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comparison ped2bed/ped2bed.xml @ 10:c6640c49fd01 draft

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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 09:00:24 -0400
parents 98c37a5d67f4
children
comparison
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9:98c37a5d67f4 10:c6640c49fd01
1 <tool id="ped2bed" name="plink: ped2bed" version="1.24"> 1 <tool id="ped2bed" name="PLINK: ped2bed" version="2.0.0">
2 <description>Convert ped to bed</description> 2 <description>Convert ped to bed</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">perl</requirement> 4 <requirement type="binary">perl</requirement>
5 <requirement type="package" version="1.6.924">perl-bioperl</requirement> 5 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
6 <requirement type="package" version="1.90b4">plink</requirement> 6 <requirement type="package" version="1.90b4">plink</requirement>
33 <output name="bed" file="ped2bed-result.bed" /> 33 <output name="bed" file="ped2bed-result.bed" />
34 <output name="fam" file="ped2bed-result.fam" /> 34 <output name="fam" file="ped2bed-result.fam" />
35 <output name="bim" file="ped2bed-result.bim" /> 35 <output name="bim" file="ped2bed-result.bim" />
36 </test> 36 </test>
37 </tests> 37 </tests>
38 <help> 38 <help><![CDATA[
39 39
40 40
41 .. class:: infomark 41 .. class:: infomark
42 42
43 **Authors** plink_ 43 Ped to Bed format conversion is done with PLINK.
44 **Authors** PLINK: Shaun Purcell (https://www.cog-genomics.org/plink)
44 45
45 .. _plink: http://pngu.mgh.harvard.edu/purcell/plink/ 46 | **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.
46 47 | **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).
47 | "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.
48 48
49 .. class:: infomark 49 .. class:: infomark
50 50
51 **Galaxy integration** South Green. 51 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
52 52
53 .. class:: infomark 53 .. class:: infomark
54 54
55 **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). 55 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
56
57 56
58 --------------------------------------------------- 57 ---------------------------------------------------
59
60
61 58
62 ======= 59 =======
63 Ped2Bed 60 Ped2Bed
64 ======= 61 =======
65 62
66 ----------- 63 -----------
67 Description 64 Description
68 ----------- 65 -----------
69 66
67 | Ped to Bed format conversion is done with PLINK
70 | 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. 68 | 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.
71 | For further informations, please visite the plink website_. 69 | For further informations, please visit the PLINK website_.
72 70
73 .. _website: http://pngu.mgh.harvard.edu/purcell/plink/ 71 .. _website: https://www.cog-genomics.org/plink
74 72
73 ------------
74 Dependencies
75 ------------
76 PLINK
77 plink_ 1.90b4, Conda version
78 Bioperl
79 perl-bioperl_ 1.6.924, Conda version
75 80
76 ----------------- 81 .. _plink: https://anaconda.org/bioconda/plink
77 Workflow position 82 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
78 -----------------
79 83
80 **Upstream tool** 84 -----------
81 85 Input files
82 =============== ========================== =========== 86 -----------
83 Name output file(s) format
84 =============== ========================== ===========
85 VCFtools filter PED and map files ped and map
86 =============== ========================== ===========
87
88
89 **Downstream tool**
90
91 =========== ========================== =======
92 Name input file(s) format
93 =========== ========================== =======
94 Admixture Bed, fam and bim file txt
95 =========== ========================== =======
96
97
98 ----------
99 Input file
100 ----------
101 87
102 PED file 88 PED file
103 Allelic file in PED format
104 89
105 MAP file 90 MAP file
106
107
108 91
109 ------------ 92 ------------
110 Output files 93 Output files
111 ------------ 94 ------------
112 95
115 Fam file 98 Fam file
116 99
117 Bim file 100 Bim file
118 101
119 All logs 102 All logs
120 Log file
121
122
123 ------------
124 Dependencies
125 ------------
126 plink
127 version 1.07
128 103
129 --------------------------------------------------- 104 ---------------------------------------------------
130 105
131 --------------- 106 ---------------
132 Working example 107 Working example
179 154
180 0 Chr1:4299 0 4299 A G 155 0 Chr1:4299 0 4299 A G
181 0 Chr8:18058 0 18058 C T 156 0 Chr8:18058 0 18058 C T
182 157
183 158
184 </help> 159 ]]></help>
185 <citations> 160 <citations>
186 <!-- [HELP] As DOI or BibTex entry --> 161 <!-- [HELP] As DOI or BibTex entry -->
187 <citation type="bibtex">@article{Dereeper03062015, 162 <citation type="bibtex">@article{Dereeper03062015,
188 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}, 163 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},
189 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, 164 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},