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1 <tool id="ggplot_histogram" name="Histogram w ggplot2" version="0.1.1">
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2 <requirements>
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3 <requirement type="package">r-getopt</requirement>
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4 <requirement type="package">r-ggplot2</requirement>
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5 <requirement type="package">r-reshape2</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command><![CDATA[
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11 Rscript ${__tool_directory__}/ggplotscripthistogram.R --input "$input1" --title "$title"
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12 --xlab "$xlab" --ylab "$ylab" --transform "$transformation.transform" --scaling "$scaling.Plot_scaling"
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13 --colorscheme "$coloring.colorscheme" --dim "$dimensions.plotdim" --facet "$group.facet"
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14 --size "$size" --binwidth "$binwidth" --legend "$showlegend.legend" --output "Rplot.pdf"
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15 #if str( $coloring.colorscheme ) == "Defined":
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16 --colors ${coloring.colors}
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17 --colororder ${coloring.colororder}
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18 #else:
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19 --colors=irrelevant
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20 --colororder=1
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21 #end if
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22
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23 #if str( $scaling.Plot_scaling ) == "Defined":
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24 --xaxismin=${scaling.xaxismin}
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25 --xaxismax=${scaling.xaxismax}
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26 --yaxismin=${scaling.yaxismin}
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27 --yaxismax=${scaling.yaxismax}
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28 #else:
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29 --xaxismin=0
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30 --xaxismax=1
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31 --yaxismin=2
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32 --yaxismax=3
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33 #end if
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34
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35 #if str( $dimensions.plotdim ) == "Defined":
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36 --woutputdim ${dimensions.woutputdim}
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37 --houtputdim ${dimensions.houtputdim}
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38 #else:
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39 --woutputdim=7
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40 --houtputdim=7
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41 #end if
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42
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43 ]]></command>
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44 <inputs>
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45 <param name="input1" type="data" format="tabular" label="Input should have column headers - these will be the columns that are plotted"/>
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46 <param name="title" size="30" type="text" format="txt"/>
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47 <param name="xlab" size="30" type="text" value="title of x-axis" label="Label for x-axis"/>
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48 <param name="ylab" size="30" type="text" value="title of y-axis" label="Label for y-axis"/>
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49 <param name="size" size="4" type="float" value="1" label="relative line width" />
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50 <param name="binwidth" size="4" type="float" value="0.5" label="Bin width for plotting"/>
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51 <conditional name="transformation">
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52 <param name="transform" type="select" label="Advanced - log transformation">
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53 <option value="none">Plot the data as it is</option>
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54 <option value="log2">Log2(value) transform my data</option>
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55 <option value="log2plus1">Log2(value+1) transform my data</option>
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56 <option value="log10">Log10(value) transform my data</option>
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57 <option value="log10plus1">Log10(value+1) transform my data</option>
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58 </param>
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59 </conditional>
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60 <conditional name="group">
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61 <param name="facet" type="select" label="Advanced - faceting">
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62 <option value="none">Plot my groups on one plot</option>
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63 <option value="facet">Plot my groups on individual plots</option>
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64 </param>
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65 </conditional>
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66 <conditional name="coloring">
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67 <param name="colorscheme" type="select" label="Advanced - coloring groups" >
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68 <option value="Default" selected="True">No thanks - just use the default scheme to color code my groups (columns)</option>
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69 <option value="Defined">I want to use defined color palettes to differentiate my groups (columns) </option>
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70 </param>
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71 <when value="Default">
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72 </when>
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73 <when value="Defined">
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74 <param name="colors" type="select" label="Color schemes to differentiate your groups" >
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75 <option value="Default">Default color scheme</option>
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76 <option value="YlOrRd">Yellow to orange to red (discrete, max=9 colors)</option>
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77 <option value="YlOrBr">Yellow to orange to brown (discrete, max=9 colors)</option>
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78 <option value="YlGnBu">Yellow to green to blue (discrete, max=9 colors)</option>
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79 <option value="YlGn">Yellow to green (discrete, max=9 colors)</option>
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80 <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option>
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81 <option value="RdPu">Red to purple (discrete, max=9 colors)</option>
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82 <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option>
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83 <option value="PuRd">Purple to red (discrete, max=9 colors)</option>
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84 <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option>
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85 <option value="PuBu">Purple to blue(discrete, max=9 colors)</option>
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86 <option value="OrRd">Orange to red (discrete, max=9 colors)</option>
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87 <option value="Oranges">Shades of orange from light to dark (discrete, max=9 colors)</option>
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88 <option value="Greys">Shades of grey from light to dark (discrete, max=9 colors)</option>
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89 <option value="Greens">Shades of greens from light to dark (discrete, max=9 colors)</option>
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90 <option value="GnBu">Green to blue (discrete, max=9 colors)</option>
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91 <option value="BuPu">Blue to purple (discrete, max=9 colors)</option>
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92 <option value="BuGn">Blue to green (discrete, max=9 colors)</option>
