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+++ b/qiime2-2020.8/qiime_phylogeny_raxml.xml	Thu Sep 03 09:33:04 2020 +0000
@@ -0,0 +1,101 @@
+<?xml version="1.0" ?>
+<tool id="qiime_phylogeny_raxml" name="qiime phylogeny raxml"
+      version="2020.8">
+  <description>Construct a phylogenetic tree with RAxML.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime phylogeny raxml
+
+--i-alignment=$ialignment
+
+#if str($pseed):
+  --p-seed=$pseed
+#end if
+--p-n-searches=$pnsearches
+
+--p-n-threads=$pnthreads
+
+#if str($praxmlversion) != 'None':
+--p-raxml-version=$praxmlversion
+#end if
+
+#if str($psubstitutionmodel) != 'None':
+--p-substitution-model=$psubstitutionmodel
+#end if
+
+--o-tree=otree
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp otree.qza $otree
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction.                           [required]" name="ialignment" optional="False" type="data" />
+    <param label="--p-seed: INTEGER        Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]" name="pseed" optional="False" type="text" />
+    <param label="--p-n-searches: INTEGER  The number of independent maximum likelihood Range(1, None)        searches to perform. The single best scoring tree is returned.                               [default: 1]" min="1" name="pnsearches" optional="True" type="integer" value="1" />
+    <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Standard">Standard</option>
+      <option value="SSE3">SSE3</option>
+      <option value="AVX2">AVX2</option>
+    </param>
+    <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="GTRGAMMA">GTRGAMMA</option>
+      <option value="GTRGAMMAI">GTRGAMMAI</option>
+      <option value="GTRCAT">GTRCAT</option>
+      <option value="GTRCATI">GTRCATI</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Construct a phylogenetic tree with RAxML.
+###############################################################
+
+Construct a phylogenetic tree with RAxML. See:
+https://sco.h-its.org/exelixis/web/software/raxml/
+
+Parameters
+----------
+alignment : FeatureData[AlignedSequence]
+    Aligned sequences to be used for phylogenetic reconstruction.
+seed : Int, optional
+    Random number seed for the parsimony starting tree. This allows you to
+    reproduce tree results. If not supplied then one will be randomly
+    chosen.
+n_searches : Int % Range(1, None), optional
+    The number of independent maximum likelihood searches to perform. The
+    single best scoring tree is returned.
+n_threads : Int % Range(1, None), optional
+    The number of threads to use for multithreaded processing. Using more
+    than one thread will enable the PTHREADS version of RAxML.
+raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
+    Select a specific CPU optimization of RAxML to use. The SSE3 versions
+    will run approximately 40% faster than the standard version. The AVX2
+    version will run 10-30% faster than the SSE3 version.
+substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
+    Model of Nucleotide Substitution.
+
+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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