<?xml version="1.0" ?>
<tool id="qiime_alignment_mask" name="qiime alignment mask" version="2018.4">
	<description> - Positional conservation and gap filtering.</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
  
  qiime alignment mask --i-alignment=$ialignment

  #if str($cmdconfig) != 'None':
   --cmd-config=$cmdconfig
  #end if
 
   --o-masked-alignment=omaskedalignment

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

  #if $pmaxgapfrequency:
   --p-max-gap-frequency=$pmaxgapfrequency
  #end if
  ;
  cp omaskedalignment.qza $omaskedalignment

]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-alignment: FeatureData[AlignedSequence] - The alignment to be masked.  [required]" name="ialignment" optional="False" type="data"/>
		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
		<param label="--p-min-conservation: 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" value="0.4"/>
		<param label="--p-max-gap-frequency: 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" value="1.0"/>
	</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.

Parameters
----------
alignment : FeatureData[AlignedSequence]
    The alignment to be masked.
max_gap_frequency : Float, 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, 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>
</tool>