<?xml version="1.0" ?>
<tool id="qiime_emperor_procrustes-plot" name="qiime emperor procrustes-plot" version="2018.4">
	<description> - Visualize and Interact with a procrustes plot</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
  qiime emperor procrustes-plot --i-reference-pcoa=$ireferencepcoa
  
  #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
  
   --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --i-other-pcoa=$iotherpcoa
  
  #if str($pcustomaxes):
   --p-custom-axes="$pcustomaxes"
  #end if
  
  #if str($cmdconfig) != 'None':
   --cmd-config=$cmdconfig
  #end if
  
   --o-visualization=ovisualization;
   
  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-reference-pcoa: PCoAResults The reference ordination matrix to be plotted.  [required]" name="ireferencepcoa" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-other-pcoa: PCoAResults The 'other' ordination matrix to be plotted (the one that was fitted to the reference). [required]" name="iotherpcoa" optional="False" type="data"/>

		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata.  [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />

		</repeat>

		<param label="--p-custom-axes: Numeric sample metadata columns that should be included as axes in the Emperor plot. [optional]" name="pcustomaxes" optional="True" type="text"/>

		<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[
Visualize and Interact with a procrustes plot
----------------------------------------------

Plot two procrustes-fitted matrices

Parameters
----------
reference_pcoa : PCoAResults
    The reference ordination matrix to be plotted.
other_pcoa : PCoAResults
    The "other" ordination matrix to be plotted (the one that was fitted to
    the reference).
metadata : Metadata
    The sample metadata.
custom_axes : List[Str], optional
    Numeric sample metadata columns that should be included as axes in the
    Emperor plot.

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