<tool id="ped2bed" name="PLINK: ped2bed" version="2.0.0">
	<description>Convert ped to bed</description>
	<requirements>
        	<requirement type="binary">perl</requirement>
        	<requirement type="package" version="1.6.924">perl-bioperl</requirement>
        	<requirement type="package" version="1.90b4">plink</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>
    <command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs
    </command>
	<inputs>
		<param format="txt" name="ped" type="data" label="Allelic file in PED format" help="Allelic file in PED format"/>
		<param format="txt" name="map" type="data" label="Map file" help="Map file"/>
	</inputs>
	<outputs>
		<data format="txt" name="bed" label="Bed file"/>
		<data format="txt" name="fam" label="Fam file"/>
		<data format="txt" name="bim" label="Bim file"/>
		<data format="txt" name="logs" label="All Logs"/>
	</outputs>
    
    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
    <tests>
        <!-- [HELP] Test files have to be in the ~/test-data directory -->
        <!-- [HELP] Multiple tests can be defined with different parameters -->
        <test>
         <param name="ped" value="ped2bed-input.ped" />
	 <param name="map" value="ped2bed-input.map" />
         <output name="bed" file="ped2bed-result.bed" />
         <output name="fam" file="ped2bed-result.fam" />
         <output name="bim" file="ped2bed-result.bim" />
        </test>
    </tests>
	<help><![CDATA[
	

.. class:: infomark

Ped to Bed format conversion is done with PLINK.
**Authors** PLINK: Shaun Purcell (https://www.cog-genomics.org/plink)

  | **Please cite** "PLINK: a toolset for whole-genome association and population-based linkage analysis.", **Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC.**, American Journal of Human Genetics, 81, 2007.
  | **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** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)

.. class:: infomark

**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr

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

=======
Ped2Bed
=======

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

  | Ped to Bed format conversion is done with PLINK
  | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
  | For further informations, please visit the PLINK website_.

.. _website: https://www.cog-genomics.org/plink

------------
Dependencies
------------
PLINK
	plink_ 1.90b4, Conda version
Bioperl
        perl-bioperl_ 1.6.924, Conda version

.. _plink: https://anaconda.org/bioconda/plink
.. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl

-----------
Input files
-----------

PED file

MAP file

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

Bed file

Fam file

Bim file

All logs 

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

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

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

PED file
--------

::
	
	AZUCENA	AZUCENA	0	0	0	0	G	G	A	A	C	C	T	T	T	
	BULUPANDAK	BULUPANDAK	0	0	0	0	G	G	A	A	A	A	T	

MAP file
--------

::
	
	0	Chr1:4299	0	4299
	0	Chr1:26710	0	26710
	0	Chr1:56184	0	56184
	0	Chr1:93272	0	93272


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

Bed file
--------

::

	binary file

Fam file
--------

::

	AZUCENA AZUCENA 0 0 0 -9
	BULUPANDAK BULUPANDAK 0 0 0 -9

Bim file
--------

::

	0	Chr1:4299	0	4299	A	G
	0	Chr8:18058	0	18058	C	T


	]]></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>