Mercurial > repos > q2d2 > qiime2_core__tools__export

changeset 2:ddff0f6d5740 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 19:53:25 +0000
parents d3b1853c4efd
children f47ed6c69f5d
files qiime2_core__tools__export.xml
diffstat 1 files changed, 102 insertions(+), 68 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2_core__tools__export.xml	Fri Jan 13 23:02:16 2023 +0000
+++ b/qiime2_core__tools__export.xml	Thu Jun 08 19:53:25 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 export" id="qiime2_core__tools__export" version="2022.11.1+dist.h2bda5906.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools export" id="qiime2_core__tools__export" version="2023.5.0+dist.h193f7cc9.2" profile="22.05" license="BSD-3-Clause">
     <description>Export data from a QIIME 2 artifact</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2022.11</container>
+        <container type="docker">quay.io/qiime2/core:2023.5</container>
     </requirements>
     <command detect_errors="exit_code">q2galaxy run tools export '$inputs'</command>
     <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__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>
@@ -61,6 +62,7 @@
                 <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>
@@ -153,6 +155,12 @@
                     <option value="BLAST6Format">BLAST6 Format</option>
                 </param>
             </when>
+            <when value="FeatureData__ob__DecontamScore__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="DecontamScoreFormat">Decontam Score 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>
@@ -262,6 +270,12 @@
                     <option value="NewickFormat">Newick Format</option>
                 </param>
             </when>
+            <when value="ImmutableMetadata">
+                <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="ImmutableMetadataFormat">Immutable Metadata Format</option>
+                </param>
+            </when>
             <when value="MultiplexedPairedEndBarcodeInSequence">
                 <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>
@@ -434,7 +448,7 @@
     </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 {'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>
+            <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'QIIME1DemuxFormat', 'DNAFASTAFormat', 'PlacementsDirFmt', 'ImmutableMetadataFormat', 'Bowtie2IndexDirFmt', 'QIIME1DemuxDirFmt', 'AlignedDNASequencesDirectoryFormat', 'DADA2StatsDirFmt', 'AlignedRNASequencesDirectoryFormat', 'OrdinationFormat', 'ProteinFASTAFormat', 'LSMatFormat', 'PairedRNASequencesDirectoryFormat', 'DifferentialFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'AlignedProteinFASTAFormat', 'ArtificialGroupingDirectoryFormat', 'RNAFASTAFormat', 'SeppReferenceDirFmt', 'FastqGzFormat', 'ProcrustesStatisticsDirFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'QualityFilterStatsFmt', 'PlacementsFormat', 'ProbabilitiesDirectoryFormat', 'ImportanceDirectoryFormat', 'FirstDifferencesFormat', 'TrueTargetsDirectoryFormat', 'ImmutableMetadataDirectoryFormat', 'UchimeStatsDirFmt', 'NewickDirectoryFormat', 'DADA2StatsFormat', 'AlignedDNAFASTAFormat', 'PredictionsDirectoryFormat', 'AlphaDiversityDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'DeblurStatsDirFmt', 'DNASequencesDirectoryFormat', 'SingleLanePerSamplePairedEndFastqDirFmt', 'UchimeStatsFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'ErrorCorrectionDetailsDirFmt', 'BLAST6DirectoryFormat', 'DecontamScoreDirFmt', 'SampleEstimatorDirFmt', 'FirstDifferencesDirectoryFormat', 'QualityFilterStatsDirFmt', 'DistanceMatrixDirectoryFormat', 'DecontamScoreFormat', 'EMPSingleEndDirFmt', 'EMPPairedEndDirFmt', 