Mercurial > repos > q2d2 > qiime2_core__tools__export

changeset 1:d3b1853c4efd draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 23:02:16 +0000
parents 0214b9ae8a6e
children ddff0f6d5740
files qiime2_core__tools__export.xml
diffstat 1 files changed, 79 insertions(+), 63 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2_core__tools__export.xml	Mon Aug 29 20:37:34 2022 +0000
+++ b/qiime2_core__tools__export.xml	Fri Jan 13 23:02:16 2023 +0000
@@ -1,21 +1,21 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2022, QIIME 2 development team.
+Copyright (c) 2023, 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)
+    q2galaxy (version: 2022.11.1)
 for:
-    qiime2 (version: 2022.8.1)
+    qiime2 (version: 2022.11.1)
 -->
-<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2022.8.1+dist.h91e3be72.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2022.11.1+dist.h2bda5906.2" profile="22.05" license="BSD-3-Clause">
     <description>Export data from a QIIME 2 artifact</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2022.8</container>
+        <container type="docker">quay.io/qiime2/core:2022.11</container>
     </requirements>
-    <command>q2galaxy run tools export '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run tools export '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
@@ -44,6 +44,7 @@
                 <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__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>
@@ -152,6 +153,12 @@
                     <option value="BLAST6Format">BLAST6 Format</option>
                 </param>
             </when>
+            <when value="FeatureData__ob__DifferentialAbundance__cb__">
+                <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
+                    <option value="None" selected="true">export as is (no conversion)</option>
+                    <option value="DataLoafPackageDirFmt">Data Loaf Package Directory Format</option>
+                </param>
+            </when>
             <when value="FeatureData__ob__Differential__cb__">
                 <param name="output_format" type="select" label="QIIME 2 file format to convert to:">
                     <option value="None" selected="true">export as is (no conversion)</option>
@@ -427,7 +434,7 @@
     </inputs>
     <outputs>
         <collection name="exported" type="list" label="${tool.name} on ${on_string} as ${fmt_peek}">
-            <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'NewickFormat', 'DADA2StatsFormat', 'AlignedProteinFASTAFormat', 'QualityFilterStatsDirFmt', 'ProbabilitiesFormat', 'OrdinationFormat', 'SingleLanePerSamplePairedEndFastqDirFmt', 'EMPPairedEndDirFmt', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'AlignedDNASequencesDirectoryFormat', 'TSVTaxonomyDirectoryFormat', 'AlignedRNAFASTAFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'BooleanSeriesFormat', 'QualityFilterStatsFmt', 'BIOMV210DirFmt', 'EMPSingleEndDirFmt', 'Bowtie2IndexDirFmt', 'PlacementsFormat', 'TrueTargetsDirectoryFormat', 'AlignedRNASequencesDirectoryFormat', 'ProbabilitiesDirectoryFormat', 'ArtificialGroupingDirectoryFormat', 'DifferentialDirectoryFormat', 'AlignedDNAFASTAFormat', 'LSMatFormat', 'FastqGzFormat', 'RNASequencesDirectoryFormat', 'ProteinSequencesDirectoryFormat', 'DADA2StatsDirFmt', 'SeppReferenceDirFmt', 'DNAFASTAFormat', 'QIIME1DemuxDirFmt', 'BooleanSeriesDirectoryFormat', 'PairedRNASequencesDirectoryFormat', 'AlphaDiversityFormat', 'PlacementsDirFmt', 'ProcrustesStatisticsDirFmt', 'ImportanceFormat', 'NewickDirectoryFormat', 'TSVTaxonomyFormat', 'DifferentialFormat', 'QIIME1DemuxFormat', 'CasavaOneEightSingleLanePerSampleDirFmt', 'BLAST6Format', 'UchimeStatsFmt', 'FirstDifferencesFormat', 'PredictionsDirectoryFormat', 'ProcrustesStatisticsFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'AlignedProteinSequencesDirectoryFormat', 'SampleEstimatorDirFmt', 'RNAFASTAFormat', 'ProteinFASTAFormat', 'ArtificialGroupingFormat', 'AlphaDiversityDirectoryFormat', 'UchimeStatsDirFmt', 'TaxonomicClassiferTemporaryPickleDirFmt', 'PairedDNASequencesDirectoryFormat', 'DNASequencesDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'DeblurStatsFmt', 'DeblurStatsDirFmt', 'ErrorCorrectionDetailsDirFmt', 'OrdinationDirectoryFormat', 'BLAST6DirectoryFormat', 'BIOMV210Format', 'PredictionsFormat', 'ImportanceDirectoryFormat', 'FirstDifferencesDirectoryFormat'}</filter>
