<tool id="hapmap_to_mlmm_files" name="HapmapToMLMMFiles" version="2.0.0">
    <description>Converts a hapmap file into MLMM input files</description>
    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
    <requirements>
        <requirement type="package" version="4.1.3">gawk</requirement>
    </requirements>
    <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">./HapmapToMLMMFiles.sh $input $snp_info $genot
    </command>
	<inputs>
		<param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
	</inputs>
	<outputs>
		<data format="txt" name="snp_info" label="SNP Info file"/>
		<data format="txt" name="genot" label="Genotyping file for MLMM"/>
	</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="input" value="hapmap2mlmm-hapmap" />
            <output name="snp_info" file="hapmap2mlmm-result_snp.hapmap" />
	    <output name="genot" file="hapmap2mlmm-result_genot" />
        </test>
    </tests>
	<help><![CDATA[

.. 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** 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

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

=================
HapmapToMLMMFiles
=================

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

  | HapmapToMLMMFiles converts a hapmap file into input files compatible with the MLMM software.

------------
Dependencies
------------
GAWK
        gawk_ 4.1.3, Conda version

.. _gawk: https://anaconda.org/bioconda/gawk

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

Hapmap file
	Allelic file in Hapmap format



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

SNP Info file

Genotyping file for MLMM



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

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

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

Hapmap file
-----------

::
	
	rs#	alleles	chrom	pos	strand	assembly#	center	protLSID	assayLSID	panel	QCcode	Ind1	Ind2
	SNP1	A/T	1	3102	+	assembly	NA	NA	NA	speciesname	NA	AA	AA	AA
	SNP2	A/T	1	4648	+	assembly	NA	NA	NA	speciesname	NA	AA	AA	AA


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

SNP Info file
-------------

::

	SNP	Chr	Pos
	SNP1	1	3102
	SNP2	1	4648
	SNP3	1	7601


Genotyping file for MLMM
------------------------

::

	Ind_id	SNP1	SNP2	SNP3	SNP4	SNP5	SNP6	SNP7	SNP8	SNP9	SNP10	SNP11	SNP12	SNP13	SNP14
	Ind1	0	0	0	0	0	0	2	0	2	0	0	0	2	0
	Ind2	0	0	0	0	0	2	2	0	0	0	0	0	0	0


	]]></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>