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1 <tool id="ks_distribution" name="KsDistribution" version="@WRAPPER_VERSION@.3.0">
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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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4
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6 <requirements>
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7 <requirement type="package" version="1.3.2">r-optparse</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 Rscript '$__tool_directory__/ks_distribution.R'
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11 -k '$input'
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12 -c '$components'
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13 -n $components.metadata.number_comp
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14 -o '$output'
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15 #if str($choose_colors_cond.choose_colors) == 'yes':
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16 #set specified_colors = list()
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17 #for $selection in $choose_colors_cond.colors:
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18 $specified_colors.append(str($selection.color))
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19 #end for
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20 #set specified_colors = ",".join($specified_colors)
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21 -s '$specified_colors'
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22 #end if
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0
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23 ]]></command>
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24 <inputs>
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25 <param name="input" format="tabular" type="data" label="KaKsAnalysis tabular file" />
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26 <param name="components" format="tabular" type="data" label="Significant components" />
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27 <conditional name="choose_colors_cond">
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28 <param name="choose_colors" type="select" label="Choose colors for significant components">
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29 <option value="no" selected="true">No</option>
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30 <option value="yes">Yes</option>
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31 </param>
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32 <when value="no" />
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33 <when value="yes">
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34 <repeat name="colors" title="Component colors" min="1">
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35 <param name="color" type="select" label="Color">
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36 <option value="red" selected="True">red</option>
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37 <option value="green">green</option>
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38 <option value="blue">blue</option>
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39 <option value="yellow">yellow</option>
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40 <option value="darkorange">dark orange</option>
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41 <option value="black">black</option>
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42 </param>
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43 </repeat>
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44 </when>
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45 </conditional>
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46 </inputs>
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47 <outputs>
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48 <data name="output" format="pdf"/>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="input" value="kaks_input1.tabular" ftype="tabular" />
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53 <param name="components" value="components.ptkscmp" ftype="ptkscmp" />
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54 <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
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55 </test>
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56 </tests>
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57 <help>
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58 **What it does**
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59
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60 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary analyses of
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61 genome-scale gene families and transcriptomes. This tool uses the analysis results produced by the KaKsAnalysis tool to plot the
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62 distribution of synonymous substitution (Ks) rates and fit the estimated significant normal mixtures component(s) onto the distribution.
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63
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64 -----
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65
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66 **Options**
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67
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68 * **Synonymous substitution rates** - estimated synonymous substitution (Ks) rates output file produced by the KaKsAnalysis tool selected from your history.
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69 * **Synonymous components** - estimated significant component(s) output file produced by the KaKsAnalysis tool selected from your history.
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1
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70 * **Choose colors for significant components** - select 'Yes' to specify component colors or 'No' for colors chosen randlomly.
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71
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72 * **Component colors** - select a color from the palette for each component (colors will be chosen randomly for unspecified components).
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73 </help>
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74 <citations>
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75 <expand macro="citation1" />
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76 <citation type="bibtex">
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77 @article{Wall2008,
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78 journal = {Nucleic Acids Research},
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79 author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
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80 title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
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81 year = {2008},
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82 volume = {36},
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83 number = {suppl 1},
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84 pages = {D970-D976},}
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85 </citation>
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86 <citation type="bibtex">
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87 @article{Altschul1990,
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88 journal = {Journal of molecular biology}
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89 author = {3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ},
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90 title = {Basic local alignment search tool},
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91 year = {1990},
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92 volume = {215},
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93 number = {3},
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94 pages = {403-410},}
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95 </citation>
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96 <citation type="bibtex">
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97 @article{Katoh2013,
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98 journal = {Molecular biology and evolution},
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99 author = {4. Katoh K, Standley DM},
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100 title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
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101 year = {2013},
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102 volume = {30},
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103 number = {4},
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104 pages = {772-780},}
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105 </citation>
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106 <citation type="bibtex">
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107 @article{Yang2007,
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108 journal = {Molecular biology and evolution},
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109 author = {5. Yang Z},
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110 title = {PAML 4: phylogenetic analysis by maximum likelihood},
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111 year = {2007},
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112 volume = {24},
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113 number = {8},
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114 pages = {1586-1591},}
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115 </citation>
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116 <citation type="bibtex">
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117 @article{Cui2006,
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118 journal = {Genome Research},
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119 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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120 title = {Widespread genome duplications throughout the history of flowering plants},
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121 year = {2006},
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122 volume = {16},
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123 number = {6},
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124 pages = {738-749},}
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125 </citation>
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126 <citation type="bibtex">
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127 @article{McLachlan1999,
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128 journal = {Journal of Statistical Software},
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129 author = {7. McLachlan GJ, Peel D, Basford KE, Adams P},
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130 title = {The EMMIX software for the fitting of mixtures of normal and t-components},
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131 year = {1999},
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132 volume = {4},
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133 number = {2},
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134 pages = {1-14},}
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135 </citation>
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136 </citations>
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137 </tool>
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138
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