<tool id="sniplay_pedToFasta" name="Ped2Fasta" version="1.0.0">
    
    <!-- [REQUIRED] Tool description displayed after the tool name -->
    <description> Convert PED file to Fasta File </description>
    
    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
    <requirements>
        <requirement type="binary">perl</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>
    
    <!-- [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">
	Ped2Fasta.pl --in $filein --out $fileout 
    </command>
     
    <!-- [REQUIRED] Input files and tool parameters -->
    <inputs>
	<param name="filein" type="data" format="txt" optional="false" label="PED input" />
	<param name="fileout_label" type="text" value="filtered" optional="false" label="Output file name"/>
    </inputs>
    
    <!-- [REQUIRED] Output files -->
    <outputs>
	<data name="fileout" type="data" format="fasta" label="${fileout_label}.fa" />
    </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="filein" value="ped2fasta-sample.ped" />
         <output name="fileout" file="ped2fasta-result.fa" />
        </test>
    </tests>
    
    <!-- [OPTIONAL] Help displayed in Galaxy -->
    <help>

.. class:: infomark

**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform

 | **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).

.. class:: infomark

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

.. class:: infomark

**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr 

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

=========
Ped2Fasta
=========

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

  Convert PED file to Fasta File

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

**Upstream tool**

=============== ========================== =======
Name            output file(s)             format 
=============== ========================== =======
VCFtools Filter VCF file  	 	   VCF
=============== ========================== =======


**Downstream tool**

=========== ========================== =======
Name            input file(s)          format
=========== ========================== =======
Readseq     Fasta alignment	       fasta
=========== ========================== =======


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

PED file
	PED file usually from VCF tools

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

Output file name
	Prefix for the output fasta file

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

Fasta file
	PED file conversion 

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

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

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

PED file
---------

::

	CATB1   CATB1   0       0       0       0       C       T       T       A       C       T       A       T       A       T       A       G       G       A

Parameters
==========

Output name -> pedFile

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

pedFile.fa
----------

::

        YWYWWRRSYYMKRRKMYRKSRKYRYRYKRKRSKKSYRWYSYRRYRRRWYWWYYWRRYRSRWSSRMYRRKSWMSKWRRYYWMYKYWRSYRWRYMWYYYMKYKYWRYRYRY


    </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>