Mercurial > repos > dereeper > sniplay
view MDSplot/mdsplot.xml @ 8:6bf69b40365c draft
Uploaded
author | dereeper |
---|---|
date | Wed, 07 Feb 2018 21:37:59 -0500 |
parents | ec22fcacb66c |
children | c6640c49fd01 |
line wrap: on
line source
<tool id="sniplay_mdsplot" name="MDS plot" version="1.2.0"> <!-- [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="1.6.924">perl-bioperl</requirement> <requirement type="package" version="1.90b4">plink</requirement> </requirements> <!-- [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] 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_matrix $fileout_plot $fileout_log $groups </command> <!-- [REQUIRED] Input files and tool parameters --> <inputs> <param name="fileped" type="data" format="txt" optional="false" label="PED input" /> <param name="filemap" type="data" format="txt" optional="false" label="MAP input" help="4 columns tabular file: chromosome, snp id, genetic distance, bp position"/> <param name="groups" type="data" format="txt" optional="true" label="Groups" help="Groups defined by sNMF"/> <param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" /> </inputs> <!-- [REQUIRED] Output files --> <outputs> <data name="fileout_matrix" type="data" format="txt" label="${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" /> </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> .. 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 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). --------------------------------------------------- ======== MDS plot ======== ----------- 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 =============== ========================== =============== ---------- 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 ------------ Dependencies ------------ plink version 1.07 --------------------------------------------------- --------------- 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> <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>