<?xml version="1.0" ?>
<tool id="qiime_phylogeny_align-to-tree-mafft-fasttree" name="qiime phylogeny align-to-tree-mafft-fasttree"
      version="2020.8">
  <description>Build a phylogenetic tree using fasttree and mafft alignment</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime phylogeny align-to-tree-mafft-fasttree

--i-sequences=$isequences

#if str($pnthreads) != 'None':
--p-n-threads=$pnthreads
#end if

--p-mask-max-gap-frequency=$pmaskmaxgapfrequency

--p-mask-min-conservation=$pmaskminconservation

#if $pparttree:
 --p-parttree
#end if

--o-alignment=oalignment

--o-masked-alignment=omaskedalignment

--o-tree=otree

--o-rooted-tree=orootedtree

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp orootedtree.qza $orootedtree

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be used for creating a fasttree based rooted phylogenetic tree.           [required]" name="isequences" optional="False" type="data" />
    <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="Int % Range(1">Int % Range(1</option>
      <option value="None">None</option>
    </param>
    <param exclude_max="False" label="--p-mask-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. This value is used when masking the aligned sequences. [default: 1.0]" max="1" min="0" name="pmaskmaxgapfrequency" optional="True" type="float" value="1.0" />
    <param exclude_max="False" label="--p-mask-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. This value is used when masking the aligned sequences. [default: 0.4]" max="1" min="0" name="pmaskminconservation" optional="True" type="float" value="0.4" />
    <param label="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default.                            [default: False]" name="pparttree" selected="False" type="boolean" />
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
    <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
    <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
    <data format="qza" label="${tool.name} on ${on_string}: rootedtree.qza" name="orootedtree" />
    
  </outputs>

  <help><![CDATA[
Build a phylogenetic tree using fasttree and mafft alignment
###############################################################

This pipeline will start by creating a sequence alignment using MAFFT,
after which any alignment columns that are phylogenetically uninformative
or ambiguously aligned will be removed (masked). The resulting masked
alignment will be used to infer a phylogenetic tree and then subsequently
rooted at its midpoint. Output files from each step of the pipeline will be
saved. This includes both the unmasked and masked MAFFT alignment from
q2-alignment methods, and both the rooted and unrooted phylogenies from
q2-phylogeny methods.

Parameters
----------
sequences : FeatureData[Sequence]
    The sequences to be used for creating a fasttree based rooted
    phylogenetic tree.
n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
    The number of threads. (Use `auto` to automatically use all available
    cores) This value is used when aligning the sequences and creating the
    tree with fasttree.
mask_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. This value is used when masking the aligned
    sequences.
mask_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.
    This value is used when masking the aligned sequences.
parttree : Bool, optional
    This flag is required if the number of sequences being aligned are
    larger than 1000000. Disabled by default.

Returns
-------
alignment : FeatureData[AlignedSequence]
    The aligned sequences.
masked_alignment : FeatureData[AlignedSequence]
    The masked alignment.
tree : Phylogeny[Unrooted]
    The unrooted phylogenetic tree.
rooted_tree : Phylogeny[Rooted]
    The rooted phylogenetic tree.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>