Mercurial > repos > dereeper > sniplay
annotate ped2bed/ped2bed.xml @ 12:88748d846a20 draft
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
| author | dereeper |
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| date | Tue, 14 Aug 2018 08:21:55 -0400 |
| parents | c6640c49fd01 |
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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> |