annotate ped2bed/ped2bed.xml @ 10:c6640c49fd01 draft

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date Mon, 16 Apr 2018 09:00:24 -0400
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1 <tool id="ped2bed" name="PLINK: ped2bed" version="2.0.0">
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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><![CDATA[
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40
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41 .. class:: infomark
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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)
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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).
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48
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49 .. class:: infomark
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50
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51 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
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52
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53 .. class:: infomark
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54
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55 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
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57 ---------------------------------------------------
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58
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59 =======
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60 Ped2Bed
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61 =======
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62
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63 -----------
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64 Description
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65 -----------
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67 | Ped to Bed format conversion is done with PLINK
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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 visit the PLINK website_.
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70
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71 .. _website: https://www.cog-genomics.org/plink
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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
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81 .. _plink: https://anaconda.org/bioconda/plink
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82 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
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84 -----------
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85 Input files
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86 -----------
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87
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88 PED file
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89
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90 MAP file
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91
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92 ------------
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93 Output files
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94 ------------
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96 Bed file
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98 Fam file
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99
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100 Bim file
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101
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102 All logs
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103
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104 ---------------------------------------------------
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105
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106 ---------------
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107 Working example
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108 ---------------
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109
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110 Input files
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111 ===========
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112
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113 PED file
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114 --------
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115
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116 ::
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118 AZUCENA AZUCENA 0 0 0 0 G G A A C C T T T
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119 BULUPANDAK BULUPANDAK 0 0 0 0 G G A A A A T
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120
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121 MAP file
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122 --------
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123
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124 ::
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125
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126 0 Chr1:4299 0 4299
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127 0 Chr1:26710 0 26710
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128 0 Chr1:56184 0 56184
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129 0 Chr1:93272 0 93272
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132 Output files
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133 ============
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134
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135 Bed file
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136 --------
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138 ::
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140 binary file
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141
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142 Fam file
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143 --------
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145 ::
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147 AZUCENA AZUCENA 0 0 0 -9
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148 BULUPANDAK BULUPANDAK 0 0 0 -9
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149
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150 Bim file
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151 --------
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153 ::
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155 0 Chr1:4299 0 4299 A G
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156 0 Chr8:18058 0 18058 C T
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157
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159 ]]></help>
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160 <citations>
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161 <!-- [HELP] As DOI or BibTex entry -->
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162 <citation type="bibtex">@article{Dereeper03062015,
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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},
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164 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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165 year = {2015},
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166 doi = {10.1093/nar/gkv351},
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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.},
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168 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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169 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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170 journal = {Nucleic Acids Research}
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171 }
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172
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173 </citation>
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174
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175 </citations>
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176 </tool>