--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_nmit.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,92 @@
+<?xml version="1.0" ?>
+<tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit" version="2019.4">
+	<description> - Nonparametric microbial interdependence test</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime longitudinal nmit
+
+--i-table=$itable
+--p-individual-id-column="$pindividualidcolumn"
+
+#if str($pcorrmethod) != 'None':
+ --p-corr-method=$pcorrmethod
+#end if
+
+#if str($pdistmethod) != 'None':
+ --p-dist-method=$pdistmethod
+#end if
+
+
+#if $input_files_mmetadatafile:
+#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 + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
+	#end for
+	#return $file_list
+#end def
+ --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+#end if
+
+
+--o-distance-matrix=odistancematrix
+;
+cp odistancematrix.qza $odistancematrix
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to use for microbial interdependence test.                                       [required]" name="itable" optional="False" type="data"/>
+		<param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects.                                   [required]" name="pindividualidcolumn" optional="False" type="text"/>
+		<param label="--p-corr-method: " name="pcorrmethod" optional="True" type="select">
+			<option selected="True" value="None">Selection is Optional</option>
+			<option value="kendall">kendall</option>
+			<option value="pearson">pearson</option>
+			<option value="spearman">spearman</option>
+		</param>
+		<param label="--p-dist-method: " name="pdistmethod" optional="True" type="select">
+			<option selected="True" value="None">Selection is Optional</option>
+			<option value="fro">fro</option>
+			<option value="nuc">nuc</option>
+		</param>
+
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+		</repeat>
+
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: distancematrix.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>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>