<?xml version="1.0" ?>
<tool id="qiime_taxa_collapse" name="qiime taxa collapse"
      version="2020.8">
  <description>Collapse features by their taxonomy at the specified level</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime taxa collapse

--i-table=$itable

--i-taxonomy=$itaxonomy

--p-level=$plevel

--o-collapsed-table=ocollapsedtable

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

;
cp ocollapsedtable.qza $ocollapsedtable

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be collapsed.             [required]" name="itable" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored.                           [required]" name="itaxonomy" optional="False" type="data" />
    <param label="--p-level: INTEGER      The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation.       [required]" name="plevel" optional="False" type="text" />
    <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}: collapsedtable.qza" name="ocollapsedtable" />
    
  </outputs>

  <help><![CDATA[
Collapse features by their taxonomy at the specified level
###############################################################

Collapse groups of features that have the same taxonomic assignment through
the specified level. The frequencies of all features will be summed when
they are collapsed.

Parameters
----------
table : FeatureTable[Frequency]
    Feature table to be collapsed.
taxonomy : FeatureData[Taxonomy]
    Taxonomic annotations for features in the provided feature table. All
    features in the feature table must have a corresponding taxonomic
    annotation. Taxonomic annotations that are not present in the feature
    table will be ignored.
level : Int
    The taxonomic level at which the features should be collapsed. All
    ouput features will have exactly this many levels of taxonomic
    annotation.

Returns
-------
collapsed_table : FeatureTable[Frequency]
    The resulting feature table, where all features are now taxonomic
    annotations with the user-specified number of levels.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>