--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_gradient-clustering.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,79 @@
+<?xml version="1.0" ?>
+<tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering" version="2019.4">
+	<description> - Hierarchical clustering using gradient information.</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime gneiss gradient-clustering
+
+--i-table=$itable
+--m-gradient-column="$mgradientcolumn"
+
+
+#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 $file_list
+#end def
+
+--m-gradient-file=$list_dict_to_string($input_files_mgradientfile)
+
+
+#if $pnoweighted:
+ --p-no-weighted
+#end if
+
+--o-clustering=oclustering
+;
+cp oclustering.qza $oclustering
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | Composition]       The feature table containing the samples in which the columns will be clustered.                   [required]" name="itable" optional="False" type="data"/>
+		<param label="--m-gradient-column: COLUMN  MetadataColumn[Numeric] Contains gradient values to sort the features and samples.                                     [required]" name="mgradientcolumn" optional="False" type="text"/>
+		<param label="--p-no-weighted : Specifies if abundance or presence/absence information should be used to perform the clustering. [default: False]" name="pnoweighted" selected="False" type="boolean"/>
+
+		<repeat name="input_files_mgradientfile" optional="False" title="--m-gradient-file">
+			<param label="--m-gradient-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+		</repeat>
+
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering"/>
+	</outputs>
+	<help><![CDATA[
+Hierarchical clustering using gradient information.
+###################################################
+
+Build a bifurcating tree that represents a hierarchical clustering of
+features.  The hiearchical clustering uses Ward hierarchical clustering
+based on the mean difference of gradients that each feature is observed in.
+This method is primarily used to sort the table to reveal the underlying
+block-like structures.
+
+Parameters
+----------
+table : FeatureTable[Frequency | RelativeFrequency | Composition]
+    The feature table containing the samples in which the columns will be
+    clustered.
+gradient : MetadataColumn[Numeric]
+    Contains gradient values to sort the features and samples.
+weighted : Bool, optional
+    Specifies if abundance or presence/absence information should be used
+    to perform the clustering.
+
+Returns
+-------
+clustering : Hierarchy
+    A hierarchy of feature identifiers where each tip corresponds to the
+    feature identifiers in the table. This tree can contain tip ids that
+    are not present in the table, but all feature ids in the table must be
+    present in this tree.
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>