<?xml version="1.0" ?>
<tool id="qiime_feature-table_core-features" name="qiime feature-table core-features" version="2018.4">
	<description> - Identify core features in table</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
		<![CDATA[
	qiime feature-table core-features --i-table=$itable

	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#end if

	#if $pminfraction:
	 --p-min-fraction=$pminfraction
	#end if

	#if $pmaxfraction:
	 --p-max-fraction=$pmaxfraction
	#end if
	 --o-visualization=ovisualization
	#if $psteps:
	 --p-steps=$psteps
	#end if
	;
	qiime tools export ovisualization.qzv --output-dir out   && mkdir -p '$ovisualization.files_path'
	&& cp -r out/* '$ovisualization.files_path'
	&& mv '$ovisualization.files_path/index.html' '$ovisualization';
]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table to use in core features calculations.  [required]" name="itable" optional="False" type="data"/>

		<param label="--p-min-fraction: The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature.  [default: 0.5]" name="pminfraction" optional="True" type="float" value="0.5"/>
		<param label="--p-max-fraction: The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature.  [default: 1.0]" name="pmaxfraction" optional="True" type="float" value="1.0"/>

		<param label="--p-steps: The number of steps to take between `min_fraction` and `max_fraction` for core features calculations. This parameter has no effect if `min_fraction` and `max_fraction` are the same value.  [default: 11]" name="psteps" optional="True" type="integer" value="11"/>

		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
	</outputs>
	<help>
		<![CDATA[
Identify core features in table
--------------------------------

Identify "core" features, which are features observed in a user-defined
fraction of the samples. Since the core features are a function of the
fraction of samples that the feature must be observed in to be considered
core, this is computed over a range of fractions defined by the
`min_fraction`, `max_fraction`, and `steps` parameters.

Parameters
----------
table : FeatureTable[Frequency]
    The feature table to use in core features calculations.
min_fraction : Float % Range(0.0, 1.0, inclusive_start=False), optional
    The minimum fraction of samples that a feature must be observed in for
    that feature to be considered a core feature.
max_fraction : Float % Range(0.0, 1.0, inclusive_end=True), optional
    The maximum fraction of samples that a feature must be observed in for
    that feature to be considered a core feature.
steps : Int % Range(2, None), optional
    The number of steps to take between `min_fraction` and `max_fraction`
    for core features calculations. This parameter has no effect if
    `min_fraction` and `max_fraction` are the same value.

Returns
-------
visualization : Visualization
		\
		]]>
	</help>
</tool>