<?xml version="1.0" ?>
<tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2019.7">
	<description> - Collapse features by their taxonomy at the specified level</description>
	<requirements>
		<requirement type="package" version="2019.7">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime taxa collapse

#if str( $id_to_taxonomy_fp.selector ) == 'history'
	#set $tax = $id_to_taxonomy_fp.taxonomy_fp
	--i-taxonomy '$tax'
#else:
	#set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
	--i-taxonomy '$tax'
#end if


--i-table=$itable

#if str($plevel):
 --p-level="$plevel"
#end if

--o-collapsed-table=ocollapsedtable
;
cp ocollapsedtable.qza $ocollapsedtable
	]]></command>
	<inputs>

		<conditional name="id_to_taxonomy_fp" optional="True">
		   <param name="selector" type="select" label="Reference taxonomy to query">
			  <option value="cached">Public databases</option>
			  <option value="history">Databases from your history</option>
		   </param>
		   <when value="cached">
			  <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
				 <options from_data_table="qiime_taxonomy" />
			  </param>
		   </when>
		   <when value="history">
			  <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
		   </when>
		</conditional>
		

		<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 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>