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1 <tool id="ks_distribution" name="KsDistribution" version="1.0.0">
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2 <description>plots the distribution of synonymous substitution (Ks) rates and fits significant component(s)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements_ks_distribution" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript $__tool_directory__/ks_distribution.R
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9 -k '$input'
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10 -c '$components'
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11 -o '$output'
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12 ]]></command>
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13 <inputs>
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14 <param name="input" format="tabular" type="data" label="KaKsAnalysis tabular file" />
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15 <param name="components" format="tabular" type="data" label="Significant components" />
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16 </inputs>
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17 <outputs>
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18 <data name="output" format="pdf"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input" value="kaks_input1.tabular" ftype="tabular" />
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23 <param name="components" value="components.tabular" ftype="tabular" />
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24 <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
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25 </test>
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26 </tests>
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27 <help>
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28 **What it does**
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29
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30 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary analyses of
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31 genome-scale gene families and transcriptomes. This tool uses the analysis results produced by the KaKsAnalysis tool to plot the
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32 distribution of synonymous substitution (Ks) rates and fit the estimated significant normal mixtures component(s) onto the distribution.
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33
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34 -----
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35
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36 **Options**
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37
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38 * **Synonymous substitution rates** - estimated synonymous substitution (Ks) rates output file produced by the KaKsAnalysis tool selected from your history.
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39 * **Synonymous components** - estimated significant component(s) output file produced by the KaKsAnalysis tool selected from your history.
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40 </help>
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41 <citations>
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42 <expand macro="citation1" />
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43 <citation type="bibtex">
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44 @article{Wall2008,
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45 journal = {Nucleic Acids Research},
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46 author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
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47 title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
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48 year = {2008},
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49 volume = {36},
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50 number = {suppl 1},
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51 pages = {D970-D976},}
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52 </citation>
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53 <citation type="bibtex">
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54 @article{Altschul1990,
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55 journal = {Journal of molecular biology}
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56 author = {3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ},
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57 title = {Basic local alignment search tool},
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58 year = {1990},
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59 volume = {215},
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60 number = {3},
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61 pages = {403-410},}
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62 </citation>
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63 <citation type="bibtex">
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64 @article{Katoh2013,
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65 journal = {Molecular biology and evolution},
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66 author = {4. Katoh K, Standley DM},
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67 title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
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68 year = {2013},
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69 volume = {30},
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70 number = {4},
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71 pages = {772-780},}
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72 </citation>
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73 <citation type="bibtex">
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74 @article{Yang2007,
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75 journal = {Molecular biology and evolution},
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76 author = {5. Yang Z},
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77 title = {PAML 4: phylogenetic analysis by maximum likelihood},
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78 year = {2007},
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79 volume = {24},
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80 number = {8},
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81 pages = {1586-1591},}
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82 </citation>
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83 <citation type="bibtex">
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84 @article{Cui2006,
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85 journal = {Genome Research},
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86 author = {6. Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA},
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87 title = {Widespread genome duplications throughout the history of flowering plants},
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88 year = {2006},
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89 volume = {16},
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90 number = {6},
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91 pages = {738-749},}
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92 </citation>
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93 <citation type="bibtex">
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94 @article{McLachlan1999,
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95 journal = {Journal of Statistical Software},
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96 author = {7. McLachlan GJ, Peel D, Basford KE, Adams P},
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97 title = {The EMMIX software for the fitting of mixtures of normal and t-components},
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98 year = {1999},
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99 volume = {4},
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100 number = {2},
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101 pages = {1-14},}
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102 </citation>
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103 </citations>
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104 </tool>
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105
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