<?xml version="1.0" ?>
<tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2019.4">
	<description> - Collapse features by their taxonomy at the specified level</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime taxa collapse

--i-table=$itable
--i-taxonomy=$itaxonomy
--p-level="$plevel"

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