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+++ b/qiime2-2020.8/qiime_diversity-lib_alpha-passthrough.xml	Thu Sep 03 09:33:04 2020 +0000
@@ -0,0 +1,88 @@
+<?xml version="1.0" ?>
+<tool id="qiime_diversity-lib_alpha-passthrough" name="qiime diversity-lib alpha-passthrough"
+      version="2020.8">
+  <description>Alpha Passthrough (non-phylogenetic)</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime diversity-lib alpha-passthrough
+
+--i-table=$itable
+
+--p-metric=$pmetric
+
+--o-vector=ovector
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp ovector.qza $ovector
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples for which a selected metric should be computed.          [required]" name="itable" optional="False" type="data" />
+    <param label="--p-metric: " name="pmetric" optional="False" type="select">
+      <option value="gini_index">gini_index</option>
+      <option value="simpson_e">simpson_e</option>
+      <option value="osd">osd</option>
+      <option value="mcintosh_e">mcintosh_e</option>
+      <option value="esty_ci">esty_ci</option>
+      <option value="berger_parker_d">berger_parker_d</option>
+      <option value="robbins">robbins</option>
+      <option value="doubles">doubles</option>
+      <option value="michaelis_menten_fit">michaelis_menten_fit</option>
+      <option value="singles">singles</option>
+      <option value="kempton_taylor_q">kempton_taylor_q</option>
+      <option value="fisher_alpha">fisher_alpha</option>
+      <option value="strong">strong</option>
+      <option value="heip_e">heip_e</option>
+      <option value="dominance">dominance</option>
+      <option value="goods_coverage">goods_coverage</option>
+      <option value="ace">ace</option>
+      <option value="enspie">enspie</option>
+      <option value="mcintosh_d">mcintosh_d</option>
+      <option value="chao1_ci">chao1_ci</option>
+      <option value="lladser_pe">lladser_pe</option>
+      <option value="brillouin_d">brillouin_d</option>
+      <option value="menhinick">menhinick</option>
+      <option value="simpson">simpson</option>
+      <option value="margalef">margalef</option>
+      <option value="chao1">chao1</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: vector.qza" name="ovector" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Alpha Passthrough (non-phylogenetic)
+###############################################################
+
+Computes a vector of values (one value for each samples in a feature table)
+using the scikit-bio implementation of the selected alpha diversity metric.
+
+Parameters
+----------
+table : FeatureTable[Frequency]
+    The feature table containing the samples for which a selected metric
+    should be computed.
+metric : Str % Choices('ace', 'berger_parker_d', 'simpson_e', 'doubles', 'gini_index', 'michaelis_menten_fit', 'chao1_ci', 'dominance', 'robbins', 'lladser_pe', 'brillouin_d', 'goods_coverage', 'mcintosh_e', 'esty_ci', 'chao1', 'margalef', 'heip_e', 'enspie', 'menhinick', 'simpson', 'strong', 'fisher_alpha', 'osd', 'singles', 'kempton_taylor_q', 'mcintosh_d')
+    The alpha diversity metric to be computed.
+
+Returns
+-------
+vector : SampleData[AlphaDiversity]
+    Vector containing per-sample values for the chosen metric.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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