annotate egglib/CalculateDiversityIndexes.xml @ 15:31c23d943c29 draft default tip

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1 <tool id="calculate_diversity" name="Diversity by gene" version="2.0.0">
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2 <description>Calculates various diversity indexes with EggLib</description>
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3 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
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4 <requirements>
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5 <requirement type="binary">perl</requirement>
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6 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
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7 <requirement type="package" version="1.90b4">plink</requirement>
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8 </requirements>
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9 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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10 <stdio>
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11 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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12 <exit_code range="1:" level="fatal" />
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13 </stdio>
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14 <command interpreter="bash">./CalculateDiversityIndexes.sh $input $output $log
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15 </command>
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16 <inputs>
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17 <param format="fasta" name="input" type="data" label="Fasta alignment" help="..."/>
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18 </inputs>
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19 <outputs>
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20 <data format="txt" name="output" label="Diversity"/>
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21 <data format="txt" name="log" label="Logfile"/>
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22 </outputs>
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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 <test>
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29 <param name="input" value="egglib-alignment.fa" />
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30 <output name="output" file="egglib-result.txt" compare="sim_size" delta="0" />
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34
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35 .. class:: infomark
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36
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37 **Authors** EggLib : http://mycor.nancy.inra.fr/egglib/
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38
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39 | **Please cite** "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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40 | **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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41
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42 .. class:: infomark
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43
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44 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
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45
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46 .. class:: infomark
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47
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48 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
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50 ---------------------------------------------------
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51
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52 ==================
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53 Diversity by genes
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54 ==================
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55
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56 -----------
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57 Description
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58 -----------
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59
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60 | Provides various diversity indexes using EggLib library.
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61 | For further informations, please visit the EggLib website_.
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62
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63 .. _website: http://egglib.sourceforge.net/
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64
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65 ------------
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66 Dependencies
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67 ------------
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68 PLINK
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69 plink_ 1.90b4, Conda version
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70 Bioperl
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71 perl-bioperl_ 1.6.924, Conda version
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72 egglib
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73 egglib_ 2.1.5, supplied with the wrapper
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74
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75 .. _plink: https://anaconda.org/bioconda/plink
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76 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
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77 .. _egglib: https://anaconda.org/bioconda/egglib
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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 Output files
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88 ------------
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89
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90 Diversity
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91 Diversity indexes
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92
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93 Log file
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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 ---------------
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99 Working example
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100 ---------------
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101
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102 Input file
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103 ==========
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104
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105 Fasta 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 >LOCOs11g09160_AZUCENA_1
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111 ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
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112 CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
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113 GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
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114 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
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115 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
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116 >LOCOs11g09160_AZUCENA_2
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117 ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
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118 CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
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119 GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
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120 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
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121 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
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122 >LOCOs11g09160_BULUPANDAK_1
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123 ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
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124 CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
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125 GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
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126 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
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127 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
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128 >LOCOs11g09160_BULUPANDAK_2
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129 ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
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130 CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
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131 GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
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132 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
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133 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
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134 >LOCOs07g23169_AZUCENA_1
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135 ACTAGTGAAGTGTTGCCCGTTGGGTTTGGTGGAGTTTGAAGAGCTCTGTCGCCGTCTTCACTCCTCGCAGTCAGACGGGAGTGGACTACTGGAGGGAGAGAGAGGGTGAGCGAGGTGTGGGA
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136 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
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137 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
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138
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139 Output file
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140 ===========
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141
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142 Diversity
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143 ---------
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145 ::
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146
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147 LOCOs07g23169;8;10494;10494;2;7.35039e-05;8.16793e-05;0.414213;2;0.428571;0.857143;0;1;
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148 LOCOs11g09160;8;6577;6577;2;0.00011728;0.000130324;0.414213;2;0.428571;0.857143;0;1;
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149
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150
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151 ]]></help>
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152 <citations>
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153 <!-- [HELP] As DOI or BibTex entry -->
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154 <citation type="bibtex">@article{Dereeper03062015,
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155 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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156 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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157 year = {2015},
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158 doi = {10.1093/nar/gkv351},
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159 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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160 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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161 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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162 journal = {Nucleic Acids Research}
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163 }
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164
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165 </citation>
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166
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167 </citations>
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168 </tool>