Mercurial > repos > dereeper > sniplay

comparison ped2bed/ped2bed.xml @ 1:420b57c3c185 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dereeper
date Fri, 10 Jul 2015 04:39:30 -0400
parents
children 10627af23f10
comparison
equal deleted inserted replaced
0:3e19d0dfcf3e 1:420b57c3c185
1 <tool id="ped2bed" name="plink: ped2bed" version="1.24">
2 <description>Convert ped to bed</description>
3 <requirements>
4 <requirement type="package" version="1.07">plink</requirement>
5 </requirements>
6 <command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs
7 </command>
8 <inputs>
9 <param format="txt" name="ped" type="data" label="Allelic file in PED format" help="Allelic file in PED format"/>
10 <param format="txt" name="map" type="data" label="Map file" help="Map file"/>
11 </inputs>
12 <outputs>
13 <data format="txt" name="bed" label="Bed file"/>
14 <data format="txt" name="fam" label="Fam file"/>
15 <data format="txt" name="bim" label="Bim file"/>
16 <data format="txt" name="logs" label="All Logs"/>
17 </outputs>
18 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
19 <stdio>
20 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
21 <exit_code range="1:" level="fatal" />
22 </stdio>
23
24 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
25 <tests>
26 <!-- [HELP] Test files have to be in the ~/test-data directory -->
27 <!-- [HELP] Multiple tests can be defined with different parameters -->
28 <!--
29 <test>
30 </test>
31 -->
32 </tests>
33 <help>
34
35
36 .. class:: infomark
37
38 **Authors** plink_
39
40 .. _plink: http://pngu.mgh.harvard.edu/purcell/plink/
41
42 | "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.
43
44 .. class:: infomark
45
46 **Galaxy integration** South Green.
47
48 .. class:: infomark
49
50 **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).
51
52
53 ---------------------------------------------------
54
55
56
57 =======
58 Ped2Bed
59 =======
60
61 -----------
62 Description
63 -----------
64
65 | 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.
66 | For further informations, please visite the plink website_.
67
68 .. _website: http://pngu.mgh.harvard.edu/purcell/plink/
69
70
71 -----------------
72 Workflow position
73 -----------------
74
75 **Upstream tool**
76
77 =============== ========================== ===========
78 Name output file(s) format
79 =============== ========================== ===========
80 VCFtools filter PED and map files ped and map
81 =============== ========================== ===========
82
83
84 **Downstream tool**
85
86 =========== ========================== =======
87 Name input file(s) format
88 =========== ========================== =======
89 Admixture Bed, fam and bim file txt
90 =========== ========================== =======
91
92
93 ----------
94 Input file
95 ----------
96
97 PED file
98 Allelic file in PED format
99
100 MAP file
101
102
103
104 ------------
105 Output files
106 ------------
107
108 Bed file
109
110 Fam file
111
112 Bim file
113
114 All logs
115 Log file
116
117
118 ------------
119 Dependencies
120 ------------
121 plink
122 version 1.07
123
124 ---------------------------------------------------
125
126 ---------------
127 Working example
128 ---------------
129
130 Input files
131 ===========
132
133 PED file
134 --------
135
136 ::
137
138 AZUCENA AZUCENA 0 0 0 0 G G A A C C T T T
139 BULUPANDAK BULUPANDAK 0 0 0 0 G G A A A A T
140
141 MAP file
142 --------
143
144 ::
145
146 0 Chr1:4299 0 4299
147 0 Chr1:26710 0 26710
148 0 Chr1:56184 0 56184
149 0 Chr1:93272 0 93272
150
151
152 Output files
153 ============
154
155 Bed file
156 --------
157
158 ::
159
160 binary file
161
162 Fam file
163 --------
164
165 ::
166
167 AZUCENA AZUCENA 0 0 0 -9
168 BULUPANDAK BULUPANDAK 0 0 0 -9
169
170 Bim file
171 --------
172
173 ::
174
175 0 Chr1:4299 0 4299 A G
176 0 Chr8:18058 0 18058 C T
177
178
179 </help>
180 <citations>
181 <!-- [HELP] As DOI or BibTex entry -->
182 <citation type="bibtex">@article{Dereeper03062015,
183 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},
184 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
185 year = {2015},
186 doi = {10.1093/nar/gkv351},
187 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.},
188 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
189 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
190 journal = {Nucleic Acids Research}
191 }
192
193 </citation>
194
195 </citations>
196 </tool>