<?xml version="1.0" ?>
<tool id="qiime_emperor_biplot" name="qiime emperor biplot" version="2019.4">
	<description> - Visualize and Interact with Principal Coordinates Analysis Biplot</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime emperor biplot

--i-biplot=$ibiplot


#def list_dict_to_string(list_dict):
#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
#for d in list_dict[1:]:
	#set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
#end for
#return $file_list
#end def

#if $m_sample_metadatafile:
--m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile)
#end if

if $m_feature_metadatafile:
--m-feature-metadata-file=$list_dict_to_string($m_feature_metadatafile)
#end if


#if $pignoremissingsamples:
 --p-ignore-missing-samples
#end if

#if $pnumberoffeatures:
 --p-number-of-features=$pnumberoffeatures
#end if
 
--o-visualization=ovisualization
;
qiime tools export --input-path ovisualization.qzv --output-path 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-biplot: ARTIFACT PCoAResults % Properties('biplot') The principal coordinates matrix to be plotted. [required]" name="ibiplot" optional="False" type="data"/>
		<param label="--p-ignore-missing-samples: --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: 'This sample has no metadata'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.               [default: False]" name="pignoremissingsamples" selected="False" type="boolean"/>
		<param label="--p-number-of-features: INTEGER Range(1, None)     The number of most important features (arrows) to display in the ordination.                 [default: 5]" name="pnumberoffeatures" optional="True" type="integer" min="1" value="5"/>

		<repeat name="m_sample_metadatafile" optional="False" title="--m-metadata-file">
			<param label="--m-sample-metadata-file: (multiple arguments will be merged)  The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>

		<repeat name="m_feature_metadatafile" optional="True" title="--m-metadata-file">
			<param label="--m-feature-metadata-file: (multiple arguments will be merged)  The feature metadata (useful to manipulate the arrows in the plot).  [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>

	</inputs>
	<outputs>
		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
	</outputs>
	<help><![CDATA[
Visualize and Interact with Principal Coordinates Analysis Biplot
#################################################################

Generates an interactive ordination biplot where the user can visually
integrate sample and feature metadata.

Parameters
----------
biplot : PCoAResults % Properties('biplot')
    The principal coordinates matrix to be plotted.
sample_metadata : Metadata
    The sample metadata
feature_metadata : Metadata, optional
    The feature metadata (useful to manipulate the arrows in the plot).
ignore_missing_samples : Bool, optional
    This will suppress the error raised when the coordinates matrix
    contains samples that are not present in the metadata. Samples without
    metadata are included by setting all metadata values to: "This sample
    has no metadata". This flag is only applied if at least one sample is
    present in both the coordinates matrix and the metadata.
number_of_features : Int % Range(1, None), optional
    The number of most important features (arrows) to display in the
    ordination.

Returns
-------
visualization : Visualization
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>