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

Uploaded

0:3e19d0dfcf3e

    <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>
<!--

    </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.

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

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Workflow position
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**Upstream tools**

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


**Downstream tools**

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


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

	File to construct mds plot

Output_name.log
	Log file

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

	IAC25	-0.0918126	0.0501177

	

    </help>
    
</tool>

1:420b57c3c185

    <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="1.07">plink</requirement>
    </requirements>
    
    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
    <version_command>
<!--

    </tests>
    
    <!-- [OPTIONAL] Help displayed in Galaxy -->
    <help>


.. class:: infomark

**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).

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



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

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

**Upstream tool**

=============== ========================== ===============
Name            output file(s)             format 
=============== ========================== ===============
VCFtools Filter PED and MAP file	   tabular and MAP
=============== ========================== ===============



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

	File to construct mds plot

Output_name.log
	Log file

------------
Dependencies
------------
plink 
	version 1.07
	
---------------------------------------------------

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

	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>