annotate fastMe_main/fastme.xml @ 0:3ef62be50f9d draft

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<tool id="sniplay_fastme" name="FastME" version="1.0.2">
    
    <!-- [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>
    
    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
    <version_command>
<!--
        tool_binary -v
-->
    </version_command>
    
    <!-- [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>
    
    <!-- [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>
    
    <!-- [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="filein" value="phylip" />
	 <param name="model" value="4"/>
	 <param name="distance" value="I"/>
         <output name="fileout" file="newick" />
	 <output name="fileout_log" file="newick.log" />
        </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>
    
</tool>