Mercurial > repos > dereeper > sniplay
annotate 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 |
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1 <tool id="ped2bed" name="PLINK: ped2bed" version="2.0.0"> |
9 | 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> | |
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38 <help><![CDATA[ |
9 | 39 |
40 | |
41 .. class:: infomark | |
42 | |
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43 Ped to Bed format conversion is done with PLINK. |
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44 **Authors** PLINK: Shaun Purcell (https://www.cog-genomics.org/plink) |
9 | 45 |
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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. |
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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). |
9 | 48 |
49 .. class:: infomark | |
50 | |
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51 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) |
9 | 52 |
53 .. class:: infomark | |
54 | |
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55 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
9 | 56 |
57 --------------------------------------------------- | |
58 | |
59 ======= | |
60 Ped2Bed | |
61 ======= | |
62 | |
63 ----------- | |
64 Description | |
65 ----------- | |
66 | |
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67 | Ped to Bed format conversion is done with PLINK |
9 | 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. |
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69 | For further informations, please visit the PLINK website_. |
9 | 70 |
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71 .. _website: https://www.cog-genomics.org/plink |
9 | 72 |
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73 ------------ |
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74 Dependencies |
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75 ------------ |
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76 PLINK |
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77 plink_ 1.90b4, Conda version |
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78 Bioperl |
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79 perl-bioperl_ 1.6.924, Conda version |
9 | 80 |
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81 .. _plink: https://anaconda.org/bioconda/plink |
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82 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl |
9 | 83 |
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84 ----------- |
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85 Input files |
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86 ----------- |
9 | 87 |
88 PED file | |
89 | |
90 MAP file | |
91 | |
92 ------------ | |
93 Output files | |
94 ------------ | |
95 | |
96 Bed file | |
97 | |
98 Fam file | |
99 | |
100 Bim file | |
101 | |
102 All logs | |
103 | |
104 --------------------------------------------------- | |
105 | |
106 --------------- | |
107 Working example | |
108 --------------- | |
109 | |
110 Input files | |
111 =========== | |
112 | |
113 PED file | |
114 -------- | |
115 | |
116 :: | |
117 | |
118 AZUCENA AZUCENA 0 0 0 0 G G A A C C T T T | |
119 BULUPANDAK BULUPANDAK 0 0 0 0 G G A A A A T | |
120 | |
121 MAP file | |
122 -------- | |
123 | |
124 :: | |
125 | |
126 0 Chr1:4299 0 4299 | |
127 0 Chr1:26710 0 26710 | |
128 0 Chr1:56184 0 56184 | |
129 0 Chr1:93272 0 93272 | |
130 | |
131 | |
132 Output files | |
133 ============ | |
134 | |
135 Bed file | |
136 -------- | |
137 | |
138 :: | |
139 | |
140 binary file | |
141 | |
142 Fam file | |
143 -------- | |
144 | |
145 :: | |
146 | |
147 AZUCENA AZUCENA 0 0 0 -9 | |
148 BULUPANDAK BULUPANDAK 0 0 0 -9 | |
149 | |
150 Bim file | |
151 -------- | |
152 | |
153 :: | |
154 | |
155 0 Chr1:4299 0 4299 A G | |
156 0 Chr8:18058 0 18058 C T | |
157 | |
158 | |
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159 ]]></help> |
9 | 160 <citations> |
161 <!-- [HELP] As DOI or BibTex entry --> | |
162 <citation type="bibtex">@article{Dereeper03062015, | |
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}, | |
164 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, | |
165 year = {2015}, | |
166 doi = {10.1093/nar/gkv351}, | |
167 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.}, | |
168 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, | |
169 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, | |
170 journal = {Nucleic Acids Research} | |
171 } | |
172 | |
173 </citation> | |
174 | |
175 </citations> | |
176 </tool> |