<tool id="sniplay_mdsplot" name="PLINK: MDS plot" version="2.0.0">
    
    <!-- [REQUIRED] Tool description displayed after the tool name -->
    <description> IBS matrix / multi-dimensional scaling</description>
    
    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
    <requirements>
        <requirement type="binary">perl</requirement>
        <requirement type="package">rsync</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>

    
    <!-- [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="bash">
	mdsplot.sh $fileped $filemap $fileout_matrix $fileout_plot $fileout_log $groups
    </command>
   
    <!-- [REQUIRED] Input files and tool parameters -->
    <inputs>
	<param name="fileped" type="data" format="txt" optional="false" label="PED input" />
	<param name="filemap" type="data" format="txt" optional="false" label="MAP input" help="4 columns tabular file: chromosome, snp id, genetic distance, bp position"/>
	<param name="groups" type="data" format="txt" optional="true" label="Groups" help="Groups defined by sNMF"/>
	<param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" />
    </inputs>
    
    <!-- [REQUIRED] Output files -->
    <outputs>
	<data name="fileout_matrix" format="txt" label="${fileout_label}.ibs_matrix.txt" />
	<data name="fileout_plot" format="txt" label="${fileout_label}.mds_plot.txt" />
	<data name="fileout_log" format="txt" label="${fileout_label}.log" />
    </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="fileped" value="MDSplot-input.ped" />
	 <param name="filemap" value="MDSplot-input.map" />
         <output name="fileout_matrix" file="MDSplot-output.ibs_matrix.txt" />
	 <output name="fileout_plot" file="MDSplot-output.mds_plot.txt" />
        </test>
    </tests>
    
    <!-- [OPTIONAL] Help displayed in Galaxy -->
    <help><![CDATA[


.. class:: infomark

MDS plot 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 & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA)

.. class:: infomark

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

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

========
MDS plot
========

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

  | MDS plot compute an IBS matrix and a multi-dimensional scaling.
  |
  | MDS plot 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
Rsync
        rsync_, Conda version


.. _plink: https://anaconda.org/bioconda/plink
.. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
.. _rsync: https://anaconda.org/conda-forge/rsync

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

PED file
	PED file usually from VCF tools

MAP file
	4 columns tabular file: chromosome, snp id, genetic distance, bp position 


---------
Parameter
---------

Output name
        Output base name for the ouput files


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

Output_name.ibs_matrix.txt
	Tabular file with IBS matrix 

Output_name.mds_plot.txt
	File to construct mds plot

Output_name.log
	Log file
	
---------------------------------------------------

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

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

PED file
-----------

::

	IRAT112	1	0	0	1	1	1 1	4 4	...
	IAC25	1	0	0	1	1	1 1	4 4	...
	CIRAD409	1	0	0	1	1	3 3	1 1	...


MAP file
-----------

::

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



Parameter
=========

Output name -> densities


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

densities.ibs_matrix.txt
------------------------

::

	Individuals	IRAT112	IAC25	IAC165	KARASUKARASURANKASU	DOURADOPRECOCE	...
	IRAT112	1	0.93691	0.937407	0.734724	0.943368	...
	IAC25	0.93691	1	0.958768	0.723299	0.965723	...


densities.mds_plot.txt
----------------------

::

	IRAT112	-0.0969382	0.0376036
	IAC25	-0.0918126	0.0501177

	

    ]]></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>