<?xml version="1.0" ?>
<tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2018.4">
	<description>- Collapse features by their taxonomy at the specified level</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
	qiime taxa collapse --p-level="$plevel"

	#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=$itable --o-collapsed-table=ocollapsedtable
	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#end if
	;
	cp ocollapsedtable.qza $ocollapsedtable;
	]]>
	</command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table to be collapsed.  [required]" name="itable" optional="False" type="data"/>

		<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 label="--p-level: 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="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: collapsed-table.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>
</tool>