<tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.0">
	<description>checks concordance between input files for GWAS analysis</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>

	<command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats
    </command>
	<inputs>
		<param format="text" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
		<param format="text" name="trait" type="data" label="Trait file" help="Phenotypic file"/>
	</inputs>
	<outputs>
		<data format="txt" name="out_hapmap" label="Hapmap output"/>
		<data format="txt" name="out_trait" label="Trait output"/>
		<data format="txt" name="stats" label="Logfile and statistics"/>
	</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="hapmap" value="gwas-hapmap" />
         <param name="trait" value="gwas-trait" />
         <output name="out_hapmap" file="gwas-result.hapmap" />
         <output name="out_trait" file="gwas-result.trait" />
         <output name="stats" file="gwas-result.stats" />
        </test>
    </tests>
	<help>
	
        <![CDATA[


.. class:: infomark

**Authors** South Green

  | **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** South Green.

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


===============
CheckGWASInputs
===============

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

  | CheckGWASInputs checks concordance between input files for GWAS analysis.


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

**Upstream tool**

=============== ====================== ===========
Name            output file(s)         format 
=============== ====================== ===========
VCF to Hapmap   Hapmap file	       hapmap
=============== ====================== ===========




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

Hapmap file
	Allelic file in Hapmap format

Trait file
	Phenotypic file

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

Hapmap output

Trait output

Logfile and statistics

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

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

Trait file
----------

::
	
	<Trait>	Test
	Ind1	-2.9985936006411
	Ind2	-2.68669426456267

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

Hapmap output
-------------

::

        rs#     alleles chrom   pos     strand  assembly#       center  protLSID        assayLSID       panel   QCcode  Ind1    Ind2    Ind3    Ind4
        SNP1    A/T     1       3102    +       assembly        NA      NA      NA      speciesname     NA      AA      AA      AA      AA      AA
        SNP2    A/T     1       4648    +       assembly        NA      NA      NA      speciesname     NA      AA      AA      AA      AA      TT
	

Trait output
------------

::

        <Trait> Test
        Ind429  -26.2142525264157
        Ind373  12.0306115988504
        Ind81   1.98118654229534

Logfile and statistics
----------------------

::


        ==============================================
        Individuals
        ==============================================
        Individuals in hapmap file: 500
        Individuals in trait file: 500
        Individuals found in both files: 500
        ==============================================
        Markers
        ==============================================
        Discarded markers:
        Monomorphic: 0
        Not biallelic: 0
        Modified markers:
        Difference in variation: 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>