--- a/MDSplot/mdsplot.xml	Wed Feb 07 22:08:47 2018 -0500
+++ b/MDSplot/mdsplot.xml	Mon Apr 16 09:00:24 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="sniplay_mdsplot" name="MDS plot" version="1.2.0">
+<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>
@@ -39,58 +39,44 @@
     
     <!-- [REQUIRED] Output files -->
     <outputs>
-	<data name="fileout_matrix" type="data" format="txt" label="${fileout_label}.ibs_matrix.txt" />
-	<data name="fileout_plot" type="data" format="txt" label="${fileout_label}.mds_plot.txt" />
-	<data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
+	<data name="fileout_matrix" format="txt" label="${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>
-
-        <!-- [HELP] Multiple tests can be defined with different parameters -->
-<!--
-        <test>
-        </test>
--->
     </tests>
     
     <!-- [OPTIONAL] Help displayed in Galaxy -->
-    <help>
+    <help><![CDATA[
 
 
 .. class:: infomark
 
-**Authors** plink_
+MDS plot is done with PLINK.
+**Authors** PLINK: Shaun Purcell (https://www.cog-genomics.org/plink)
 
-.. _plink: http://pngu.mgh.harvard.edu/purcell/plink/
-
-  | "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** "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** Andres Gwendoline, Institut Français de Bioinformatique.
+**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 support.abims@sb-roscoff.fr
-
-.. class:: infomark
-
-**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).
+**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
 
 ---------------------------------------------------
 
-
-
 ========
 MDS plot
 ========
@@ -99,36 +85,41 @@
 Description
 -----------
 
-  Compute an IBS matrix and a multi-dimensional scaling.
-
-
------------------
-Workflow position
------------------
-
-**Upstream tool**
-
-=============== ========================== ===============
-Name            output file(s)             format 
-=============== ========================== ===============
-VCFtools Filter PED and MAP file	   tabular and MAP
-=============== ========================== ===============
+  | 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_.
 
 
 
-----------
-Input file
-----------
+.. _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
+	PED file usually from VCF tools
 
 MAP file
 	4 columns tabular file: chromosome, snp id, genetic distance, bp position 
 
 
-----------
-Parameters
-----------
+---------
+Parameter
+---------
 
 Output name
         Output base name for the ouput files
@@ -146,12 +137,6 @@
 
 Output_name.log
 	Log file
-
-------------
-Dependencies
-------------
-plink 
-	version 1.07
 	
 ---------------------------------------------------
 
@@ -184,8 +169,8 @@
 
 
 
-Parameters
-==========
+Parameter
+=========
 
 Output name -> densities
 
@@ -213,7 +198,7 @@
 
 	
 
-    </help>
+    ]]></help>
     <citations>
         <!-- [HELP] As DOI or BibTex entry -->
     	<citation type="bibtex">@article{Dereeper03062015,