<tool id="sniplay_mdsplot" name="MDS plot" version="1.1.1">
    
    <!-- [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" version="0.1.13">plink</requirement>
    </requirements>
    
    <!-- [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_label $fileout_matrix $fileout_plot $fileout_log
    </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="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" />
    </inputs>
    
    <!-- [REQUIRED] Output files -->
    <outputs>
	<data name="fileout_matrix" type="data" format="tabular" label="${fileout_label}.ibs_matrix.txt" />
	<data name="fileout_plot" type="data" format="tabular" label="${fileout_label}.mds_plot.txt" />
	<data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
    </outputs>
    
    <!-- [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] 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="input.ped" />
	 <param name="filemap" value="input.map" />
         <output name="fileout_matrix" file="output.ibs_matrix.txt" />
	 <output name="fileout_plot" file="output.mds_plot.txt" />
	 <output name="fileout_log" file="output.log" />
        </test>

        <!-- [HELP] Multiple tests can be defined with different parameters -->
<!--
        <test>
        </test>
-->
    </tests>
    
    <!-- [OPTIONAL] Help displayed in Galaxy -->
    <help>

.. class:: infomark

**Authors** 

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

.. class:: infomark

**Please cite** If you use this tool, please cite dereeper et al. 2015 in prep.

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

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

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

  Compute an IBS matrix and a multi-dimensional scaling.


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

**Upstream tools**

=========== ========================== =======
Name            output file(s)         format 
=========== ========================== =======
=========== ========================== =======


**Downstream tools**

=========== ========================== =======
Name            output file(s)         format
=========== ========================== =======
=========== ========================== =======


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

PED file

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


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

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



Parameters
==========

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>
    
</tool>