+            <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'TSVTaxonomyDirectoryFormat', 'EMPPairedEndDirFmt', 'AlignedRNASequencesDirectoryFormat', 'AlignedProteinFASTAFormat', 'QualityFilterStatsDirFmt', 'OrdinationFormat', 'DeblurStatsFmt', 'ImportanceDirectoryFormat', 'ArtificialGroupingDirectoryFormat', 'Bowtie2IndexDirFmt', 'BooleanSeriesDirectoryFormat', 'ArtificialGroupingFormat', 'SampleEstimatorDirFmt', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'TaxonomicClassiferTemporaryPickleDirFmt', 'AlphaDiversityFormat', 'TrueTargetsDirectoryFormat', 'PairedDNASequencesDirectoryFormat', 'UchimeStatsDirFmt', 'DifferentialFormat', 'AlignedDNASequencesDirectoryFormat', 'PredictionsDirectoryFormat', 'DADA2StatsDirFmt', 'SingleLanePerSamplePairedEndFastqDirFmt', 'DNAFASTAFormat', 'DADA2StatsFormat', 'RNAFASTAFormat', 'AlignedRNAFASTAFormat', 'UchimeStatsFmt', 'ErrorCorrectionDetailsDirFmt', 'FastqGzFormat', 'QIIME1DemuxDirFmt', 'PairedRNASequencesDirectoryFormat', 'ProcrustesStatisticsDirFmt', 'DeblurStatsDirFmt', 'ImportanceFormat', 'AlignedProteinSequencesDirectoryFormat', 'DifferentialDirectoryFormat', 'NewickDirectoryFormat', 'NewickFormat', 'OrdinationDirectoryFormat', 'LSMatFormat', 'BooleanSeriesFormat', 'ProteinFASTAFormat', 'EMPSingleEndDirFmt', 'QIIME1DemuxFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'PlacementsFormat', 'PredictionsFormat', 'ProteinSequencesDirectoryFormat', 'QualityFilterStatsFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'FirstDifferencesDirectoryFormat', 'FirstDifferencesFormat', 'PlacementsDirFmt', 'DNASequencesDirectoryFormat', 'SeppReferenceDirFmt', 'TSVTaxonomyFormat', 'ProcrustesStatisticsFmt', 'RNASequencesDirectoryFormat', 'BIOMV210DirFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'BIOMV210Format', 'AlphaDiversityDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'BLAST6Format', 'AlignedDNAFASTAFormat', 'ProbabilitiesFormat', 'ProbabilitiesDirectoryFormat', 'BLAST6DirectoryFormat', 'DataLoafPackageDirFmt'}</filter>
             <discover_datasets pattern="__designation_and_ext__" visible="false"/>
         </collection>
         <data name="AlignedDNAFASTAFormat" label="${tool.name} on ${on_string} as AlignedDNAFASTAFormat">
@@ -523,6 +530,14 @@
             <filter>fmt_finder['output_format'] == 'DNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNASequencesDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;dna-sequences)\.(?P&lt;ext&gt;fasta)" visible="true"/>
         </data>
+        <collection name="DataLoafPackageDirFmt_data_slices" type="list" label="${tool.name} on ${on_string} as DataLoafPackageDirFmt (data_slices)">
+            <filter>fmt_finder['output_format'] == 'DataLoafPackageDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DataLoafPackageDirFmt')</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;csv)" visible="false"/>
+        </collection>
+        <data name="DataLoafPackageDirFmt" label="${tool.name} on ${on_string} as DataLoafPackageDirFmt">
+            <filter>fmt_finder['output_format'] == 'DataLoafPackageDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DataLoafPackageDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;datapackage)\.(?P&lt;ext&gt;json)" visible="true"/>
+        </data>
         <data name="DeblurStatsDirFmt" label="${tool.name} on ${on_string} as DeblurStatsDirFmt">
