<tool id="raxml_boot" name="RAxML_boot" version="1.0.0" force_history_refresh='True'>
    <description> Bootstrapped Maximum Likelihood Phylogenetic Analysis </description>
    <requirements>
        <requirement type="package">raxml</requirement>
    </requirements>
    <command interpreter="perl">
        raxml.pl $GAMMA $PROT $protmodel $morphmodel $data_file $part_file $constraint 
		$ML $INVAR $Boot $seed Boot $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='GAMMA' type='boolean' checked='false' truevalue='GTR' falsevalue='CAT' label='Gamma model of rate heterogeneity' help='If not checked, CAT model will be used.'/>
        <param name='INVAR' type='boolean' checked='false' truevalue='INVAR' falsevalue='no' label='Estimate proportion of invariant sites' help=''/>
	<param name='PROT' type='boolean' checked='false' truevalue='PROT' falsevalue='DNA' label='Protein Sequences' help='If not checked, DNA sequences will be assumed'/>
    <param name="protmodel" type="select" label="Protein Model">
      <option value="WAG">WAG</option>
      <option value="DAYHOFF">DAYHOFF</option>
      <option value="DCMUT">DCMUT</option>
      <option value="JTT">JTT</option>
      <option value="MTREV">MTREV</option>
      <option value="RTREV">RTREV</option>
      <option value="CPREV">CPREV</option>
      <option value="VT">VT</option>
      <option value="BLOSUM62">BLOSUM62</option>
      <option value="MTMAM">MTMAM</option>
      <option value="LG">LG</option>
      <option value="MTART">MTART</option>
      <option value="MTZOA">MTZOA</option>
      <option value="PMB">PMB</option>
      <option value="HIVB">HIVB</option>
      <option value="HIVW">HIVW</option>
      <option value="JTTDCMUT">JTTDCMUT</option>
      <option value="FLU">FLU</option>
      <option value="GTR">GTR</option>
    </param>
    <param name="morphmodel" type="select" optional="true" label="Multi-state morphological char model" help="Ignored unless specifying MULTI in model partition">
      <option value="MK">MK</option>
      <option value="ORDERED">ORDERED</option>
      <option value="GTR">GTR</option>
    </param>
	<param name="Boot" type="integer" value="100" label="Specify Number of bootstrap replicates" help='100 tends to be sufficient, do not exceed 1000'/>
	<param name="seed" type="integer" value="1234567" label="Random Number Seed"/>
        <param format="txt" name="part_file" type="data" optional="true" label="Partition file" help="You may provide an alignment partition file."/>
	<param format="newick" name="constraint" type="data" label="BINARY Constraint Tree" optional="true" help="This option allows you to specify an incomplete or comprehensive multifurcating constraint tree in NEWICK format."/>
        <param name='ML' type='boolean' checked='false' truevalue='no' falsevalue='no' 
label='Maximum Likelihood Search' help='DISABLED for MPI.'/>
	<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 ${on_string}" />
        <data format="txt" name="boot_tree" label="$Run: ${tool.name} Bootstrap Trees on ${on_string}" from_work_dir="RAxML_bootstrap.galaxy" />
        <data format="txt" name="bipartitions" label="$Run: ${tool.name} Bootstrap bipartitions on ${on_string}" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" />
        <data format="txt" name="branchlabelboots" label="$Run: ${tool.name} Branchlabel bootstrap bipartitions on ${on_string}" from_work_dir="RAxML_bipartitions.galaxy" />
        <data format="txt" name="raxml_info" label="$Run: ${tool.name} Log File on ${on_string}" from_work_dir="RAxML_info.galaxy" />
        <data format="txt" name="best_trees" label="$Run: ${tool.name} ML Tree ${on_string}" from_work_dir="RAxML_bestTree.galaxy" />
    </outputs>
    <tests>
    </tests>
    <help>
**What it does**

RAxML_boot is a copy of RAxML for longer bootstrap-only analysis. RAxML estimates phylogenetic trees using Maximum Likelihood.

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**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). In addition, if bootstrapping was selected, the individual bootstrap trees and the ML tree with support are written as separate newick files.

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**Additional Information**

The reason to have a copy is to allow Galaxy to request more resources from the cluster job runner.  Both raxml and raxml_boot call raxml.pl, but raxml_boot calls the perl script with the 'Boot' flag, which then calls the MPI version of RAxML to spread bootstraps across many processors. The number of processors specified in the call in the raxml.pl file must match the resources requested in Galaxy's universe.ini file for raxml_boot.

raxml Home Page.
http://www.exelixis-lab.org/software.html
   
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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>