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comparison ped2bed/ped2bed.xml @ 9:98c37a5d67f4 draft

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author dereeper
date Wed, 07 Feb 2018 22:08:47 -0500
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8:6bf69b40365c 9:98c37a5d67f4
1 <tool id="ped2bed" name="plink: ped2bed" version="1.24">
2 <description>Convert ped to bed</description>
3 <requirements>
4 <requirement type="binary">perl</requirement>
5 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
6 <requirement type="package" version="1.90b4">plink</requirement>
7 </requirements>
8 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
9 <stdio>
10 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
11 <exit_code range="1:" level="fatal" />
12 </stdio>
13 <command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs
14 </command>
15 <inputs>
16 <param format="txt" name="ped" type="data" label="Allelic file in PED format" help="Allelic file in PED format"/>
17 <param format="txt" name="map" type="data" label="Map file" help="Map file"/>
18 </inputs>
19 <outputs>
20 <data format="txt" name="bed" label="Bed file"/>
21 <data format="txt" name="fam" label="Fam file"/>
22 <data format="txt" name="bim" label="Bim file"/>
23 <data format="txt" name="logs" label="All Logs"/>
24 </outputs>
25
26 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
27 <tests>
28 <!-- [HELP] Test files have to be in the ~/test-data directory -->
29 <!-- [HELP] Multiple tests can be defined with different parameters -->
30 <test>
31 <param name="ped" value="ped2bed-input.ped" />
32 <param name="map" value="ped2bed-input.map" />
33 <output name="bed" file="ped2bed-result.bed" />
34 <output name="fam" file="ped2bed-result.fam" />
35 <output name="bim" file="ped2bed-result.bim" />
36 </test>
37 </tests>
38 <help>
39
40
41 .. class:: infomark
42
43 **Authors** plink_
44
45 .. _plink: http://pngu.mgh.harvard.edu/purcell/plink/
46
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
49 .. class:: infomark
50
51 **Galaxy integration** South Green.
52
53 .. class:: infomark
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).
56
57
58 ---------------------------------------------------
59
60
61
62 =======
63 Ped2Bed
64 =======
65
66 -----------
67 Description
68 -----------
69
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.
71 | For further informations, please visite the plink website_.
72
73 .. _website: http://pngu.mgh.harvard.edu/purcell/plink/
74
75
76 -----------------
77 Workflow position
78 -----------------
79
80 **Upstream tool**
81
82 =============== ========================== ===========
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
102 PED file
103 Allelic file in PED format
104
105 MAP file
106
107
108
109 ------------
110 Output files
111 ------------
112
113 Bed file
114
115 Fam file
116
117 Bim file
118
119 All logs
120 Log file
121
122
123 ------------
124 Dependencies
125 ------------
126 plink
127 version 1.07
128
129 ---------------------------------------------------
130
131 ---------------
132 Working example
133 ---------------
134
135 Input files
136 ===========
137
138 PED file
139 --------
140
141 ::
142
143 AZUCENA AZUCENA 0 0 0 0 G G A A C C T T T
144 BULUPANDAK BULUPANDAK 0 0 0 0 G G A A A A T
145
146 MAP file
147 --------
148
149 ::
150
151 0 Chr1:4299 0 4299
152 0 Chr1:26710 0 26710
153 0 Chr1:56184 0 56184
154 0 Chr1:93272 0 93272
155
156
157 Output files
158 ============
159
160 Bed file
161 --------
162
163 ::
164
165 binary file
166
167 Fam file
168 --------
169
170 ::
171
172 AZUCENA AZUCENA 0 0 0 -9
173 BULUPANDAK BULUPANDAK 0 0 0 -9
174
175 Bim file
176 --------
177
178 ::
179
180 0 Chr1:4299 0 4299 A G
181 0 Chr8:18058 0 18058 C T
182
183
184 </help>
185 <citations>
186 <!-- [HELP] As DOI or BibTex entry -->
187 <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},
189 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
190 year = {2015},
191 doi = {10.1093/nar/gkv351},
192 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.},
193 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
194 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
195 journal = {Nucleic Acids Research}
196 }
197
198 </citation>
199
200 </citations>
201 </tool>