - ProcrustesStatisticsFmt
+ - CasavaOneEightLanelessPerSampleDirFmt
+ - EMPSingleEndDirFmt
+ - DecontamScoreFormat
+ - OrdinationFormat
+ - SingleLanePerSampleSingleEndFastqDirFmt
+ - Bowtie2IndexDirFmt
+ - BIOMV210Format
+ - PairedEndFastqManifestPhred33V2
+ - SampleEstimatorDirFmt
+ - EMPSingleEndCasavaDirFmt
+ - PairedRNASequencesDirectoryFormat
+ - EMPPairedEndCasavaDirFmt
  - CasavaOneEightSingleLanePerSampleDirFmt
- - ErrorCorrectionDetailsFmt
- - ImportanceFormat
- - SingleEndFastqManifestPhred33V2
- - DNAFASTAFormat
+ - SingleEndFastqManifestPhred64V2
  - MultiplexedFastaQualDirFmt
- - PredictionsFormat
+ - DifferentialFormat
+ - AlphaDiversityFormat
  - MultiplexedPairedEndBarcodeInSequenceDirFmt
  - PairedEndFastqManifestPhred33
- - AlphaDiversityFormat
+ - ArtificialGroupingFormat
  - ProbabilitiesFormat
- - EMPSingleEndDirFmt
- - PairedRNASequencesDirectoryFormat
+ - SeppReferenceDirFmt
+ - MixedCaseAlignedRNAFASTAFormat
  - SingleEndFastqManifestPhred33
- - UchimeStatsFmt
- - EMPPairedEndCasavaDirFmt
- - NewickFormat
- - SampleEstimatorDirFmt
- - DifferentialFormat
- - LSMatFormat
- - SingleLanePerSamplePairedEndFastqDirFmt
- - QualityFilterStatsFmt
- - PairedEndFastqManifestPhred64V2
- - MixedCaseAlignedRNAFASTAFormat
- - SingleEndFastqManifestPhred64V2
+ - ImportanceFormat
  - AlignedRNAFASTAFormat
- - BooleanSeriesFormat
- - SeppReferenceDirFmt
+ - PredictionsFormat
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>