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1 <tool id="ped2bed" name="plink: ped2bed" version="1.24">
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2 <description>Convert ped to bed</description>
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3 <requirements>
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4 <requirement type="package" version="1.07">plink</requirement>
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5 </requirements>
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4
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6 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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7 <stdio>
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8 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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9 <exit_code range="1:" level="fatal" />
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10 </stdio>
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11 <command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs
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1
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12 </command>
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13 <inputs>
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14 <param format="txt" name="ped" type="data" label="Allelic file in PED format" help="Allelic file in PED format"/>
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15 <param format="txt" name="map" type="data" label="Map file" help="Map file"/>
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16 </inputs>
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17 <outputs>
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18 <data format="txt" name="bed" label="Bed file"/>
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19 <data format="txt" name="fam" label="Fam file"/>
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20 <data format="txt" name="bim" label="Bim file"/>
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21 <data format="txt" name="logs" label="All Logs"/>
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22 </outputs>
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23
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24 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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25 <tests>
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26 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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27 <!-- [HELP] Multiple tests can be defined with different parameters -->
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28 <test>
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4
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29 <param name="ped" value="ped2bed-input.ped" />
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30 <param name="map" value="ped2bed-input.map" />
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31 <output name="bed" file="ped2bed-result.bed" />
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32 <output name="fam" file="ped2bed-result.fam" />
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33 <output name="bim" file="ped2bed-result.bim" />
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1
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34 </test>
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35 </tests>
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36 <help>
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37
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38
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39 .. class:: infomark
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40
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41 **Authors** plink_
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42
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43 .. _plink: http://pngu.mgh.harvard.edu/purcell/plink/
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44
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45 | "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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46
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47 .. class:: infomark
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48
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49 **Galaxy integration** South Green.
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50
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51 .. class:: infomark
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52
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53 **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).
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54
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55
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56 ---------------------------------------------------
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57
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58
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59
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60 =======
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61 Ped2Bed
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62 =======
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63
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64 -----------
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65 Description
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66 -----------
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67
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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 visite the plink website_.
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70
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71 .. _website: http://pngu.mgh.harvard.edu/purcell/plink/
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72
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73
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74 -----------------
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75 Workflow position
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76 -----------------
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77
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78 **Upstream tool**
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79
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80 =============== ========================== ===========
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81 Name output file(s) format
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82 =============== ========================== ===========
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83 VCFtools filter PED and map files ped and map
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84 =============== ========================== ===========
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85
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86
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87 **Downstream tool**
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88
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89 =========== ========================== =======
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90 Name input file(s) format
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91 =========== ========================== =======
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92 Admixture Bed, fam and bim file txt
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93 =========== ========================== =======
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94
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95
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96 ----------
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97 Input file
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98 ----------
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99
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100 PED file
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101 Allelic file in PED format
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102
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103 MAP file
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104
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105
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106
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107 ------------
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108 Output files
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109 ------------
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110
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111 Bed file
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112
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113 Fam file
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114
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115 Bim file
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116
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117 All logs
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118 Log file
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119
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120
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121 ------------
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122 Dependencies
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123 ------------
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124 plink
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125 version 1.07
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126
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127 ---------------------------------------------------
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128
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129 ---------------
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130 Working example
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131 ---------------
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132
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133 Input files
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134 ===========
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135
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136 PED file
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137 --------
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138
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139 ::
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140
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141 AZUCENA AZUCENA 0 0 0 0 G G A A C C T T T
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142 BULUPANDAK BULUPANDAK 0 0 0 0 G G A A A A T
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143
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144 MAP file
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145 --------
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146
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147 ::
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148
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149 0 Chr1:4299 0 4299
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150 0 Chr1:26710 0 26710
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151 0 Chr1:56184 0 56184
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152 0 Chr1:93272 0 93272
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153
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154
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155 Output files
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156 ============
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157
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158 Bed file
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159 --------
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160
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161 ::
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162
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163 binary file
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164
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165 Fam file
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166 --------
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167
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168 ::
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169
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170 AZUCENA AZUCENA 0 0 0 -9
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171 BULUPANDAK BULUPANDAK 0 0 0 -9
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172
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173 Bim file
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174 --------
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175
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176 ::
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177
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178 0 Chr1:4299 0 4299 A G
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179 0 Chr8:18058 0 18058 C T
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180
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181
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182 </help>
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183 <citations>
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184 <!-- [HELP] As DOI or BibTex entry -->
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185 <citation type="bibtex">@article{Dereeper03062015,
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186 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},
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187 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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188 year = {2015},
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189 doi = {10.1093/nar/gkv351},
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190 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.},
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191 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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192 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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193 journal = {Nucleic Acids Research}
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194 }
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195
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196 </citation>
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197
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198 </citations>
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199 </tool>
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