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1 <tool id="sniplay_pedToFasta" name="Ped2Fasta" version="1.0.0">
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2
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description> Convert PED file to Fasta File </description>
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5
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6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
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7 <requirements>
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8 <requirement type="binary">perl</requirement>
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9 </requirements>
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10
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11 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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12 <stdio>
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13 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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14 <exit_code range="1:" level="fatal" />
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15 </stdio>
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16
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17 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
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18 <version_command>
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19 <!--
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20 tool_binary -v
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21 -->
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22 </version_command>
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23
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24 <!-- [REQUIRED] The command to execute -->
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25 <command interpreter="perl">
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26 Ped2Fasta.pl --in $filein --out $fileout
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27 </command>
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28
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29 <!-- [REQUIRED] Input files and tool parameters -->
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30 <inputs>
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31 <param name="filein" type="data" format="txt" optional="false" label="PED input" />
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32 <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file name"/>
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33 </inputs>
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34
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35 <!-- [REQUIRED] Output files -->
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36 <outputs>
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37 <data name="fileout" type="data" format="fasta" label="${fileout_label}.fa" />
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38 </outputs>
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39
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40 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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41 <tests>
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42 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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43 <test>
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44 <param name="filein" value="ped2fasta-sample.ped" />
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45 <output name="fileout" file="ped2fasta-result.fa" />
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46 </test>
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47 </tests>
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48
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49 <!-- [OPTIONAL] Help displayed in Galaxy -->
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50 <help>
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51
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52 .. class:: infomark
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53
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54 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
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55
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56 | **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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57
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58 .. class:: infomark
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59
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60 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
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61
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62 .. class:: infomark
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63
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64 **Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr
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65
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66 ---------------------------------------------------
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67
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68 =========
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69 Ped2Fasta
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70 =========
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71
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72 -----------
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73 Description
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74 -----------
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75
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76 Convert PED file to Fasta File
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77
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78 -----------------
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79 Workflow position
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80 -----------------
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81
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82 **Upstream tool**
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83
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84 =============== ========================== =======
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85 Name output file(s) format
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86 =============== ========================== =======
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87 VCFtools Filter VCF file VCF
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88 =============== ========================== =======
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89
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90
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91 **Downstream tool**
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92
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93 =========== ========================== =======
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94 Name input file(s) format
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95 =========== ========================== =======
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96 Readseq Fasta alignment fasta
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97 =========== ========================== =======
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98
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99
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100 ----------
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101 Input file
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102 ----------
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103
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104 PED file
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105 PED file usually from VCF tools
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106
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107 ----------
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108 Parameters
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109 ----------
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110
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111 Output file name
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112 Prefix for the output fasta file
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113
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114 ------------
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115 Output files
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116 ------------
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117
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118 Fasta file
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119 PED file conversion
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120
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121 ---------------------------------------------------
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122
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123 ---------------
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124 Working example
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125 ---------------
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126
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127 Input files
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128 ===========
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129
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130 PED file
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131 ---------
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132
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133 ::
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134
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135 CATB1 CATB1 0 0 0 0 C T T A C T A T A T A G G A
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136
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137 Parameters
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138 ==========
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139
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140 Output name -> pedFile
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141
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142 Output files
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143 ============
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144
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145 pedFile.fa
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146 ----------
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147
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148 ::
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149
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150 YWYWWRRSYYMKRRKMYRKSRKYRYRYKRKRSKKSYRWYSYRRYRRRWYWWYYWRRYRSRWSSRMYRRKSWMSKWRRYYWMYKYWRSYRWRYMWYYYMKYKYWRYRYRY
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151
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152
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153 </help>
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154
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155 <citations>
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156 <!-- [HELP] As DOI or BibTex entry -->
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157 <citation type="bibtex">@article{Dereeper03062015,
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158 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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159 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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160 year = {2015},
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161 doi = {10.1093/nar/gkv351},
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162 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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163 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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164 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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165 journal = {Nucleic Acids Research}
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166 }
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167
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168 </citation>
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169
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170 </citations>
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171 </tool>
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