             <filter>fmt_finder['output_format'] == 'DeblurStatsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DeblurStatsDirFmt')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;stats)\.(?P&lt;ext&gt;csv)" visible="true"/>
@@ -817,73 +832,74 @@
 
 Additional formats without documentation:
 *****************************************
- - AlignedRNASequencesDirectoryFormat
+ - QIIME1DemuxDirFmt
+ - ArtificialGroupingDirectoryFormat
+ - DeblurStatsFmt
+ - DADA2StatsFormat
+ - ImportanceDirectoryFormat
+ - BIOMV210Format
+ - AlphaDiversityDirectoryFormat
+ - AlignedDNAFASTAFormat
+ - DataLoafPackageDirFmt
  - MultiplexedSingleEndBarcodeInSequenceDirFmt
- - AlignedDNASequencesDirectoryFormat
- - NewickFormat
- - SeppReferenceDirFmt
- - ProcrustesStatisticsDirFmt
- - PairedRNASequencesDirectoryFormat
- - BIOMV210DirFmt
+ - QualityFilterStatsDirFmt
+ - BLAST6Format
+ - PairedDNASequencesDirectoryFormat
  - EMPPairedEndDirFmt
- - DistanceMatrixDirectoryFormat
- - AlphaDiversityDirectoryFormat
- - OrdinationDirectoryFormat
- - ArtificialGroupingFormat
- - BLAST6Format
- - RNASequencesDirectoryFormat
- - ProbabilitiesFormat
+ - NewickDirectoryFormat
  - PlacementsFormat
- - DADA2StatsFormat
- - SampleEstimatorDirFmt
- - ImportanceFormat
+ - FirstDifferencesDirectoryFormat
  - AlignedProteinFASTAFormat
- - DNASequencesDirectoryFormat
- - BIOMV210Format
+ - BIOMV210DirFmt
+ - DistanceMatrixDirectoryFormat
  - TSVTaxonomyDirectoryFormat
- - QualityFilterStatsDirFmt
- - SingleLanePerSampleSingleEndFastqDirFmt
- - CasavaOneEightSingleLanePerSampleDirFmt
+ - FirstDifferencesFormat
+ - TrueTargetsDirectoryFormat
+ - Bowtie2IndexDirFmt
+ - ProcrustesStatisticsFmt
  - ProteinFASTAFormat
+ - RNAFASTAFormat
  - ProbabilitiesDirectoryFormat
+ - SingleLanePerSampleSingleEndFastqDirFmt
+ - OrdinationFormat
+ - AlignedRNASequencesDirectoryFormat
+ - PlacementsDirFmt
+ - TaxonomicClassiferTemporaryPickleDirFmt
+ - ArtificialGroupingFormat
+ - CasavaOneEightSingleLanePerSampleDirFmt
+ - ImportanceFormat
+ - DifferentialDirectoryFormat
+ - DNAFASTAFormat
  - DADA2StatsDirFmt
- - Bowtie2IndexDirFmt
- - DifferentialFormat
- - QIIME1DemuxDirFmt
+ - BooleanSeriesDirectoryFormat
+ - AlignedDNASequencesDirectoryFormat
+ - PredictionsFormat
+ - MultiplexedPairedEndBarcodeInSequenceDirFmt
+ - AlphaDiversityFormat
+ - ProbabilitiesFormat
+ - EMPSingleEndDirFmt
+ - BLAST6DirectoryFormat
+ - PairedRNASequencesDirectoryFormat
+ - PredictionsDirectoryFormat
  - UchimeStatsFmt
- - DeblurStatsFmt
- - DeblurStatsDirFmt
- - AlignedRNAFASTAFormat
- - NewickDirectoryFormat
- - EMPSingleEndDirFmt
- - PredictionsDirectoryFormat
- - AlignedDNAFASTAFormat
- - ArtificialGroupingDirectoryFormat
- - FirstDifferencesDirectoryFormat
- - ProcrustesStatisticsFmt
- - FirstDifferencesFormat
- - BLAST6DirectoryFormat
- - PairedDNASequencesDirectoryFormat
- - ErrorCorrectionDetailsDirFmt
- - MultiplexedPairedEndBarcodeInSequenceDirFmt
+ - AlignedProteinSequencesDirectoryFormat
+ - NewickFormat
+ - UchimeStatsDirFmt
+ - SampleEstimatorDirFmt
+ - ProcrustesStatisticsDirFmt
+ - DifferentialFormat
+ - ProteinSequencesDirectoryFormat
+ - RNASequencesDirectoryFormat
  - LSMatFormat
- - AlphaDiversityFormat
- - PlacementsDirFmt
- - OrdinationFormat
+ - SingleLanePerSamplePairedEndFastqDirFmt
+ - QualityFilterStatsFmt
+ - OrdinationDirectoryFormat
+ - ErrorCorrectionDetailsDirFmt
+ - AlignedRNAFASTAFormat
+ - DNASequencesDirectoryFormat
  - BooleanSeriesFormat
- - ImportanceDirectoryFormat
- - AlignedProteinSequencesDirectoryFormat
- - RNAFASTAFormat
- - SingleLanePerSamplePairedEndFastqDirFmt
- - TaxonomicClassiferTemporaryPickleDirFmt
- - PredictionsFormat
- - TrueTargetsDirectoryFormat
- - ProteinSequencesDirectoryFormat
- - DNAFASTAFormat
- - QualityFilterStatsFmt
- - BooleanSeriesDirectoryFormat
- - DifferentialDirectoryFormat
- - UchimeStatsDirFmt
+ - SeppReferenceDirFmt
+ - DeblurStatsDirFmt
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>