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