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diff qiime2/qiime_phylogeny_raxml-rapid-bootstrap.xml @ 14:a0a8d77a991c draft

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Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
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--- a/qiime2/qiime_phylogeny_raxml-rapid-bootstrap.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_phylogeny_raxml-rapid-bootstrap.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,70 +1,73 @@
-<?xml version="1.0" ?>
-<tool id="qiime_phylogeny_raxml-rapid-bootstrap" name="qiime phylogeny raxml-rapid-bootstrap" version="2019.7">
-	<description> - Construct a phylogenetic tree with bootstrap supports using RAxML.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<?xml version="1.0" ?>
+<tool id="qiime_phylogeny_raxml-rapid-bootstrap" name="qiime phylogeny raxml-rapid-bootstrap"
+      version="2020.8">
+  <description>Construct a phylogenetic tree with bootstrap supports using RAxML.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime phylogeny raxml-rapid-bootstrap
 
 --i-alignment=$ialignment
 
 #if str($pseed):
- --p-seed="$pseed"
+  --p-seed=$pseed
 #end if
-
 #if str($prapidbootstrapseed):
- --p-rapid-bootstrap-seed="$prapidbootstrapseed"
+  --p-rapid-bootstrap-seed=$prapidbootstrapseed
 #end if
+--p-bootstrap-replicates=$pbootstrapreplicates
 
-#if str($pbootstrapreplicates):
- --p-bootstrap-replicates=$pbootstrapreplicates
-#end if
-
-#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 $otree
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction.                           [required]" name="ialignment" optional="False" type="data"/>
-		<param label="--p-seed: INTEGER        Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]" name="pseed" optional="True" type="integer"/>
-		<param label="--p-rapid-bootstrap-seed: INTEGER Specify a random seed for rapid bootstrapping. This allows you to reproduce rapid bootstrap results. If not supplied then one will be randomly chosen. [optional]" name="prapidbootstrapseed" optional="True" type="integer"/>
-		<param label="--p-bootstrap-replicates: INTEGER Range(10, None)       The number of bootstrap searches to perform. [default: 100]" name="pbootstrapreplicates" optional="True" type="integer" value="100"/>
-		<param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="Standard">Standard</option>
-			<option value="SSE3">SSE3</option>
-			<option value="AVX2">AVX2</option>
-		</param>
-		<param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="GTRGAMMA">GTRGAMMA</option>
-			<option value="GTRGAMMAI">GTRGAMMAI</option>
-			<option value="GTRCAT">GTRCAT</option>
-			<option value="GTRCATI">GTRCATI</option>
-		</param>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
-	</outputs>
-	<help><![CDATA[
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction.                           [required]" name="ialignment" optional="False" type="data" />
+    <param label="--p-seed: INTEGER        Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]" name="pseed" optional="False" type="text" />
+    <param label="--p-rapid-bootstrap-seed: INTEGER Specify a random seed for rapid bootstrapping. This allows you to reproduce rapid bootstrap results. If not supplied then one will be randomly chosen. [optional]" name="prapidbootstrapseed" optional="False" type="text" />
+    <param label="--p-bootstrap-replicates: INTEGER Range(10, None)       The number of bootstrap searches to perform. [default: 100]" min="10" name="pbootstrapreplicates" optional="True" type="integer" value="100" />
+    <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Standard">Standard</option>
+      <option value="SSE3">SSE3</option>
+      <option value="AVX2">AVX2</option>
+    </param>
+    <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="GTRGAMMA">GTRGAMMA</option>
+      <option value="GTRGAMMAI">GTRGAMMAI</option>
+      <option value="GTRCAT">GTRCAT</option>
+      <option value="GTRCATI">GTRCATI</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Construct a phylogenetic tree with bootstrap supports using RAxML.
-##################################################################
+###############################################################
 
 Construct a phylogenetic tree with RAxML with the addition of rapid
 bootstrapping support values. See:
@@ -79,11 +82,14 @@
     reproduce tree results. If not supplied then one will be randomly
     chosen.
 rapid_bootstrap_seed : Int, optional
-    Specify a random seed for rapid bootstrapping. This allows you to
+    Specify a random seed for rapid bootstrapping. This allows you to
     reproduce rapid bootstrap results. If not supplied then one will be
     randomly chosen.
 bootstrap_replicates : Int % Range(10, None), optional
     The number of bootstrap searches to perform.
+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
@@ -95,9 +101,9 @@
 -------
 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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