diff qiime2/qiime_phylogeny_raxml.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_phylogeny_raxml.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_phylogeny_raxml.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,65 +1,69 @@
 <?xml version="1.0" ?>
-<tool id="qiime_phylogeny_raxml" name="qiime phylogeny raxml" version="2019.7">
-	<description> - Construct a phylogenetic tree with RAxML.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<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
-
-#if str($pnsearches):
- --p-n-searches=$pnsearches
+  --p-seed=$pseed
 #end if
+--p-n-searches=$pnsearches
 
-#set $pnthreads = '${GALAXY_SLOTS:-4}'
-#if str($pnthreads):
- --p-n-threads="$pnthreads"
-#end if
-
+--p-n-threads=$pnthreads
 
 #if str($praxmlversion) != 'None':
- --p-raxml-version=$praxmlversion
+--p-raxml-version=$praxmlversion
 #end if
 
 #if str($psubstitutionmodel) != 'None':
- --p-substitution-model=$psubstitutionmodel
+--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="True" type="integer"/>
-		<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]" name="pnsearches" optional="True" type="integer" min="1" 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>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
-	</outputs>
-	<help><![CDATA[
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction.                           [required]" name="ialignment" optional="False" type="data" />
+    <param label="--p-seed: INTEGER        Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]" name="pseed" optional="False" type="text" />
+    <param label="--p-n-searches: INTEGER  The number of independent maximum likelihood Range(1, None)        searches to perform. The single best scoring tree is returned.                               [default: 1]" min="1" name="pnsearches" optional="True" type="integer" value="1" />
+    <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Standard">Standard</option>
+      <option value="SSE3">SSE3</option>
+      <option value="AVX2">AVX2</option>
+    </param>
+    <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="GTRGAMMA">GTRGAMMA</option>
+      <option value="GTRGAMMAI">GTRGAMMAI</option>
+      <option value="GTRCAT">GTRCAT</option>
+      <option value="GTRCATI">GTRCATI</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${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/
@@ -75,6 +79,9 @@
 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
@@ -86,9 +93,9 @@
 -------
 tree : Phylogeny[Unrooted]
     The resulting phylogenetic tree.
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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