<?xml version="1.0" ?>
<tool id="qiime_alignment_mask" name="qiime alignment mask" version="2019.4">
	<description> - Positional conservation and gap filtering.</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime alignment mask

--i-alignment=$ialignment

--o-masked-alignment=omaskedalignment

#if $pmaxgapfrequency:
 --p-max-gap-frequency=$pmaxgapfrequency
#end if

#if $pminconservation:
 --p-min-conservation=$pminconservation
#end if

;
cp omaskedalignment.qza $omaskedalignment
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] The alignment to be masked.               [required]" name="ialignment" optional="False" type="data"/>
		<param label="--p-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. [default: 1.0]" name="pmaxgapfrequency" optional="True" type="float" min="0" max="1" exclude_max="False" value="1.0"/>
		<param label="--p-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. [default: 0.4]" name="pminconservation" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.4"/>
	</inputs>
	<outputs>
		<data format="qza" label="${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>