'DataLoafPackageDirFmt', 'PairedDNASequencesDirectoryFormat', 'BIOMV210DirFmt', 'AlignedRNAFASTAFormat', 'OrdinationDirectoryFormat', 'BIOMV210Format', 'AlphaDiversityFormat', 'ArtificialGroupingFormat', 'DeblurStatsFmt', 'TSVTaxonomyDirectoryFormat', 'PredictionsFormat', 'BooleanSeriesFormat', 'DifferentialDirectoryFormat', 'ProcrustesStatisticsFmt', 'BooleanSeriesDirectoryFormat', 'AlignedProteinSequencesDirectoryFormat', 'TSVTaxonomyFormat', 'NewickFormat', 'ProteinSequencesDirectoryFormat', 'BLAST6Format', 'ImportanceFormat', 'RNASequencesDirectoryFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'ProbabilitiesFormat'}</filter>
             <discover_datasets pattern="__designation_and_ext__" visible="false"/>
         </collection>
         <data name="AlignedDNAFASTAFormat" label="${tool.name} on ${on_string} as AlignedDNAFASTAFormat">
@@ -546,6 +560,14 @@
             <filter>fmt_finder['output_format'] == 'DeblurStatsFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DeblurStatsFmt')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <data name="DecontamScoreDirFmt" label="${tool.name} on ${on_string} as DecontamScoreDirFmt">
+            <filter>fmt_finder['output_format'] == 'DecontamScoreDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DecontamScoreDirFmt')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;stats)\.(?P&lt;ext&gt;tsv)" visible="true"/>
+        </data>
+        <data name="DecontamScoreFormat" label="${tool.name} on ${on_string} as DecontamScoreFormat">
+            <filter>fmt_finder['output_format'] == 'DecontamScoreFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DecontamScoreFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
+        </data>
         <data name="DifferentialDirectoryFormat" label="${tool.name} on ${on_string} as DifferentialDirectoryFormat">
             <filter>fmt_finder['output_format'] == 'DifferentialDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DifferentialDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;differentials)\.(?P&lt;ext&gt;tsv)" visible="true"/>
@@ -585,6 +607,14 @@
             <filter>fmt_finder['output_format'] == 'FirstDifferencesFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'FirstDifferencesFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
         </data>
+        <data name="ImmutableMetadataDirectoryFormat" label="${tool.name} on ${on_string} as ImmutableMetadataDirectoryFormat">
+            <filter>fmt_finder['output_format'] == 'ImmutableMetadataDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ImmutableMetadataDirectoryFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;metadata)\.(?P&lt;ext&gt;tsv)" visible="true"/>
+        </data>
+        <data name="ImmutableMetadataFormat" label="${tool.name} on ${on_string} as ImmutableMetadataFormat">
+            <filter>fmt_finder['output_format'] == 'ImmutableMetadataFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ImmutableMetadataFormat')</filter>
+            <discover_datasets assign_primary_output="true" pattern="__designation_and_ext__" visible="true"/>
+        </data>
         <data name="ImportanceDirectoryFormat" label="${tool.name} on ${on_string} as ImportanceDirectoryFormat">
             <filter>fmt_finder['output_format'] == 'ImportanceDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ImportanceDirectoryFormat')</filter>
             <discover_datasets assign_primary_output="true" pattern="(?P&lt;designation&gt;importance)\.(?P&lt;ext&gt;tsv)" visible="true"/>
@@ -775,21 +805,6 @@
 --------
 These formats have documentation available.
 
-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.
@@ -824,6 +839,21 @@
 - 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.
