diff qiime2/qiime_diversity_alpha-phylogenetic-alt.xml @ 9:f190567fe3f6 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_alpha-phylogenetic-alt.xml	Wed Aug 14 15:12:48 2019 -0400
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+<?xml version="1.0" ?>
+<tool id="qiime_diversity_alpha-phylogenetic-alt" name="qiime diversity alpha-phylogenetic-alt" version="2019.7">
+	<description> - Alpha diversity (phylogenetic) - alternative implementation</description>
+	<requirements>
+		<requirement type="package" version="2019.7">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime diversity alpha-phylogenetic-alt
+
+--i-table=$itable
+--i-phylogeny=$iphylogeny
+
+--p-metric=$pmetric
+
+--o-alpha-diversity=oalphadiversity
+
+;
+cp oalphadiversity.qza $oalphadiversity
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples for which alpha diversity should be computed.       [required]" name="itable" optional="False" type="data"/>
+		<param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" optional="False" type="data"/>
+		<param label="--p-metric: " name="pmetric" optional="False" type="select">
+			<option value="faith_pd">faith_pd</option>
+		</param>
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: alphadiversity.qza" name="oalphadiversity"/>
+	</outputs>
+	<help><![CDATA[
+Alpha diversity (phylogenetic) - alternative implementation
+############################################################
+
+Computes a user-specified phylogenetic alpha diversity metric for all
+samples in a feature table. This implementation is recommended for large
+datasets, otherwise the results are identical to alpha_phylogenetic.   This
+method is an implementation of the Stacked Faith Algorithm (manuscript in
+preparation).
+
+Parameters
+----------
+table : FeatureTable[Frequency]
+    The feature table containing the samples for which alpha diversity
+    should be computed.
+phylogeny : Phylogeny[Rooted]
+    Phylogenetic tree containing tip identifiers that correspond 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.
+metric : Str % Choices('faith_pd')
+    The alpha diversity metric to be computed.
+
+Returns
+-------
+alpha_diversity : SampleData[AlphaDiversity] % Properties('phylogenetic')
+    Vector containing per-sample alpha diversities.
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>