diff qiime2-2020.8/qiime_diversity-lib_faith-pd.xml @ 0:5c352d975ef7 draft

Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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+++ b/qiime2-2020.8/qiime_diversity-lib_faith-pd.xml	Thu Sep 03 09:33:04 2020 +0000
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+<?xml version="1.0" ?>
+<tool id="qiime_diversity-lib_faith-pd" name="qiime diversity-lib faith-pd"
+      version="2020.8">
+  <description>Faith\'s Phylogenetic Diversity</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime diversity-lib faith-pd
+
+#if $itable:
+ --i-table
+#end if
+
+--i-phylogeny=$iphylogeny
+
+--o-vector=ovector
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp ovector.qza $ovector
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: --i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]      The feature table containing the samples for which Faith\'s phylogenetic diversity should be computed. Table values will be converted to presence/absence. [required]" name="itable" selected="False" type="boolean" />
+    <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" optional="False" type="data" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: vector.qza" name="ovector" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Faith\'s Phylogenetic Diversity
+###############################################################
+
+Computes Faith's Phylogenetic Diversity for all samples in a feature table.
+
+Parameters
+----------
+table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
+    The feature table containing the samples for which Faith's phylogenetic
+    diversity should be computed. Table values will be converted to
+    presence/absence.
+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.
+
+Returns
+-------
+vector : SampleData[AlphaDiversity]
+    Vector containing per-sample values for Faith's Phylogenetic Diversity.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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