--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__alignment__mask.xml	Mon Aug 29 19:19:18 2022 +0000
@@ -0,0 +1,73 @@
+<?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 alignment mask" id="qiime2__alignment__mask" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Positional conservation and gap filtering.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version alignment</version_command>
+    <command detect_errors="aggressive">q2galaxy run alignment mask '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required]  The alignment to be masked.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[AlignedSequence]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="max_gap_frequency" type="float" min="0" max="1" value="1.0" label="max_gap_frequency: Float % Range(0, 1, inclusive_end=True)" help="[default: 1.0]  The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency."/>
+            <param name="min_conservation" type="float" min="0" max="1" value="0.4" label="min_conservation: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.4]  The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="masked_alignment" format="qza" label="${tool.name} on ${on_string}: masked_alignment.qza" from_work_dir="masked_alignment.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: alignment mask
+=======================
+Positional conservation and gap filtering.
+
+
+Outputs:
+--------
+:masked_alignment.qza: The masked alignment.
+
+|  
+
+Description:
+------------
+Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="bibtex">@incollection{cite1,
+ address = {New York},
+ author = {Lane, DJ},
+ booktitle = {Nucleic Acid Techniques in Bacterial Systematics},
+ editor = {Stackebrandt, E and Goodfellow, M},
+ pages = {115--175},
+ publisher = {John Wiley and Sons},
+ title = {16S/23S rRNA sequencing},
+ year = {1991}
+}
+</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>