diff qiime2-2020.8/qiime_gneiss_correlation-clustering.xml @ 20:d93d8888f0b0 draft

Uploaded

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+++ b/qiime2-2020.8/qiime_gneiss_correlation-clustering.xml	Fri Sep 04 12:44:24 2020 +0000
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+<?xml version="1.0" ?>
+<tool id="qiime_gneiss_correlation-clustering" name="qiime gneiss correlation-clustering"
+      version="2020.8">
+  <description>Hierarchical clustering using feature correlation.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime gneiss correlation-clustering
+
+--i-table=$itable
+
+--p-pseudocount=$ppseudocount
+
+--o-clustering=oclustering
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp oclustering.qza $oclustering
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples in which the columns will be clustered.            [required]" name="itable" optional="False" type="data" />
+    <param label="--p-pseudocount: NUMBER  The value to add to zero counts in the feature table.                                [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Hierarchical clustering using feature correlation.
+###############################################################
+
+Build a bifurcating tree that represents a hierarchical clustering of
+features.  The hiearchical clustering uses Ward hierarchical clustering
+based on the degree of proportionality between features.
+
+Parameters
+----------
+table : FeatureTable[Frequency]
+    The feature table containing the samples in which the columns will be
+    clustered.
+pseudocount : Float, optional
+    The value to add to zero counts in the feature table.
+
+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>
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