diff qiime2/qiime_diversity_alpha-group-significance.xml @ 0:370e0b6e9826 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_alpha-group-significance.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,69 @@
+<?xml version="1.0" ?>
+<tool id="qiime_diversity_alpha-group-significance" name="qiime diversity alpha-group-significance" version="2019.4">
+	<description> - Alpha diversity comparisons</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime diversity alpha-group-significance
+
+--i-alpha-diversity=$ialphadiversity
+
+
+#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($input_files_mmetadatafile)
+
+--o-visualization=ovisualization
+;
+qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization';
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample.  [required]" name="ialphadiversity" optional="False" type="data"/>
+
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+		</repeat>
+	</inputs>
+	<outputs>
+		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
+	</outputs>
+	<help><![CDATA[
+Beta diversity group significance
+#################################
+
+Determine whether groups of samples are significantly different from one
+another using a permutation-based statistical test.
+
+Parameters
+----------
+distance_matrix : DistanceMatrix
+    Matrix of distances between pairs of samples.
+metadata : MetadataColumn[Categorical]
+    Categorical sample metadata column.
+method : Str % Choices('permanova', 'anosim', 'permdisp'), optional
+    The group significance test to be applied.
+pairwise : Bool, optional
+    Perform pairwise tests between all pairs of groups in addition to the
+    test across all groups. This can be very slow if there are a lot of
+    groups in the metadata column.
+permutations : Int, 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>