# HG changeset patch
# User q2d2
# Date 1673649744 0
# Node ID bbaba170747524a24b7db8f6f4194334329e48ad
# Parent  4218e31465183aa67377f7f00ece45f69ff31798
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732

diff -r 4218e3146518 -r bbaba1707475 qiime2__dada2__denoise_paired.xml
--- a/qiime2__dada2__denoise_paired.xml	Mon Aug 29 19:23:50 2022 +0000
+++ b/qiime2__dada2__denoise_paired.xml	Fri Jan 13 22:42:24 2023 +0000
@@ -1,22 +1,22 @@
 <?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 dada2 denoise-paired" id="qiime2__dada2__denoise_paired" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 dada2 denoise-paired" id="qiime2__dada2__denoise_paired" version="2022.11.2+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
     <description>Denoise and dereplicate paired-end sequences</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 dada2</version_command>
-    <command detect_errors="aggressive">q2galaxy run dada2 denoise_paired '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run dada2 denoise_paired '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
@@ -57,7 +57,34 @@
         <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/>
         <data name="denoising_stats" format="qza" label="${tool.name} on ${on_string}: denoising_stats.qza" from_work_dir="denoising_stats.qza"/>
     </outputs>
-    <tests/>
+    <tests>
+        <test>
+            <param name="demultiplexed_seqs" value="denoise_paired.test0.demux-paired.qza" ftype="qza"/>
+            <param name="trunc_len_f" value="150"/>
+            <param name="trunc_len_r" value="140"/>
+            <output name="representative_sequences" 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\[Sequence\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+            <output name="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>
+            <output name="denoising_stats" 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: SampleData\[DADA2Stats\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help>
 QIIME 2: dada2 denoise-paired
 =============================
@@ -76,6 +103,18 @@
 ------------
 This method denoises paired-end sequences, dereplicates them, and filters chimeras.
 
+Examples:
+---------
+
+denoise_paired
+**************
+Using the ``qiime2 dada2 denoise-paired`` tool:
+ #. Set *"demultiplexed_seqs"* to ``#: demux-paired.qza``
+ #. Set *"trunc_len_f"* to ``150``
+ #. Set *"trunc_len_r"* to ``140``
+ #. Press the ``Execute`` button.
+
+
 
 |  
 
diff -r 4218e3146518 -r bbaba1707475 test-data/.gitkeep
diff -r 4218e3146518 -r bbaba1707475 test-data/denoise_paired.test0.demux-paired.qza
Binary file test-data/denoise_paired.test0.demux-paired.qza has changed
diff -r 4218e3146518 -r bbaba1707475 test-data/denoise_single.test0.demux-single.qza
Binary file test-data/denoise_single.test0.demux-single.qza has changed