+
+
 FastqGzFormat
 *************
 
@@ -832,74 +862,78 @@
 
 Additional formats without documentation:
 *****************************************
- - QIIME1DemuxDirFmt
- - ArtificialGroupingDirectoryFormat
- - DeblurStatsFmt
- - DADA2StatsFormat
- - ImportanceDirectoryFormat
- - BIOMV210Format
+ - FirstDifferencesFormat
+ - DecontamScoreDirFmt
+ - OrdinationDirectoryFormat
+ - EMPPairedEndDirFmt
+ - ImmutableMetadataFormat
+ - PredictionsDirectoryFormat
  - AlphaDiversityDirectoryFormat
+ - DataLoafPackageDirFmt
  - AlignedDNAFASTAFormat
- - DataLoafPackageDirFmt
- - MultiplexedSingleEndBarcodeInSequenceDirFmt
- - QualityFilterStatsDirFmt
+ - DADA2StatsDirFmt
+ - TrueTargetsDirectoryFormat
+ - UchimeStatsFmt
  - BLAST6Format
  - PairedDNASequencesDirectoryFormat
- - EMPPairedEndDirFmt
- - NewickDirectoryFormat
- - PlacementsFormat
- - FirstDifferencesDirectoryFormat
+ - QIIME1DemuxDirFmt
+ - QualityFilterStatsFmt
+ - DADA2StatsFormat
  - AlignedProteinFASTAFormat
- - BIOMV210DirFmt
- - DistanceMatrixDirectoryFormat
- - TSVTaxonomyDirectoryFormat
- - FirstDifferencesFormat
- - TrueTargetsDirectoryFormat
- - Bowtie2IndexDirFmt
- - ProcrustesStatisticsFmt
+ - PlacementsFormat
+ - NewickFormat
+ - ProbabilitiesDirectoryFormat
+ - ErrorCorrectionDetailsDirFmt
  - ProteinFASTAFormat
  - RNAFASTAFormat
- - ProbabilitiesDirectoryFormat
- - SingleLanePerSampleSingleEndFastqDirFmt
- - OrdinationFormat
+ - MultiplexedSingleEndBarcodeInSequenceDirFmt
+ - BooleanSeriesFormat
+ - LSMatFormat
+ - ImportanceDirectoryFormat
+ - DeblurStatsFmt
  - AlignedRNASequencesDirectoryFormat
- - PlacementsDirFmt
+ - QualityFilterStatsDirFmt
  - TaxonomicClassiferTemporaryPickleDirFmt
- - ArtificialGroupingFormat
- - CasavaOneEightSingleLanePerSampleDirFmt
- - ImportanceFormat
+ - BooleanSeriesDirectoryFormat
  - DifferentialDirectoryFormat
  - DNAFASTAFormat
- - DADA2StatsDirFmt
- - BooleanSeriesDirectoryFormat
- - AlignedDNASequencesDirectoryFormat
- - PredictionsFormat
- - MultiplexedPairedEndBarcodeInSequenceDirFmt
- - AlphaDiversityFormat
- - ProbabilitiesFormat
+ - ProcrustesStatisticsFmt
+ - PlacementsDirFmt
  - EMPSingleEndDirFmt
- - BLAST6DirectoryFormat
+ - DecontamScoreFormat
+ - BIOMV210DirFmt
+ - ImmutableMetadataDirectoryFormat
+ - AlignedDNASequencesDirectoryFormat
+ - TSVTaxonomyDirectoryFormat
+ - OrdinationFormat
+ - FirstDifferencesDirectoryFormat
+ - Bowtie2IndexDirFmt
+ - BIOMV210Format
+ - SingleLanePerSampleSingleEndFastqDirFmt
+ - SampleEstimatorDirFmt
  - PairedRNASequencesDirectoryFormat
- - PredictionsDirectoryFormat
- - UchimeStatsFmt
+ - CasavaOneEightSingleLanePerSampleDirFmt
  - AlignedProteinSequencesDirectoryFormat
- - NewickFormat
  - UchimeStatsDirFmt
- - SampleEstimatorDirFmt
- - ProcrustesStatisticsDirFmt
+ - NewickDirectoryFormat
+ - SingleLanePerSamplePairedEndFastqDirFmt
  - DifferentialFormat
  - ProteinSequencesDirectoryFormat
  - RNASequencesDirectoryFormat
- - LSMatFormat
- - SingleLanePerSamplePairedEndFastqDirFmt
- - QualityFilterStatsFmt
- - OrdinationDirectoryFormat
- - ErrorCorrectionDetailsDirFmt
+ - MultiplexedPairedEndBarcodeInSequenceDirFmt
+ - AlphaDiversityFormat
+ - DistanceMatrixDirectoryFormat
+ - ArtificialGroupingFormat
+ - ArtificialGroupingDirectoryFormat
+ - ProbabilitiesFormat
+ - DeblurStatsDirFmt
+ - SeppReferenceDirFmt
+ - ImportanceFormat
+ - BLAST6DirectoryFormat
  - AlignedRNAFASTAFormat
  - DNASequencesDirectoryFormat
- - BooleanSeriesFormat
- - SeppReferenceDirFmt
- - DeblurStatsDirFmt
+ - ProcrustesStatisticsDirFmt
+ - PredictionsFormat
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>