--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_alignment_mask.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,74 @@
+<?xml version="1.0" ?>
+<tool id="qiime_alignment_mask" name="qiime alignment mask"
+      version="2020.8">
+  <description>Positional conservation and gap filtering.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime alignment mask
+
+--i-alignment=$ialignment
+
+--p-max-gap-frequency=$pmaxgapfrequency
+
+--p-min-conservation=$pminconservation
+
+--o-masked-alignment=omaskedalignment
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp omaskedalignment.qza $omaskedalignment
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] The alignment to be masked.               [required]" name="ialignment" optional="False" type="data" />
+    <param exclude_max="False" label="--p-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. [default: 1.0]" max="1" min="0" name="pmaxgapfrequency" optional="True" type="float" value="1.0" />
+    <param exclude_max="False" label="--p-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. [default: 0.4]" max="1" min="0" name="pminconservation" optional="True" type="float" value="0.4" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Positional conservation and gap filtering.
+###############################################################
+
+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).
+
+Parameters
+----------
+alignment : FeatureData[AlignedSequence]
+    The alignment to be masked.
+max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
+    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.
+min_conservation : Float % Range(0, 1, inclusive_end=True), optional
+    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.
+
+Returns
+-------
+masked_alignment : FeatureData[AlignedSequence]
+    The masked alignment.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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