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Changeset 1:0ffd4aef0c59 (2023-01-13)

Previous changeset 0:3828e8e6487f (2022-08-29) Next changeset 2:a0c16a5250e4 (2023-06-08)

Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732

modified:
qiime2__feature_table__merge_taxa.xml
test-data/merge.test0.feature-table1.qza
test-data/merge.test0.feature-table2.qza
test-data/merge.test1.feature-table1.qza
test-data/merge.test1.feature-table2.qza
test-data/merge.test1.feature-table3.qza

diff -r 3828e8e6487f -r 0ffd4aef0c59 qiime2__feature_table__merge_taxa.xml
--- a/qiime2__feature_table__merge_taxa.xml Mon Aug 29 19:57:10 2022 +0000
+++ b/qiime2__feature_table__merge_taxa.xml Fri Jan 13 22:55:22 2023 +0000

[

@@ -1,22 +1,22 @@
<?xml version='1.0' encoding='utf-8'?>


-<tool name="qiime2 feature-table merge-taxa" id="qiime2__feature_table__merge_taxa" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 feature-table merge-taxa" id="qiime2__feature_table__merge_taxa" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
     <description>Combine collections of feature taxonomies</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2022.8</container>
+        <container type="docker">quay.io/qiime2/core:2022.11</container>
     </requirements>
     <version_command>q2galaxy version feature_table</version_command>
-    <command detect_errors="aggressive">q2galaxy run feature_table merge_taxa '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run feature_table merge_taxa '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
@@ -30,7 +30,18 @@
     <outputs>
         <data name="merged_data" format="qza" label="${tool.name} on ${on_string}: merged_data.qza" from_work_dir="merged_data.qza"/>
     </outputs>
-    <tests/>
+    <tests>
+        <test>
+            <param name="data" value="merge_taxa.test0.tax1.qza,merge_taxa.test0.tax2.qza" ftype="qza"/>
+            <output name="merged_data" ftype="qza">
+                <assert_contents>
+                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
+                        <has_line_matching expression="type: FeatureData\[Taxonomy\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help>
QIIME 2: feature-table merge-taxa
=================================
@@ -47,6 +58,20 @@
------------
Combines a pair of feature data objects which may or may not contain data for the same features. If different feature data is present for the same feature id in the inputs, the data from the first will be propagated to the result.

+Examples:
+---------
+
+feature_table_merge_taxa
+************************
+Using the ``qiime2 feature-table merge-taxa`` tool:
+ #. For *"data"*, use ctrl-(or command)-click to select the following inputs:
+
+    #. ``#: tax1.qza``
+    #. ``#: tax2.qza``
+
+ #. Press the ``Execute`` button.
+
+

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diff -r 3828e8e6487f -r 0ffd4aef0c59 test-data/filter_samples.test0.feature-table.qza

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diff -r 3828e8e6487f -r 0ffd4aef0c59 test-data/filter_samples.test0.sample-metadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples.test0.sample-metadata.tsv Fri Jan 13 22:55:22 2023 +0000

@@ -0,0 +1,36 @@
+sample-id barcode-sequence body-site year month day subject reported-antibiotic-usage days-since-experiment-start
+#q2:types categorical categorical numeric numeric numeric categorical categorical numeric
+L1S8 AGCTGACTAGTC gut 2008 10 28 subject-1 Yes 0
+L1S57 ACACACTATGGC gut 2009 1 20 subject-1 No 84
+L1S76 ACTACGTGTGGT gut 2009 2 17 subject-1 No 112
+L1S105 AGTGCGATGCGT gut 2009 3 17 subject-1 No 140
+L2S155 ACGATGCGACCA left palm 2009 1 20 subject-1 No 84
+L2S175 AGCTATCCACGA left palm 2009 2 17 subject-1 No 112
+L2S204 ATGCAGCTCAGT left palm 2009 3 17 subject-1 No 140
+L2S222 CACGTGACATGT left palm 2009 4 14 subject-1 No 168
+L3S242 ACAGTTGCGCGA right palm 2008 10 28 subject-1 Yes 0
+L3S294 CACGACAGGCTA right palm 2009 1 20 subject-1 No 84
+L3S313 AGTGTCACGGTG right palm 2009 2 17 subject-1 No 112
+L3S341 CAAGTGAGAGAG right palm 2009 3 17 subject-1 No 140
+L3S360 CATCGTATCAAC right palm 2009 4 14 subject-1 No 168
+L5S104 CAGTGTCAGGAC tongue 2008 10 28 subject-1 Yes 0
+L5S155 ATCTTAGACTGC tongue 2009 1 20 subject-1 No 84
+L5S174 CAGACATTGCGT tongue 2009 2 17 subject-1 No 112
+L5S203 CGATGCACCAGA tongue 2009 3 17 subject-1 No 140
+L5S222 CTAGAGACTCTT tongue 2009 4 14 subject-1 No 168
+L1S140 ATGGCAGCTCTA gut 2008 10 28 subject-2 Yes 0
+L1S208 CTGAGATACGCG gut 2009 1 20 subject-2 No 84
+L1S257 CCGACTGAGATG gut 2009 3 17 subject-2 No 140
+L1S281 CCTCTCGTGATC gut 2009 4 14 subject-2 No 168
+L2S240 CATATCGCAGTT left palm 2008 10 28 subject-2 Yes 0
+L2S309 CGTGCATTATCA left palm 2009 1 20 subject-2 No 84
+L2S357 CTAACGCAGTCA left palm 2009 3 17 subject-2 No 140
+L2S382 CTCAATGACTCA left palm 2009 4 14 subject-2 No 168
+L3S378 ATCGATCTGTGG right palm 2008 10 28 subject-2 Yes 0
+L4S63 CTCGTGGAGTAG right palm 2009 1 20 subject-2 No 84
+L4S112 GCGTTACACACA right palm 2009 3 17 subject-2 No 140
+L4S137 GAACTGTATCTC right palm 2009 4 14 subject-2 No 168
+L5S240 CTGGACTCATAG tongue 2008 10 28 subject-2 Yes 0
+L6S20 GAGGCTCATCAT tongue 2009 1 20 subject-2 No 84
+L6S68 GATACGTCCTGA tongue 2009 3 17 subject-2 No 140
+L6S93 GATTAGCACTCT tongue 2009 4 14 subject-2 No 168

diff -r 3828e8e6487f -r 0ffd4aef0c59 test-data/filter_samples.test1.feature-table.qza

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diff -r 3828e8e6487f -r 0ffd4aef0c59 test-data/filter_samples.test1.sample-metadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples.test1.sample-metadata.tsv Fri Jan 13 22:55:22 2023 +0000

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diff -r 3828e8e6487f -r 0ffd4aef0c59 test-data/filter_samples.test2.sample-metadata.tsv
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diff -r 3828e8e6487f -r 0ffd4aef0c59 test-data/filter_samples.test3.sample-metadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples.test3.sample-metadata.tsv Fri Jan 13 22:55:22 2023 +0000

diff -r 3828e8e6487f -r 0ffd4aef0c59 test-data/filter_samples.test4.feature-table.qza

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diff -r 3828e8e6487f -r 0ffd4aef0c59 test-data/filter_samples.test4.sample-metadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 3828e8e6487f -r 0ffd4aef0c59 test-data/group.test0.sample-metadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/group.test0.sample-metadata.tsv Fri Jan 13 22:55:22 2023 +0000

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