view phylostatistics/tree_support_raxml.xml @ 0:5b9a38ec4a39 draft default tip

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<tool id="tree_support_raxml" name="tree_support_RAxML">
	<description>Calculates support for nodes of a single tree (bootstrap) using a file of multiple trees</description>
	<requirements>
		<requirement type="package">raxml</requirement>
	</requirements>
	<command>
		raxmlHPC-PTHREADS-SSE3 -T 2 -f b -t $besttree -z $treesfile -m GTRCAT -n galaxy -o $Out 
	</command>
	<inputs>
		<param format="txt" name="treesfile" type="data" label="Input trees file" help="A file of multiple trees in newick format"/>
		<param format="txt" name="besttree" type="data" label="Target tree" help="Tree to find support for"/>
		<param name="Out" type="text" label="Outgroup (optional)" help="The name of one or more (comma-separated) outgroup(s) can be specified"/>
	</inputs>
	<outputs>
        <data format="txt" name="boot_tree" label="${tool.name} Bootstrap Trees on ${on_string}" from_work_dir="RAxML_bipartitions.galaxy" />
        <data format="txt" name="branchlabelboots" label="${tool.name} Branchlabel bootstrap bipartitions on ${on_string}" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" />
        <data format="txt" name="raxml_info" label="${tool.name} Log File on ${on_string}" from_work_dir="RAxML_info.galaxy" />
	</outputs>
    <help>
**What it does**

Tree support RAxML calculates support values for a given tree using a set of input trees. For example, it can calculate bootstrap support for the ML tree based on a set of trees from a bootstrap analysis.
This is valuable when separating bootstrap analysis from ML analysis, and when separating bootstrap replicates in different runs, which can be concatenated and used as input for this tool.

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**Inputs**

1. Newick format target tree, branch lengths are optional.

2. Set of Newick format phylogenies, branch lengths are ignored.

3. Optional outgroup specification. There can be no spaces in this entry.

------

**Outputs**

The focal tree is output with support values in Newick tree format.

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**Additional Information**

1. This tool Calls RAxML with -f b option with -t and -z options

2. A similar tool is tree_support_phyutility, which works best with nexus format trees.

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**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>