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Changeset 1:94617586f2cb (2023-01-13)

Previous changeset 0:834bb534ba6d (2022-08-29) Next changeset 2:a27ceaf4cfc2 (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__group.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 834bb534ba6d -r 94617586f2cb qiime2__feature_table__group.xml
--- a/qiime2__feature_table__group.xml Mon Aug 29 19:54:40 2022 +0000
+++ b/qiime2__feature_table__group.xml Fri Jan 13 22:55:48 2023 +0000

[

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


-<tool name="qiime2 feature-table group" id="qiime2__feature_table__group" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 feature-table group" id="qiime2__feature_table__group" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
     <description>Group samples or features by a metadata column</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 group '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run feature_table group '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
@@ -62,7 +62,25 @@
     <outputs>
         <data name="grouped_table" format="qza" label="${tool.name} on ${on_string}: grouped_table.qza" from_work_dir="grouped_table.qza"/>
     </outputs>
-    <tests/>
+    <tests>
+        <test>
+            <param name="table" value="group.test0.feature-table.qza" ftype="qza"/>
+            <param name="axis" value="sample"/>
+            <conditional name="metadata">
+                <param name="type" value="tsv"/>
+                <param name="source" value="group.test0.sample-metadata.tsv" ftype="qiime2.tabular"/>
+                <param name="column" value="3"/>
+            </conditional>
+            <param name="mode" value="median-ceiling"/>
+            <output name="grouped_table" 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: FeatureTable\[Frequency\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help>
QIIME 2: feature-table group
============================
@@ -79,6 +97,36 @@
------------
Group samples or features in a feature table using metadata to define the mapping of IDs to a group.

+Examples:
+---------
+
+group_samples
+*************
+| Combine samples from the same body-site into single sample. Feature frequencies will be the median across the samples being combined, rounded up to the nearest whole number.
+Using the ``qiime2 feature-table group`` tool:
+ #. Set *"table"* to ``#: feature-table.qza``
+ #. Set *"axis"* to ``sample``
+ #. For *"metadata"*:
+
+    #. Leave as ``Metadata from TSV``
+    #. Set *"Metadata Source"* to ``sample-metadata.tsv``
+    #. Set *"Column Name"* to ``body-site``
+
+ #. Set *"mode"* to ``median-ceiling``
+ #. Press the ``Execute`` button.
+
+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
+ (Renaming is optional, but it will make any subsequent steps easier to complete.)
+
+ .. list-table::
+    :align: left
+    :header-rows: 1
+
+    * - History Name
+      - *"Name"* to set (be sure to press ``Save``)
+    * - ``#: qiime2 feature-table group [...] : grouped_table.qza``
+      - ``body-site-table.qza``
+

|

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diff -r 834bb534ba6d -r 94617586f2cb test-data/filter_samples.test0.feature-table.qza

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diff -r 834bb534ba6d -r 94617586f2cb 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 22:55:48 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 834bb534ba6d -r 94617586f2cb test-data/filter_samples.test1.feature-table.qza

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diff -r 834bb534ba6d -r 94617586f2cb 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 22:55:48 2023 +0000

diff -r 834bb534ba6d -r 94617586f2cb test-data/filter_samples.test2.feature-table.qza

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diff -r 834bb534ba6d -r 94617586f2cb test-data/filter_samples.test2.sample-metadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples.test2.sample-metadata.tsv Fri Jan 13 22:55:48 2023 +0000

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diff -r 834bb534ba6d -r 94617586f2cb 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 22:55:48 2023 +0000

diff -r 834bb534ba6d -r 94617586f2cb test-data/filter_samples.test4.feature-table.qza

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diff -r 834bb534ba6d -r 94617586f2cb test-data/filter_samples.test4.sample-metadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples.test4.sample-metadata.tsv Fri Jan 13 22:55:48 2023 +0000

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diff -r 834bb534ba6d -r 94617586f2cb 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 22:55:48 2023 +0000

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