annotate fastme.xml @ 3:df98a0425c8d draft

planemo upload

<tool id="sniplay_fastme" name="Fastme" version="1.1.0">
    
    <!-- [REQUIRED] Tool description displayed after the tool name -->
    <description> Calculate distance tree for an alignment file</description>
    
    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
    <requirements>
        <requirement type="binary">perl</requirement>
	<requirement type="package" version="2.1.4">fastme</requirement>
    </requirements>
    
    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
    <stdio>
        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
        <exit_code range="1:" level="fatal" />
    </stdio>

    
    <!-- [REQUIRED] The command to execute -->
    <command>
	fastme --input_data=$input_data --dna=$model --output_tree=$fileout 
	#if str( $distance ) == "SPR":
	--spr
	#elif str( $distance )[:3] == "NNI"  :
	  #if str( $distance ) == "NNI_B" :
           --nni=B
          #else :
           --nni=O
          #end if

	#else :
	--method=$distance
	#end if
	> $fileout_log
    </command>
   


    <!-- [REQUIRED] Input files and tool parameters -->
    <inputs>
	<param name="input_data" type="data" format="txt" optional="false" label="Phylip input" />
	<param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" />
	<param name="model" type="select" label="Evolutionary model" >
	    <option value="p">p-distance</option>
	    <option value="Y">RY symetric</option>
	    <option value="R">RY</option>
	    <option value="J">JC69</option>
	    <option value="K">K2P</option>
	    <option value="1">F81</option>
	    <option value="4" selected="true">F84</option>
	    <option value="T">TN93</option>
	    <option value="L">LogDet</option>
        </param>
	<param name="distance" type="select" label="Distance methode" >
	    <option value="B">TaxAdd_BalME</option>
	    <option value="O">TaxAdd_OLSME</option>
	    <option value="I" selected="true">BIONJ</option>
	    <option value="N">NJ</option>
	    <option value="U">UNJ</option>
	    <option value="NNI_B">NNI_BalME</option>
	    <option value="NNI_O">NNI_OLS</option>
	    <option value="SPR">SPR</option>
        </param>
    </inputs> 
    
    <!-- [REQUIRED] Output files -->
    <outputs>
	<data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
	<data name="fileout" type="data" format="txt" label="${fileout_label}" />
    </outputs>
    
    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
    <tests>
        <!-- [HELP] Test files have to be in the ~/test-data directory -->

        <test>
         <param name="input_data" value="phylip" />
	 <param name="model" value="4"/>
	 <param name="distance" value="I"/>
         <output name="fileout" file="newick" />
        </test>

        <!-- [HELP] Multiple tests can be defined with different parameters -->
<!--
        <test>
        </test>
-->
    </tests>
    
    <!-- [OPTIONAL] Help displayed in Galaxy -->
    <help>

.. class:: infomark

**Authors** 

 | Richard Desper and Olivier Gascuel,
 |	Journal of Computational Biology 19(5), 687-705, 2002.
 |	Molecular Biology and Evolution 21(3), 587-598, 2004.
 |	Please cite these papers if you use this software in your publications.


.. class:: infomark

**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.

.. class:: infomark

**Support** For any questions about Galaxy integration, please send an e-mail to [e-mail]

---------------------------------------------------


======
FastMe
======

-----------
Description
-----------


  	FastME - A distance based phylogeny reconstruction algorithm.

	FastME showed better topological accuracy than NJ,
	BIONJ, WEIGHBOR and FITCH, in all evolutionary
	conditions we tested, which include large range
	deviations from molecular clock and substitution rates.



-----------------
Workflow position
-----------------

**Upstream tools**

=========== ========================== =======
Name            output file(s)         format 
=========== ========================== =======
Readseq     phylip conversion          phylip 
=========== ========================== =======


**Downstream tools**

=========== ========================== =======
Name            output file(s)         format
=========== ========================== =======
Rooting     out tree                   Newick 
=========== ========================== =======


----------
Input file
----------

Phylip file 
	Phylip file with sequence alignments
	

----------
Parameters
----------

Output name
        Output base name for the ouput files

Evolutionary model
	Indicate the evolutionary [model] which can be choosen from:p-distance, RY symmetric, RY, JC69, K2P, F81, F84 (default), TN93, LogDet.

Distance methode
	FastME computes a tree using a distance algorithm. You may choose this method/topologie from: TaxAdd_BalME, TaxAdd_OLSME, BIONJ (default), NJ, UNJ, NNI_BalME, NNI_OLS or SPR

------------
Output files
------------

Output_name
	Resulting tree at Newick format 

Output_name.log
	Log file

------------
Dependencies
------------
FastME
	http://www.atgc-montpellier.fr/fastme
 	


---------------------------------------------------

---------------
Working example
---------------

Input files
===========

Philip file
-----------

::

	168 5125
	IRAT112      GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT
	KARASUKARA   GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT

Parameters
==========

Output name -> Newick tree

Evolutionary model -> F84

Distance methode -> BIONJ

Output files
============

Newick tree
-----------

::

	(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...
	

    </help>
    
    <citations>
            <!-- [HELP] As DOI or BibTex entry -->
        <citation type="bibtex">    
@article{Lefort30062015,
author = {Lefort, Vincent and Desper, Richard and Gascuel, Olivier}, 
title = {FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program},
year = {2015}, 
doi = {10.1093/molbev/msv150}, 
abstract ={FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange. The new 2.0 version also includes Subtree Pruning and Regrafting, while remaining as fast as NJ and providing a number of facilities: Distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations. FastME is available using several interfaces: Command-line (to be integrated in pipelines), PHYLIP-like, and a Web server (http://www.atgc-montpellier.fr/fastme/).}, 
URL = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.abstract}, 
eprint = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.full.pdf+html}, 
journal = {Molecular Biology and Evolution} 
}

	</citation>

    </citations>


</tool>