# HG changeset patch
# User q2d2
# Date 1661804573 0
# Node ID 8bf2383917c324723c10f856dc3230b0fb5da2ba

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

diff -r 000000000000 -r 8bf2383917c3 qiime2__quality_filter__q_score.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__quality_filter__q_score.xml	Mon Aug 29 20:22:53 2022 +0000
@@ -0,0 +1,68 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2022, 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)
+for:
+    qiime2 (version: 2022.8.1)
+-->
+<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">
+    <description>Quality filter based on sequence quality scores.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version quality_filter</version_command>
+    <command detect_errors="aggressive">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[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>
+        </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."/>
+            <param name="quality_window" type="integer" value="3" label="quality_window: Int" help="[default: 3]  The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read."/>
+            <param name="min_length_fraction" type="float" value="0.75" label="min_length_fraction: Float" help="[default: 0.75]  The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length."/>
+            <param name="max_ambiguous" type="integer" value="0" label="max_ambiguous: Int" help="[default: 0]  The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min_length_fraction`."/>
+        </section>
+    </inputs>
+    <outputs>
+        <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/>
+    <help>
+QIIME 2: quality-filter q-score
+===============================
+Quality filter based on sequence quality scores.
+
+
+Outputs:
+--------
+:filtered_sequences.qza: The resulting quality-filtered sequences.
+:filter_stats.qza: Summary statistics of the filtering process.
+
+|  
+
+Description:
+------------
+This method filters sequence based on quality scores and the presence of ambiguous base calls.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/nmeth.2276</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 8bf2383917c3 test-data/.gitkeep