diff phylostatistics/SHtest.xml @ 0:5b9a38ec4a39 draft default tip

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+<tool id="SHtest" name="SHtest" version="1.0.0" force_history_refresh='True'>
+    <description> Use RAxML to calculate SHtest to compare phylogenetic tree topologies 
+    </description>
+    <requirements>
+        <requirement type="package">raxml</requirement>
+    </requirements>
+    <command interpreter="perl">
+        SHtest.pl $datatype $data_file $part_file $best_tree $alt_trees
+		  > $raxml_log
+			2>&amp;1
+    </command>
+    <inputs>
+        <param format="phylip" name="data_file" type="data" label="Raxml Phylip File" help=""/>
+    <param name="datatype" type="select" format="text">
+      <label>Model of evolution to apply to all data partitions (-m)</label>
+      <option value="GTRGAMMA">GTRGAMMA</option> <option value="PROTGAMMADAYHOFF">PROTGAMMADAYHOFF</option> <option value="PROTGAMMADCMUT">PROTGAMMADCMUT</option> <option value="PROTGAMMAJTT">PROTGAMMAJTT</option> <option value="PROTGAMMAMTREV">PROTGAMMAMTREV</option> <option value="PROTGAMMAWAG">PROTGAMMAWAG</option> <option value="PROTGAMMARTREV">PROTGAMMARTREV</option> <option value="PROTGAMMACPREV">PROTGAMMACPREV</option> <option value="PROTGAMMAVT">PROTGAMMAVT</option> <option value="PROTGAMMABLOSUM62">PROTGAMMABLOSUM62</option> <option value="PROTGAMMAMTMAM">PROTGAMMAMTMAM</option> <option value="PROTGAMMALG">PROTGAMMALG</option> <option value="PROTGAMMAMTART">PROTGAMMAMTART</option> <option value="PROTGAMMAMTZOA">PROTGAMMAMTZOA</option> <option value="PROTGAMMAPMB">PROTGAMMAPMB</option> <option value="PROTGAMMAHIVB">PROTGAMMAHIVB</option> <option value="PROTGAMMAHIVW">PROTGAMMAHIVW</option> <option value="PROTGAMMAJTTDCMUT">PROTGAMMAJTTDCMUT</option> <option value="PROTGAMMAFLU">PROTGAMMAFLU</option> <option value="PROTGAMMAGTR">PROTGAMMAGTR</option>
+    </param>
+        <param format="txt" name="part_file" type="data" optional="true" label="Partition file" help="You may provide an alignment partition file."/>
+        <param format="txt" name="best_tree" type="data" optional="true" label="ML Tree" help="ML Tree in newick format."/>
+        <param format="txt" name="alt_trees" type="data" optional="true" label="Alt Tree(s)" help="Alternative Hypothesis Tree(s) in newick format."/>
+    </inputs>
+    <outputs>
+	<data format="txt" name="raxml_log" label="${tool.name} Screen Output on ${on_string}" />
+        <data format="txt" name="raxml_info" label="${tool.name} Log File on ${on_string}" from_work_dir="RAxML_info.SH" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+**What it does**
+
+SHtest performs the Shimodaira-Hasegawa statistical test to compare one tree topology to alternative tree(s). The test is implemented with RAxML.
+
+------
+
+**Inputs**
+
+#. A file in RAxML (phylipE) format. This can be made with Osiris tools phylocatenator or fasta2phylipE. 
+#. Model of evolution assumed for likelihood calculations.
+#. An optional RAxML partition file delineates data set partitions. This can be made with Osiris tool phylocatenator.
+#. Target phylogeny in newick format.
+#. Alternative hypothesis phylogenetic tree(s) in newick format.
+
+------
+
+**Outputs**
+
+The output is text output from RAxML, which details the statistical value of the SH test(s).
+
+-------    
+
+**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
+
+Shimodaira H., M. Hasegawa, 1999 Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol. Biol. Evol 16:1114-1116
+
+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>