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0
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1 <tool id="ks_distribution" name="KsDistribution" version="1.0.0">
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5
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2 <description>plots the distribution of synonymous substitution (Ks) rates and fits significant component(s)</description>
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0
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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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2
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 Rscript $__tool_directory__/ks_distribution.R
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10 -k '$input'
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11 -c '$components'
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12 -o '$output'
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param name="input" format="tabular" type="data" label="KaKsAnalysis tabular file" />
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17 <param name="rates" format="tabular" type="data" label="Synonymous substitution rates" />
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18 <param name="components" format="tabular" type="data" label="Significant components" />
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19 </inputs>
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20 <outputs>
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21 <data name="output" format="pdf"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input" value="kaks_input1.tabular" ftype="tabular" />
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26 <param name="rates" value="rates.tabular" ftype="tabular" />
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27 <param name="components" value="components.tabular" ftype="tabular" />
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28 <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
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29 </test>
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30 </tests>
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31 <help>
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32 **What it does**
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33
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34 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary analyses of
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35 genome-scale gene families and transcriptomes. This tool uses the analysis results produced by the KaKsAnalysis tool to plot the
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36 distribution of synonymous substitution (Ks) rates and fit the estimated significant normal mixtures component(s) onto the distribution.
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37
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38 -----
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39
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40 **Options**
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41
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1
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42 * **Synonymous substitution rates** - estimated synonymous substitution (Ks) rates output file produced by the KaKsAnalysis tool selected from your history.
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43 * **Synonymous components** - estimated significant component(s) output file produced by the KaKsAnalysis tool selected from your history.
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0
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44 </help>
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45 <citations>
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46 <expand macro="citation1" />
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47 <citation type="bibtex">
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48 @article{Wall2008,
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49 journal = {Nucleic Acids Research},
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50 author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
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51 title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
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52 year = {2008},
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53 volume = {36},
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54 number = {suppl 1},
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55 pages = {D970-D976},}
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56 </citation>
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57 <citation type="bibtex">
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58 @article{Altschul1990,
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59 journal = {Journal of molecular biology}
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60 author = {3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ},
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61 title = {Basic local alignment search tool},
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62 year = {1990},
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63 volume = {215},
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64 number = {3},
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65 pages = {403-410},}
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66 </citation>
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67 <citation type="bibtex">
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68 @article{Katoh2013,
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69 journal = {Molecular biology and evolution},
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70 author = {4. Katoh K, Standley DM},
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71 title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
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72 year = {2013},
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73 volume = {30},
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74 number = {4},
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75 pages = {772-780},}
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76 </citation>
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77 <citation type="bibtex">
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78 @article{Yang2007,
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79 journal = {Molecular biology and evolution},
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80 author = {5. Yang Z},
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81 title = {PAML 4: phylogenetic analysis by maximum likelihood},
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82 year = {2007},
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83 volume = {24},
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84 number = {8},
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85 pages = {1586-1591},}
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86 </citation>
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87 <citation type="bibtex">
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88 @article{Cui2006,
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89 journal = {Genome Research},
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90 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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91 title = {Widespread genome duplications throughout the history of flowering plants},
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92 year = {2006},
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93 volume = {16},
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94 number = {6},
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95 pages = {738-749},}
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96 </citation>
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97 <citation type="bibtex">
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98 @article{McLachlan1999,
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99 journal = {Journal of Statistical Software},
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100 author = {7. McLachlan GJ, Peel D, Basford KE, Adams P},
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101 title = {The EMMIX software for the fitting of mixtures of normal and t-components},
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102 year = {1999},
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103 volume = {4},
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104 number = {2},
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105 pages = {1-14},}
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106 </citation>
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107 </citations>
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108 </tool>
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109
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