diff MDSplot/mdsplot.xml @ 1:420b57c3c185 draft

Uploaded

--- a/MDSplot/mdsplot.xml	Mon Mar 23 05:57:27 2015 -0400
+++ b/MDSplot/mdsplot.xml	Fri Jul 10 04:39:30 2015 -0400
@@ -6,7 +6,7 @@
     <!-- [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>
+	<requirement type="package" version="1.07">plink</requirement>
     </requirements>
     
     <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
@@ -63,17 +63,31 @@
     <!-- [OPTIONAL] Help displayed in Galaxy -->
     <help>
 
+
 .. class:: infomark
 
-**Authors** 
+**Authors** 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.
+
+
+.. class:: infomark
+
+**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
+
+.. class:: infomark
+
+**Support** For any questions about Galaxy integration, please send an e-mail to [e-mail]
+
+.. 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).
 
 ---------------------------------------------------
 
-.. class:: infomark
 
-**Please cite** If you use this tool, please cite dereeper et al. 2015 in prep.
-
----------------------------------------------------
 
 ========
 MDS plot
@@ -90,20 +104,14 @@
 Workflow position
 -----------------
 
-**Upstream tools**
-
-=========== ========================== =======
-Name            output file(s)         format 
-=========== ========================== =======
-=========== ========================== =======
+**Upstream tool**
 
-
-**Downstream tools**
+=============== ========================== ===============
+Name            output file(s)             format 
+=============== ========================== ===============
+VCFtools Filter PED and MAP file	   tabular and MAP
+=============== ========================== ===============
 
-=========== ========================== =======
-Name            output file(s)         format
-=========== ========================== =======
-=========== ========================== =======
 
 
 ----------
@@ -137,6 +145,11 @@
 Output_name.log
 	Log file
 
+------------
+Dependencies
+------------
+plink 
+	version 1.07
 	
 ---------------------------------------------------
 
@@ -199,5 +212,21 @@
 	
 
     </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>