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1 <tool id="calculate_diversity" name="Diversity by gene" version="2.1.6">
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2 <description>calculates various diversity indexes with EggLib.</description>
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4
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3 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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4 <stdio>
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5 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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6 <exit_code range="1:" level="fatal" />
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7 </stdio>
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8 <command interpreter="bash">./CalculateDiversityIndexes.sh $input $output $log
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9 </command>
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10 <inputs>
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11 <param format="fasta" name="input" type="data" label="Fasta alignment" help="..."/>
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12 </inputs>
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13 <outputs>
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14 <data format="txt" name="output" label="Diversity"/>
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15 <data format="txt" name="log" label="Logfile"/>
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16 </outputs>
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17
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18 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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19 <tests>
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20 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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21 <!-- [HELP] Multiple tests can be defined with different parameters -->
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22 <test>
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23 <param name="input" value="egglib-alignment.fa" />
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24 <output name="output" file="egglib-result.txt" />
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25 </test>
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26 </tests>
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27 <help>
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28
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29
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30
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31 .. class:: infomark
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32
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33 **Authors** EggLib_
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34
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35 .. _EggLib: http://egglib.sourceforge.net/
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36
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37 | "EggLib: processing, analysis and simulation tools for population genetics and genomics.", **De Mita S. and M. Siol.**, BMC Genet. 2012. 13:27.
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38
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39 .. class:: infomark
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40
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41 **Galaxy integration** South Green.
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42
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43 .. class:: infomark
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44
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45 **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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46
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47 ---------------------------------------------------
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48
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49
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50
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51 ==================
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52 Diversity by genes
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53 ==================
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54
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55 -----------
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56 Description
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57 -----------
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58
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59 | Provides various diversity indexes using EggLib library.
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60 | For further informations, please visite the EggLib website_.
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61
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62 .. _website: http://egglib.sourceforge.net/
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63
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64
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65 -----------------
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66 Workflow position
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67 -----------------
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68
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69 **Upstream tool**
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70
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71 =============== ====================== ===========
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72 Name output file(s) format
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73 =============== ====================== ===========
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74 VCF to Hapmap Fasta alignment fasta
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75 =============== ====================== ===========
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76
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77
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78
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79 ----------
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80 Input file
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81 ----------
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82
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83 Fasta file
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84 Fasta alignment
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85
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86
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87
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88 ------------
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89 Output files
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90 ------------
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91
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92 Diversity
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93
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94 Log file
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95
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96
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97 ------------
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98 Dependencies
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99 ------------
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100 EggLib
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101 version 2.1.5
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102
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103 ---------------------------------------------------
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104
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105 ---------------
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106 Working example
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107 ---------------
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108
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109 Input files
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110 ===========
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111
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112 Fasta file
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113 ----------
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114
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115 ::
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116
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117 >LOCOs11g09160_AZUCENA_1
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118 ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
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119 CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
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120 GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
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121 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
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122 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
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123 >LOCOs11g09160_AZUCENA_2
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124 ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
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125 CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
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126 GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
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127 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
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128 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
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129 >LOCOs11g09160_BULUPANDAK_1
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130 ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
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131 CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
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132 GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
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133 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
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134 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
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135 >LOCOs11g09160_BULUPANDAK_2
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136 ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
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137 CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
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138 GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
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139 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
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140 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
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141 >LOCOs07g23169_AZUCENA_1
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142 ACTAGTGAAGTGTTGCCCGTTGGGTTTGGTGGAGTTTGAAGAGCTCTGTCGCCGTCTTCACTCCTCGCAGTCAGACGGGAGTGGACTACTGGAGGGAGAGAGAGGGTGAGCGAGGTGTGGGA
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143 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
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144 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
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145
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146 Output files
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147 ============
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148
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149 Diversity
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150 ---------
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151
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152 ::
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153
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154 LOCOs07g23169;8;10494;10494;2;7.35039e-05;8.16793e-05;0.414213;2;0.428571;0.857143;0;1;
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155 LOCOs11g09160;8;6577;6577;2;0.00011728;0.000130324;0.414213;2;0.428571;0.857143;0;1;
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156
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157
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158 </help>
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159 <citations>
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160 <!-- [HELP] As DOI or BibTex entry -->
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161 <citation type="bibtex">@article{Dereeper03062015,
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162 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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163 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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164 year = {2015},
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165 doi = {10.1093/nar/gkv351},
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166 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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167 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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168 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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169 journal = {Nucleic Acids Research}
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170 }
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171
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172 </citation>
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173
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174 </citations>
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175 </tool>
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