Mercurial > repos > dereeper > sniplay
diff MDSplot/mdsplot.xml @ 10:c6640c49fd01 draft
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author | dereeper |
---|---|
date | Mon, 16 Apr 2018 09:00:24 -0400 |
parents | 6bf69b40365c |
children | 15b23cdde685 |
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--- 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,