Mercurial > repos > dereeper > sniplay
diff ped2bed/ped2bed.xml @ 10:c6640c49fd01 draft
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author | dereeper |
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date | Mon, 16 Apr 2018 09:00:24 -0400 |
parents | 98c37a5d67f4 |
children |
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--- a/ped2bed/ped2bed.xml Wed Feb 07 22:08:47 2018 -0500 +++ b/ped2bed/ped2bed.xml Mon Apr 16 09:00:24 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="ped2bed" name="plink: ped2bed" version="1.24"> +<tool id="ped2bed" name="PLINK: ped2bed" version="2.0.0"> <description>Convert ped to bed</description> <requirements> <requirement type="binary">perl</requirement> @@ -35,30 +35,27 @@ <output name="bim" file="ped2bed-result.bim" /> </test> </tests> - <help> + <help><![CDATA[ .. class:: infomark -**Authors** plink_ +Ped to Bed format conversion 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** South Green. +**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) .. 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 --------------------------------------------------- - - ======= Ped2Bed ======= @@ -67,45 +64,31 @@ Description ----------- + | Ped to Bed format conversion 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 visite the plink website_. - -.. _website: http://pngu.mgh.harvard.edu/purcell/plink/ - + | For further informations, please visit the PLINK website_. ------------------ -Workflow position ------------------ - -**Upstream tool** +.. _website: https://www.cog-genomics.org/plink -=============== ========================== =========== -Name output file(s) format -=============== ========================== =========== -VCFtools filter PED and map files ped and map -=============== ========================== =========== - - -**Downstream tool** +------------ +Dependencies +------------ +PLINK + plink_ 1.90b4, Conda version +Bioperl + perl-bioperl_ 1.6.924, Conda version -=========== ========================== ======= -Name input file(s) format -=========== ========================== ======= -Admixture Bed, fam and bim file txt -=========== ========================== ======= +.. _plink: https://anaconda.org/bioconda/plink +.. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl - ----------- -Input file ----------- +----------- +Input files +----------- PED file - Allelic file in PED format MAP file - - ------------ Output files ------------ @@ -117,14 +100,6 @@ Bim file All logs - Log file - - ------------- -Dependencies ------------- -plink - version 1.07 --------------------------------------------------- @@ -181,7 +156,7 @@ 0 Chr8:18058 0 18058 C T - </help> + ]]></help> <citations> <!-- [HELP] As DOI or BibTex entry --> <citation type="bibtex">@article{Dereeper03062015,