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93 <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option>
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94 <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option>
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95 <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option>
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96 <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option>
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97 <option value="Pastel1">Pastel 1 - predefined pastel color pallete (discrete, max=9 colors)</option>
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98 <option value="Pastel2">Pastel 2 - predefined pastel color pallete (discrete, max=8 colors)</option>
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99 <option value="Paired">Paired - predefined color pallete (discrete, max=12 colors)</option>
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100 <option value="Dark2">Dark 2 - predefined color pallete (discrete, max=12 colors)</option>
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101 <option value="Accent">Accent - predefined color pallete (discrete, max=12 colors)</option>
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102 <option value="Spectral">Spectral - Red to yellow to purple (discrete, max=11 colors)</option>
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103 <option value="RdYlGn">Red to yellow to green (discrete, max=11 colors)</option>
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104 <option value="RdYlBu">Red to yellow to blue (discrete, max=11 colors)</option>
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105 <option value="RdGy">Red to grey (discrete, max=11 colors)</option>
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106 <option value="RdBu">Red to blue (discrete, max=11 colors)</option>
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107 <option value="PuOr">Purple to orange (discrete, max=11 colors)</option>
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108 <option value="PRGn">Purple to green (discrete, max=11 colors)</option>
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109 <option value="BrBG">Brown to teal (discrete, max=11 colors)</option>
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110 </param>
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111 <param name="colororder" type="select" label="Reverse color scheme" >
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112 <option value="1">Default order of color scheme</option>
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113 <option value="-1">Reverse the order of my color scheme</option>
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114 </param>
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115 </when>
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116 </conditional>
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117 <conditional name="scaling">
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118 <param name="Plot_scaling" type="select" label="Advanced - Axis scaling">
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119 <option value="Automatic" selected="True">Automatic axis scaling</option>
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120 <option value="Defined">User deined axis scales</option>
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121 </param>
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122 <when value="Automatic">
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123 <!--Do nothing here -->
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124 </when>
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125 <when value="Defined">
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126 <param name="xaxismin" size="4" type="integer" value="0" label="minimal range of x-axis" />
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127 <param name="xaxismax" size="4" type="integer" value="3" label="maximal range of x-axis" />
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128 <param name="yaxismin" size="4" type="integer" value="0" label="minimal range of y-axis" />
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129 <param name="yaxismax" size="4" type="integer" value="3" label="maximal range of y-axis" />
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130 </when>
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131 </conditional>
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132 <conditional name="dimensions">
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133 <param name="plotdim" type="select" label="Advanced - output dimensions">
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134 <option value="Default" selected="True">Default</option>
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135 <option value="Defined">User deined output dimensions</option>
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136 </param>
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137 <when value="Default">
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138 <!--Do nothing here -->
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139 </when>
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140 <when value="Defined">
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141 <param name="woutputdim" size="4" type="float" value="7" label="width of output (inches)" />
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142 <param name="houtputdim" size="4" type="float" value="7" label="height of output (inches)" />
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143 </when>
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144 </conditional>
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145 <conditional name="showlegend">
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146 <param name="legend" type="select" label="Legend options">
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147 <option value="NULL">Include legend on plot</option>
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148 <option value="theme(legend.position="none")">Hide legend</option>
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149 </param>
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150 </conditional>
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151 </inputs>
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152 <outputs>
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153 <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/> -->
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154 <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/>
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155 </outputs>
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156 <tests>
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157 <test>
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158 <param name="input1" value="input.txt"/>
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159 <output name="output1" file="Rplot.pdf"/>
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160 </test>
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161 </tests>
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162 <help><![CDATA[
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163
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164 This tool will generate a histogram representing the distrinutions of each numerical column. Each column should have a descriptive header with no spaces, which will be used in the plot legend to represent the corresponding column (group).
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165
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166 Input data example:
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167 ID Cond_A Cond_B
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168 gene_A 10 15
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169 gene_B 8 12
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170 gene_C 10 15
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171 gene_D 6 9
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172 gene_E 9 13.5
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173 gene_F 8 12
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174
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175 ]]></help>
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176 <citations>
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177 <citation type="bibtex">
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178 @misc{renameTODO,
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179 author = {TODO, FirstTODO},
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180 year = {TODO},
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181 title = {TODO},
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182 url = {under construction},
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183 }</citation>
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184 </citations>
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185 </tool>
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