annotate Rooting/rooting.xml~ @ 2:feb40a9a8eae draft

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<tool id="sniplay_rooting" name="Rooting" version="1.0.2">
    
    <!-- [REQUIRED] Tool description displayed after the tool name -->
    <description> Midpoint rooting of newick tree </description>
    
    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
    <requirements>
        <requirement type="binary">perl</requirement>
	<requirement type="package">Rootings_54.jar</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 interpreter="perl">
	Rooting.pl -i $filein -o $fileout &amp;&amp; mv ${filein}.rooting.log $fileout_log
    </command>
   
    <!-- [REQUIRED] Input files and tool parameters -->
    <inputs>
	<param name="filein" type="data" format="txt" optional="false" label="Fasta alignment input" />
	<param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" />
    </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="newick" />
         <output name="fileout" file="out_tree" />
	 <output name="fileout_log" file="out_tree.log" />
        </test>

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


.. class:: infomark

**Authors** Jean-François Dufayard, CIRAD, South Green platform


.. 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]

.. class:: infomark

**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).

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




=======
Rooting
=======

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

  Compute a midpoint newick rooted tree.


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

**Upstream tool**

=========== ========================== =======
Name            output file(s)         format 
=========== ========================== =======
fastme      Newick tree                Newick 
=========== ========================== =======



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

Newick file
	

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

Output name
        Output base name for the ouput files


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

Output_name
	Resulting tree rooted in newick format

Output_name.log
	Log file

------------
Dependencies
------------
Rooting
	CIRAD tool. Contact [e-mail]

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

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

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

Newick file
-----------

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


Parameters
==========

Output name -> out tree


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

out tree
--------

::

	(ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662...
	

    </help>
    <citations>
        <!-- [HELP] As DOI or BibTex entry -->
    	<citation type="bibtex">@article{Dereeper03062015,
author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
year = {2015}, 
doi = {10.1093/nar/gkv351}, 
abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
journal = {Nucleic Acids Research} 
}

    	</citation>

    </citations>
    
</tool>