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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="binary">perl</requirement>
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5 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
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6 <requirement type="package" version="1.90b4">plink</requirement>
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7 </requirements>
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8 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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9 <stdio>
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10 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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11 <exit_code range="1:" level="fatal" />
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12 </stdio>
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13 <command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs
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14 </command>
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15 <inputs>
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16 <param format="txt" name="ped" type="data" label="Allelic file in PED format" help="Allelic file in PED format"/>
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17 <param format="txt" name="map" type="data" label="Map file" help="Map file"/>
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18 </inputs>
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19 <outputs>
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20 <data format="txt" name="bed" label="Bed file"/>
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21 <data format="txt" name="fam" label="Fam file"/>
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22 <data format="txt" name="bim" label="Bim file"/>
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23 <data format="txt" name="logs" label="All Logs"/>
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24 </outputs>
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25
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26 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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27 <tests>
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28 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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29 <!-- [HELP] Multiple tests can be defined with different parameters -->
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30 <test>
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31 <param name="ped" value="ped2bed-input.ped" />
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32 <param name="map" value="ped2bed-input.map" />
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33 <output name="bed" file="ped2bed-result.bed" />
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34 <output name="fam" file="ped2bed-result.fam" />
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35 <output name="bim" file="ped2bed-result.bim" />
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36 </test>
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37 </tests>
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38 <help>
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39
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40
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41 .. class:: infomark
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42
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43 **Authors** plink_
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44
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45 .. _plink: http://pngu.mgh.harvard.edu/purcell/plink/
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46
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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.
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48
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49 .. class:: infomark
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50
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51 **Galaxy integration** South Green.
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52
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53 .. class:: infomark
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54
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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).
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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
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62 =======
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63 Ped2Bed
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64 =======
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65
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66 -----------
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67 Description
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68 -----------
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69
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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.
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71 | For further informations, please visite the plink website_.
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72
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73 .. _website: http://pngu.mgh.harvard.edu/purcell/plink/
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74
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75
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76 -----------------
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77 Workflow position
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78 -----------------
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79
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80 **Upstream tool**
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81
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82 =============== ========================== ===========
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83 Name output file(s) format
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84 =============== ========================== ===========
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85 VCFtools filter PED and map files ped and map
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86 =============== ========================== ===========
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87
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88
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89 **Downstream tool**
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90
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91 =========== ========================== =======
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92 Name input file(s) format
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93 =========== ========================== =======
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94 Admixture Bed, fam and bim file txt
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95 =========== ========================== =======
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96
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97
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98 ----------
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99 Input file
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100 ----------
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101
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102 PED file
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103 Allelic file in PED format
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104
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105 MAP file
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106
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107
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108
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109 ------------
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110 Output files
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111 ------------
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112
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113 Bed file
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114
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115 Fam file
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116
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117 Bim file
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118
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119 All logs
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120 Log file
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121
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122
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123 ------------
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124 Dependencies
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125 ------------
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126 plink
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127 version 1.07
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128
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129 ---------------------------------------------------
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130
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131 ---------------
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132 Working example
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133 ---------------
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134
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135 Input files
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136 ===========
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137
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138 PED file
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139 --------
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140
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141 ::
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142
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143 AZUCENA AZUCENA 0 0 0 0 G G A A C C T T T
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144 BULUPANDAK BULUPANDAK 0 0 0 0 G G A A A A T
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145
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146 MAP file
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147 --------
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148
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149 ::
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150
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151 0 Chr1:4299 0 4299
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152 0 Chr1:26710 0 26710
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153 0 Chr1:56184 0 56184
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154 0 Chr1:93272 0 93272
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155
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156
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157 Output files
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158 ============
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159
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160 Bed file
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161 --------
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162
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163 ::
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164
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165 binary file
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166
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167 Fam file
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168 --------
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169
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170 ::
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171
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172 AZUCENA AZUCENA 0 0 0 -9
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173 BULUPANDAK BULUPANDAK 0 0 0 -9
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174
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175 Bim file
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176 --------
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177
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178 ::
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179
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180 0 Chr1:4299 0 4299 A G
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181 0 Chr8:18058 0 18058 C T
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182
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183
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184 </help>
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185 <citations>
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186 <!-- [HELP] As DOI or BibTex entry -->
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187 <citation type="bibtex">@article{Dereeper03062015,
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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},
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189 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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190 year = {2015},
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191 doi = {10.1093/nar/gkv351},
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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.},
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193 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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194 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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195 journal = {Nucleic Acids Research}
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196 }
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197
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198 </citation>
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199
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200 </citations>
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201 </tool>
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