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1 <tool id="ks_distribution" name="KsDistribution" version="1.0.1">
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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 -n $components.metadata.number_comp
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12 -o '$output'
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13 #if str($choose_colors_cond.choose_colors) == 'yes':
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14 #set specified_colors = list()
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15 #for $selection in $choose_colors_cond.colors:
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16 $specified_colors.append(str($selection.color))
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17 #end for
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18 #set specified_colors = ",".join($specified_colors)
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19 -s '$specified_colors'
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20 #end if
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21 ]]></command>
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22 <inputs>
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23 <param name="input" format="tabular" type="data" label="KaKsAnalysis tabular file" />
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24 <param name="components" format="ptkscmp" type="data" label="Significant components" />
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25 <conditional name="choose_colors_cond">
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26 <param name="choose_colors" type="select" label="Choose colors for significant components">
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27 <option value="no" selected="true">No</option>
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28 <option value="yes">Yes</option>
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29 </param>
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30 <when value="no" />
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31 <when value="yes">
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32 <repeat name="colors" title="Component colors" min="1">
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33 <param name="color" type="select" label="Color">
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34 <option value="red" selected="True">red</option>
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35 <option value="green">green</option>
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36 <option value="blue">blue</option>
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37 <option value="yellow">yellow</option>
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38 <option value="darkorange">dark orange</option>
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39 <option value="black">black</option>
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40 </param>
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41 </repeat>
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42 </when>
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43 </conditional>
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44 </inputs>
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45 <outputs>
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46 <data name="output" format="pdf"/>
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="input" value="kaks_input1.tabular" ftype="tabular" />
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51 <param name="components" value="components.ptkscmp" ftype="ptkscmp" />
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52 <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
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53 </test>
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54 </tests>
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55 <help>
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56 **What it does**
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57
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58 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary analyses of
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59 genome-scale gene families and transcriptomes. This tool uses the analysis results produced by the KaKsAnalysis tool to plot the
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60 distribution of synonymous substitution (Ks) rates and fit the estimated significant normal mixtures component(s) onto the distribution.
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61
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62 -----
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63
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64 **Options**
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65
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66 * **Synonymous substitution rates** - estimated synonymous substitution (Ks) rates output file produced by the KaKsAnalysis tool selected from your history.
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67 * **Synonymous components** - estimated significant component(s) output file produced by the KaKsAnalysis tool selected from your history.
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68 * **Choose colors for significant components** - select 'Yes' to specify component colors or 'No' for colors chosen randlomly.
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69
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70 * **Component colors** - select a color from the palette for each component (colors will be chosen randomly for unspecified components).
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71 </help>
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72 <citations>
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73 <expand macro="citation1" />
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74 <citation type="bibtex">
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75 @article{Wall2008,
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76 journal = {Nucleic Acids Research},
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77 author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
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78 title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
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79 year = {2008},
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80 volume = {36},
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81 number = {suppl 1},
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82 pages = {D970-D976},}
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83 </citation>
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84 <citation type="bibtex">
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85 @article{Altschul1990,
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86 journal = {Journal of molecular biology}
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87 author = {3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ},
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88 title = {Basic local alignment search tool},
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89 year = {1990},
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90 volume = {215},
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91 number = {3},
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92 pages = {403-410},}
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93 </citation>
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94 <citation type="bibtex">
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95 @article{Katoh2013,
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96 journal = {Molecular biology and evolution},
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97 author = {4. Katoh K, Standley DM},
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98 title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
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99 year = {2013},
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100 volume = {30},
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101 number = {4},
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102 pages = {772-780},}
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103 </citation>
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104 <citation type="bibtex">
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105 @article{Yang2007,
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106 journal = {Molecular biology and evolution},
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107 author = {5. Yang Z},
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108 title = {PAML 4: phylogenetic analysis by maximum likelihood},
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109 year = {2007},
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110 volume = {24},
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111 number = {8},
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112 pages = {1586-1591},}
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113 </citation>
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114 <citation type="bibtex">
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115 @article{Cui2006,
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116 journal = {Genome Research},
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117 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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118 title = {Widespread genome duplications throughout the history of flowering plants},
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119 year = {2006},
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120 volume = {16},
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121 number = {6},
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122 pages = {738-749},}
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123 </citation>
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124 <citation type="bibtex">
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125 @article{McLachlan1999,
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126 journal = {Journal of Statistical Software},
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127 author = {7. McLachlan GJ, Peel D, Basford KE, Adams P},
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128 title = {The EMMIX software for the fitting of mixtures of normal and t-components},
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129 year = {1999},
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130 volume = {4},
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131 number = {2},
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132 pages = {1-14},}
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133 </citation>
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134 </citations>
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135 </tool>
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136
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