diff qiime2/qiime_phylogeny_fasttree.xml @ 29:3ba9833030c1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_fasttree.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,69 @@
+<?xml version="1.0" ?>
+<tool id="qiime_phylogeny_fasttree" name="qiime phylogeny fasttree"
+      version="2020.8">
+  <description>Construct a phylogenetic tree with FastTree.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime phylogeny fasttree
+
+--i-alignment=$ialignment
+
+#if str($pnthreads) != 'None':
+--p-n-threads=$pnthreads
+#end if
+
+--o-tree=otree
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp otree.qza $otree
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction.                           [required]" name="ialignment" optional="False" type="data" />
+    <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Int % Range(1">Int % Range(1</option>
+      <option value="None">None</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Construct a phylogenetic tree with FastTree.
+###############################################################
+
+Construct a phylogenetic tree with FastTree.
+
+Parameters
+----------
+alignment : FeatureData[AlignedSequence]
+    Aligned sequences to be used for phylogenetic reconstruction.
+n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
+    The number of threads. Using more than one thread runs the non-
+    deterministic variant of `FastTree` (`FastTreeMP`), and may result in a
+    different tree than single-threading. See
+    http://www.microbesonline.org/fasttree/#OpenMP for details. (Use `auto`
+    to automatically use all available cores)
+
+Returns
+-------
+tree : Phylogeny[Unrooted]
+    The resulting phylogenetic tree.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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