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+++ b/phylogenies/raxml_pars.xml	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,73 @@
+<tool id="raxml_pars" name="raxml_pars" version="1.0.0" force_history_refresh='True'>
+    <description> Use RAxML to calculate a phylogeny with Parsimony </description>
+    <requirements>
+        <requirement type="package">raxml</requirement>
+    </requirements>
+    <command interpreter="perl">
+        raxml_pars.pl $datatype $data_file $part_file 
+		$seed $Out  > $raxml_log
+			2>&amp;1
+    </command>
+    <inputs>
+        <param format="phylip" name="data_file" type="data" label="Raxml Phylip File" help=""/>
+	<param name="Out" type="text" label="Outgroup (optional)" help="The name of one or more (comma-separated) outgroup(s) can be specified"/>
+    <param name="datatype" type="select" label="Data Type" help="If you have multiple, mixed data types, specify them in a partition file ">
+      <option value="PROTGAMMAWAG">PROTEIN</option>
+      <option value="GTRGAMMA">DNA</option>
+      <option value="BINGAMMA">BINARY</option>
+      <option value="MULTIGAMMA">Multistate Morphology</option>
+    </param>
+	<param name="seed" type="integer" value="1234567" label="Random Number Seed for search"/>
+        <param format="txt" name="part_file" type="data" optional="true" label="Partition file" help="You may provide an alignment partition file."/>
+	<param name="Run" type="text" label="Run Name" help="For Galaxy History"/>
+    </inputs>
+    <outputs>
+	<data format="txt" name="raxml_log" label="$Run: ${tool.name} Screen Output on ${on_string}" />
+        <data format="txt" name="raxml_info" label="$Run: ${tool.name} Log File on ${on_string}" from_work_dir="RAxML_info.parsimony" />
+        <data format="txt" name="best_trees" label="$Run: ${tool.name} MP Tree ${on_string}" from_work_dir="RAxML_parsimonyTree.parsimony" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+**What it does**
+
+RAxML_pars estimates phylogenetic trees, in this case calling a Parsimony algorithm.
+
+------
+
+**Inputs**
+
+Input file is a RAxML compatible text file. This can be generated by Osiris tools from an aligned fasta file with fasta2phylipE or from a PHYTAB format file with phylocatenator.
+
+------
+
+**Outputs**
+
+RAxML writes the resulting tree file in newick text format, which can be viewed in Osiris with TreeVector (of the mothur package).
+
+-------    
+
+**Additional Information**
+
+raxml Home Page.
+http://www.exelixis-lab.org/software.html
+   
+-------    
+
+**Citations**   
+
+This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following.
+
+Current Osiris Citation is here
+
+http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
+
+Additional Citations for this tool
+
+Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics.
+http://bioinformatics.oxfordjournals.org/content/22/21/2688.short
+
+    </help>
+</tool>
+
+