# HG changeset patch
# User q2d2
# Date 1673649790 0
# Node ID 222b50c1cb52f538450eb8fc1ceef40850f20645
# Parent  3e85de16634033bdc80b3e087f73c994b10f7c75
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 69da7976573cc07a363ac66bdacc9269d7cd3732

diff -r 3e85de166340 -r 222b50c1cb52 qiime2__demux__summarize.xml
--- a/qiime2__demux__summarize.xml	Mon Aug 29 19:28:01 2022 +0000
+++ b/qiime2__demux__summarize.xml	Fri Jan 13 22:43:10 2023 +0000
@@ -1,31 +1,31 @@
 <?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 demux summarize" id="qiime2__demux__summarize" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 demux summarize" id="qiime2__demux__summarize" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
     <description>Summarize counts per sample.</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 demux</version_command>
-    <command detect_errors="aggressive">q2galaxy run demux summarize '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run demux summarize '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
     <inputs>
         <param name="data" type="data" format="qza" label="data: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required]  The demultiplexed sequences to be summarized.">
             <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
-                <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
         </param>
@@ -36,7 +36,18 @@
     <outputs>
         <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
     </outputs>
-    <tests/>
+    <tests>
+        <test>
+            <param name="data" value="summarize.test0.demux.qza" ftype="qza"/>
+            <output name="visualization" ftype="qzv">
+                <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: Visualization"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help>
 QIIME 2: demux summarize
 ========================
@@ -53,6 +64,16 @@
 ------------
 Summarize counts per sample for all samples, and generate interactive positional quality plots based on `n` randomly selected sequences.
 
+Examples:
+---------
+
+demux
+*****
+Using the ``qiime2 demux summarize`` tool:
+ #. Set *"data"* to ``#: demux.qza``
+ #. Press the ``Execute`` button.
+
+
 
 |  
 
diff -r 3e85de166340 -r 222b50c1cb52 test-data/.gitkeep
diff -r 3e85de166340 -r 222b50c1cb52 test-data/emp_single.test0.sample-metadata.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emp_single.test0.sample-metadata.tsv	Fri Jan 13 22:43:10 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 3e85de166340 -r 222b50c1cb52 test-data/emp_single.test0.sequences.qza
Binary file test-data/emp_single.test0.sequences.qza has changed
diff -r 3e85de166340 -r 222b50c1cb52 test-data/summarize.test0.demux.qza
Binary file test-data/summarize.test0.demux.qza has changed