<?xml version="1.0" ?>
<tool id="qiime_composition_ancom" name="qiime composition ancom" version="2018.4">
	<description> - Apply ANCOM to identify features that differ in abundance.</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
  
  qiime composition ancom --i-table=$itable

  #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 str($pdifferencefunction) != 'None':
   --p-difference-function=$pdifferencefunction
  #end if

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

  #if str($ptransformfunction) != 'None':
   --p-transform-function=$ptransformfunction
  #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-table: FeatureTable[Composition] - The feature table to be used for ANCOM computation.  [required]" name="itable" optional="False" type="data"/>
		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
			<param format="tabular" 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"/>
		</repeat>
		<param label="--m-metadata-column: MetadataColumn[Categorical] - Column from metadata file or artifact viewable as metadata. The categorical sample metadata column to test for differential abundance across.  [required]" name="mmetadatacolumn" optional="False" type="text"/>
		<param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="mean_difference">mean_difference</option>
			<option value="f_statistic">f_statistic</option>
		</param>
		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
		<param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="log">log</option>
			<option value="clr">clr</option>
			<option value="sqrt">sqrt</option>
		</param>
	</inputs>
	<outputs>
		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
	</outputs>
	<help>
<![CDATA[
Apply ANCOM to identify features that differ in abundance.
----------------------------------------------------------

Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
that are differentially abundant across groups.

Parameters
----------
table : FeatureTable[Composition]
    The feature table to be used for ANCOM computation.
metadata : MetadataColumn[Categorical]
    The categorical sample metadata column to test for differential
    abundance across.
transform_function : Str % Choices({'clr', 'log', 'sqrt'}), optional
    The method applied to transform feature values before generating
    volcano plots.
difference_function : Str % Choices({'f_statistic', 'mean_difference'}), optional
    The method applied to visualize fold difference in feature abundances
    across groups for volcano plots.

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