# HG changeset patch
# User q2d2
# Date 1673650788 0
# Node ID 2c4de53c8903d7a9cf7d55643f1e3de69ba680af
# Parent  8bf2383917c324723c10f856dc3230b0fb5da2ba
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter commit 69da7976573cc07a363ac66bdacc9269d7cd3732

diff -r 8bf2383917c3 -r 2c4de53c8903 qiime2__quality_filter__q_score.xml
--- a/qiime2__quality_filter__q_score.xml	Mon Aug 29 20:22:53 2022 +0000
+++ b/qiime2__quality_filter__q_score.xml	Fri Jan 13 22:59:48 2023 +0000
@@ -1,32 +1,33 @@
 <?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 quality-filter q-score" id="qiime2__quality_filter__q_score" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 quality-filter q-score" id="qiime2__quality_filter__q_score" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
     <description>Quality filter based on sequence quality scores.</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 quality_filter</version_command>
-    <command detect_errors="aggressive">q2galaxy run quality_filter q_score '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run quality_filter q_score '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
     <inputs>
         <param name="demux" type="data" format="qza" label="demux: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]²" help="[required]  The demultiplexed sequence data to be quality filtered.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]"/>
+                <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
+                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
             </options>
-            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]']</validator>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[SequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]']</validator>
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
             <param name="min_quality" type="integer" value="4" label="min_quality: Int" help="[default: 4]  The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores."/>
@@ -39,7 +40,25 @@
         <data name="filtered_sequences" format="qza" label="${tool.name} on ${on_string}: filtered_sequences.qza" from_work_dir="filtered_sequences.qza"/>
         <data name="filter_stats" format="qza" label="${tool.name} on ${on_string}: filter_stats.qza" from_work_dir="filter_stats.qza"/>
     </outputs>
-    <tests/>
+    <tests>
+        <test>
+            <param name="demux" value="q_score.test0.demuxed-seqs.qza" ftype="qza"/>
+            <output name="filtered_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: SampleData\[SequencesWithQuality\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+            <output name="filter_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: QualityFilterStats"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help>
 QIIME 2: quality-filter q-score
 ===============================
@@ -57,6 +76,29 @@
 ------------
 This method filters sequence based on quality scores and the presence of ambiguous base calls.
 
+Examples:
+---------
+
+q_score
+*******
+Using the ``qiime2 quality-filter q-score`` tool:
+ #. Set *"demux"* to ``#: demuxed-seqs.qza``
+ #. Press the ``Execute`` button.
+
+Once completed, for each 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 quality-filter q-score [...] : filtered_sequences.qza``
+      - ``dumux-filtered.qza``
+    * - ``#: qiime2 quality-filter q-score [...] : filter_stats.qza``
+      - ``demux-filter-stats.qza``
+
 
 |  
 
diff -r 8bf2383917c3 -r 2c4de53c8903 test-data/.gitkeep
diff -r 8bf2383917c3 -r 2c4de53c8903 test-data/q_score.test0.demuxed-seqs.qza
Binary file test-data/q_score.test0.demuxed-seqs.qza has changed