<?xml version="1.0" ?>
<tool id="qiime_fragment-insertion_sepp" name="qiime fragment-insertion sepp"
      version="2020.8">
  <description>Insert fragment sequences using SEPP into reference phylogenies.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime fragment-insertion sepp

--i-representative-sequences=$irepresentativesequences

--i-reference-database=$ireferencedatabase

--p-alignment-subset-size=$palignmentsubsetsize

--p-placement-subset-size=$pplacementsubsetsize

--p-threads=$pthreads

#if $pdebug:
 --p-debug
#end if

--o-tree=otree

--o-placements=oplacements

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

;
cp oplacements.qza $oplacements

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences to insert into the reference tree. [required]" name="irepresentativesequences" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-reference-database: ARTIFACT SeppReferenceDatabase The reference database to insert the representative sequences into.                              [required]" name="ireferencedatabase" optional="False" type="data" />
    <param label="--p-alignment-subset-size: INTEGER Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset.                 [default: 1000]" name="palignmentsubsetsize" optional="True" type="integer" value="1000" />
    <param label="--p-placement-subset-size: INTEGER The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. Further reading: https://github.com/smirarab/sepp/blob/master/tutorial/s epp-tutorial.md#sample-datasets-default-parameters. [default: 5000]" name="pplacementsubsetsize" optional="True" type="integer" value="5000" />
    <param label="--p-debug: --p-debug: / --p-no-debug Collect additional run information to STDOUT for debugging. Temporary directories will not be removed if run fails.                             [default: False]" name="pdebug" 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 ${on_string}: tree.qza" name="otree" />
    <data format="qza" label="${tool.name} on ${on_string}: placements.qza" name="oplacements" />
    
  </outputs>

  <help><![CDATA[
Insert fragment sequences using SEPP into reference phylogenies.
###############################################################

Perform fragment insertion of sequences using the SEPP algorithm.

Parameters
----------
representative_sequences : FeatureData[Sequence]
    The sequences to insert into the reference tree.
reference_database : SeppReferenceDatabase
    The reference database to insert the representative sequences into.
alignment_subset_size : Int, optional
    Each placement subset is further broken into subsets of at most these
    many sequences and a separate HMM is trained on each subset.
placement_subset_size : Int, optional
    The tree is divided into subsets such that each subset includes at most
    these many subsets. The placement step places the fragment on only one
    subset, determined based on alignment scores. Further reading:
    https://github.com/smirarab/sepp/blob/master/tutorial/sepp-
    tutorial.md#sample-datasets-default-parameters.
threads : Int, optional
    The number of threads to use.
debug : Bool, optional
    Collect additional run information to STDOUT for debugging. Temporary
    directories will not be removed if run fails.

Returns
-------
tree : Phylogeny[Rooted]
    The tree with inserted feature data.
placements : Placements
    Information about the feature placements within the reference tree.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>