<?xml version="1.0" ?>
<tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit" version="2018.4">
	<description> - Nonparametric microbial interdependence test</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
		qiime longitudinal nmit --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) --p-individual-id-column="$pindividualidcolumn"
	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#end if

	#if str($pdistmethod) != 'None':
	 --p-dist-method=$pdistmethod
	#end if

	#if str($pcorrmethod) != 'None':
	 --p-corr-method=$pcorrmethod
	#end if
	 --o-distance-matrix=odistancematrix;

	cp odistancematrix.qza $odistancematrix;
	]]>
	</command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[RelativeFrequency] Feature table to use for microbial interdependence test.  [required]" name="itable" 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. Sample metadata file containing individual_id_column.  [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>

		<param label="--p-individual-id-column: Metadata column containing IDs for individual subjects.  [required]" name="pindividualidcolumn" optional="False" type="text"/>

		<param label="--p-corr-method: The temporal correlation test to be applied.
                                  [default: kendall]" name="pcorrmethod" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="kendall">kendall</option>
			<option value="pearson">pearson</option>
			<option value="spearman">spearman</option>
		</param>

		<param label="--p-dist-method: Temporal distance method, see
                                  numpy.linalg.norm for details.  [default:
                                  fro]" name="pdistmethod" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="fro">fro</option>
			<option value="nuc">nuc</option>
		</param>

		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: distance-matrix.qza" name="odistancematrix"/>
	</outputs>
	<help>
		<![CDATA[
Nonparametric microbial interdependence test
---------------------------------------------

Perform nonparametric microbial interdependence test to determine
longitudinal sample similarity as a function of temporal microbial
composition. For more details and citation, please see
doi.org/10.1002/gepi.22065

Parameters
----------
table : FeatureTable[RelativeFrequency]
    Feature table to use for microbial interdependence test.
metadata : Metadata
    Sample metadata file containing individual_id_column.
individual_id_column : Str
    Metadata column containing IDs for individual subjects.
corr_method : Str % Choices({'kendall', 'pearson', 'spearman'}), optional
    The temporal correlation test to be applied.
dist_method : Str % Choices({'fro', 'nuc'}), optional
    Temporal distance method, see numpy.linalg.norm for details.

Returns
-------
distance_matrix : DistanceMatrix
    The resulting distance matrix.
		]]>
	</help>
</tool>