--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_adonis.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,94 @@
+<?xml version="1.0" ?>
+<tool id="qiime_diversity_adonis" name="qiime diversity adonis" version="2019.4">
+	<description> - adonis PERMANOVA test for beta group significance</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime diversity adonis
+
+--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("$input_files_mmetadatafile")
+
+
+
+
+--p-formula="$pformula"
+
+#if $ppermutations:
+ --p-permutations=$ppermutations
+#end if
+
+#set $pnjobs = '${GALAXY_SLOTS:-4}'
+#if str($pnjobs):
+ --p-n-jobs="$pnjobs"
+#end if
+
+--o-visualization=ovisualization
+;
+qiime tools export --input-path ovisualization.qzv --output-path 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: ARTIFACT DistanceMatrix     Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
+		<param label="--p-formula: TEXT     Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula 'treatment+block' would test whether the input distance matrix partitions based on 'treatment' and 'block' sample metadata. The formula 'treatment*block' would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises.                        [required]" name="pformula" optional="False" type="text"/>
+		<param label="--p-permutations: INTEGER Range(1, None)     The number of permutations to be run when computing p-values.                                [default: 999]" name="ppermutations" optional="True" min="1" type="integer" value="999"/>
+
+		<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>
+	</inputs>
+	<outputs>
+		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
+	</outputs>
+	<help><![CDATA[
+adonis PERMANOVA test for beta group significance
+#################################################
+
+Determine whether groups of samples are significantly different from one
+another using the ADONIS permutation-based statistical test in vegan-R. The
+function partitions sums of squares of a multivariate data set, and is
+directly analogous to MANOVA (multivariate analysis of variance). This
+action differs from beta_group_signficance in that it accepts R formulae to
+perform multi-way ADONIS tests; beta_group_signficance only performs one-
+way tests. For more details see
+http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adonis.html
+
+Parameters
+----------
+distance_matrix : DistanceMatrix
+    Matrix of distances between pairs of samples.
+metadata : Metadata
+    Sample metadata containing formula terms.
+formula : Str
+    Model formula containing only independent terms contained in the sample
+    metadata. These can be continuous variables or factors, and they can
+    have interactions as in a typical R formula. E.g., the formula
+    "treatment+block" would test whether the input distance matrix
+    partitions based on "treatment" and "block" sample metadata. The
+    formula "treatment*block" would test both of those effects as well as
+    their interaction. Enclose formulae in quotes to avoid unpleasant
+    surprises.
+permutations : Int % Range(1, None), optional
+    The number of permutations to be run when computing p-values.
+
+Returns
+-------
+visualization : Visualization
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>