<?xml version="1.0" ?>
<tool id="qiime_diversity_beta-group-significance" name="qiime diversity beta-group-significance" version="2018.4">
	<description> - Beta diversity group significance</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
  qiime diversity beta-group-significance --i-distance-matrix=$idistancematrix
  
  #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) --m-metadata-column="$mmetadatacolumn"
   
  #if $ppairwise:
   --p-pairwise
  #else
    --p-no-pairwise
  #end if
  
   --o-visualization=ovisualization
   
  #if str($cmdconfig) != 'None':
   --cmd-config=$cmdconfig
  #end if
  
  #if str($pmethod) != 'None':
   --p-method=$pmethod
  #end if
  
  #if $ppermutations:
   --p-permutations=$ppermutations
  #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-distance-matrix: DistanceMatrix Matrix of distances between pairs of samples.  [required]" name="idistancematrix" 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. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>
		<param label="--m-metadata-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. Categorical sample metadata column.  [required]" name="mmetadatacolumn" optional="False" type="text"/>
		<param label="--p-method: " name="pmethod" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="anosim">anosim</option>
			<option value="permanova">permanova</option>
		</param>
		<param label="--p-pairwise: --p-no-pairwise  Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column. [default: False]" name="ppairwise" checked="False" type="boolean"/>
		<param label="--p-permutations: The number of permutations to be run when computing p-values.  [default: 999]" name="ppermutations" optional="True" type="integer" value="999"/>
		<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[
Beta diversity group significance
---------------------------------

Determine whether groups of samples are significantly different from one
another using a permutation-based statistical test.

Parameters
----------
distance_matrix : DistanceMatrix
    Matrix of distances between pairs of samples.
metadata : MetadataColumn[Categorical]
    Categorical sample metadata column.
method : Str % Choices({'anosim', 'permanova'}), optional
    The group significance test to be applied.
pairwise : Bool, optional
    Perform pairwise tests between all pairs of groups in addition to the
    test across all groups. This can be very slow if there are a lot of
    groups in the metadata column.
permutations : Int, optional
    The number of permutations to be run when computing p-values.

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