Mercurial > repos > dereeper > sniplay
annotate egglib/CalculateDiversityIndexes.xml @ 12:88748d846a20 draft
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| date | Tue, 14 Aug 2018 08:21:55 -0400 |
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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> |
| 9 | 9 <!-- [STRONGLY RECOMMANDED] Exit code rules --> |
| 10 <stdio> | |
| 11 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
| 12 <exit_code range="1:" level="fatal" /> | |
| 13 </stdio> | |
| 14 <command interpreter="bash">./CalculateDiversityIndexes.sh $input $output $log | |
| 15 </command> | |
| 16 <inputs> | |
| 17 <param format="fasta" name="input" type="data" label="Fasta alignment" help="..."/> | |
| 18 </inputs> | |
| 19 <outputs> | |
| 20 <data format="txt" name="output" label="Diversity"/> | |
| 21 <data format="txt" name="log" label="Logfile"/> | |
| 22 </outputs> | |
| 23 | |
| 24 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | |
| 25 <tests> | |
| 26 <!-- [HELP] Test files have to be in the ~/test-data directory --> | |
| 27 <!-- [HELP] Multiple tests can be defined with different parameters --> | |
| 28 <test> | |
| 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" /> |
| 9 | 31 </test> |
| 32 </tests> | |
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33 <help><![CDATA[ |
| 9 | 34 |
| 35 .. class:: infomark | |
| 36 | |
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37 **Authors** EggLib : http://mycor.nancy.inra.fr/egglib/ |
| 9 | 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). |
| 9 | 41 |
| 42 .. class:: infomark | |
| 43 | |
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44 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) |
| 9 | 45 |
| 46 .. class:: infomark | |
| 47 | |
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48 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
| 9 | 49 |
| 50 --------------------------------------------------- | |
| 51 | |
| 52 ================== | |
| 53 Diversity by genes | |
| 54 ================== | |
| 55 | |
| 56 ----------- | |
| 57 Description | |
| 58 ----------- | |
| 59 | |
| 60 | Provides various diversity indexes using EggLib library. | |
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61 | For further informations, please visit the EggLib website_. |
| 9 | 62 |
| 63 .. _website: http://egglib.sourceforge.net/ | |
| 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 |
| 9 | 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 |
| 9 | 78 |
| 79 ---------- | |
| 80 Input file | |
| 81 ---------- | |
| 82 | |
| 83 Fasta file | |
| 84 Fasta alignment | |
| 85 | |
| 86 ------------ | |
| 87 Output files | |
| 88 ------------ | |
| 89 | |
| 90 Diversity | |
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91 Diversity indexes |
| 9 | 92 |
| 93 Log file | |
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94 Log file |
| 9 | 95 |
| 96 --------------------------------------------------- | |
| 97 | |
| 98 --------------- | |
| 99 Working example | |
| 100 --------------- | |
| 101 | |
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102 Input file |
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103 ========== |
| 9 | 104 |
| 105 Fasta file | |
| 106 ---------- | |
| 107 | |
| 108 :: | |
| 109 | |
| 110 >LOCOs11g09160_AZUCENA_1 | |
| 111 ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA | |
| 112 CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG | |
| 113 GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT | |
| 114 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA | |
| 115 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC | |
| 116 >LOCOs11g09160_AZUCENA_2 | |
| 117 ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA | |
| 118 CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG | |
| 119 GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT | |
| 120 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA | |
| 121 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC | |
| 122 >LOCOs11g09160_BULUPANDAK_1 | |
| 123 ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA | |
| 124 CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG | |
| 125 GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT | |
| 126 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA | |
| 127 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC | |
| 128 >LOCOs11g09160_BULUPANDAK_2 | |
| 129 ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA | |
| 130 CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG | |
| 131 GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT | |
| 132 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA | |
| 133 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC | |
| 134 >LOCOs07g23169_AZUCENA_1 | |
| 135 ACTAGTGAAGTGTTGCCCGTTGGGTTTGGTGGAGTTTGAAGAGCTCTGTCGCCGTCTTCACTCCTCGCAGTCAGACGGGAGTGGACTACTGGAGGGAGAGAGAGGGTGAGCGAGGTGTGGGA | |
| 136 GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA | |
| 137 TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC | |
| 138 | |
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139 Output file |
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140 =========== |
| 9 | 141 |
| 142 Diversity | |
| 143 --------- | |
| 144 | |
| 145 :: | |
| 146 | |
| 147 LOCOs07g23169;8;10494;10494;2;7.35039e-05;8.16793e-05;0.414213;2;0.428571;0.857143;0;1; | |
| 148 LOCOs11g09160;8;6577;6577;2;0.00011728;0.000130324;0.414213;2;0.428571;0.857143;0;1; | |
| 149 | |
| 150 | |
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151 ]]></help> |
| 9 | 152 <citations> |
| 153 <!-- [HELP] As DOI or BibTex entry --> | |
| 154 <citation type="bibtex">@article{Dereeper03062015, | |
| 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}, | |
| 156 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, | |
| 157 year = {2015}, | |
| 158 doi = {10.1093/nar/gkv351}, | |
| 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.}, | |
| 160 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, | |
| 161 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, | |
| 162 journal = {Nucleic Acids Research} | |
| 163 } | |
| 164 | |
| 165 </citation> | |
| 166 | |
| 167 </citations> | |
| 168 </tool> |