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1 <tool id="ggplot_point" name="Scatterplot w ggplot2 to pdf 8.10.2" version="0.1.2">
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2 <requirements>
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3 <requirement type="package">getopt</requirement>
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4 <requirement type="package">ggplot2</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command><![CDATA[
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10 Rscript $__tool_directory__/ggplotpointscript.R --input "$input1" --title "$title"
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11 --theme "${theme.theme_selector}" --xplot "$xplot" --yplot "$yplot" --scaling "$scaling.Plot_scaling" --points "$points.pointoptions" --dim "$dimensions.plotdim" --factor "$factor.factoring" --transform "$transformation.transform" --xlab "$xlab" --ylab "$ylab"
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12 --axistitlecust "$axistitlecustomization.axistitlecust" --axistextcust "$axistextcustomization.axistextcust"
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13 --plottitlecust "$plottitlecustomization.plottitlecust" --gridlinecust "$gridlinecustomization.gridlinecust" --output "Rplot.pdf"
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14 #if str( $factor.factoring ) == "Single":
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15 --factorcol ${factor.factorcol}
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16 --colors ${factor.colors}
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17 --colororder ${factor.colororder}
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18 #elif str( $factor.factoring ) == "Multiple":
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19 --factorcol ${factor.factorcol}
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20 --colors=irrelevant
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21 --colororder=1
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22 #else:
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23 --factorcol=1
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24 --colors=irrelevant
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25 --colororder=1
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26 #end if
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27
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28 #if str( $points.pointoptions ) == "Defined":
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29 --size ${points.size}
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30 --alpha ${points.alpha}
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31 --pointcolor ${points.pointcolor}
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32 #else:
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33 --size=1
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34 --alpha=1
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35 --pointcolor=black
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36 #end if
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37
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38 #if str( $scaling.Plot_scaling ) == "Defined":
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39 --xaxismin=${scaling.xaxismin}
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40 --xaxismax=${scaling.xaxismax}
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41 --yaxismin=${scaling.yaxismin}
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42 --yaxismax=${scaling.yaxismax}
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43 #else:
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44 --xaxismin=0
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45 --xaxismax=1
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46 --yaxismin=2
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47 --yaxismax=3
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48 #end if
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49
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50 #if str( $axistitlecustomization.axistitlecust ) == "Defined":
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51 --axistitlesize ${axistitlecustomization.axistitlesize}
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52 --axistitlecolor ${axistitlecustomization.axistitlecolor}
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53 --axistitleface ${axistitlecustomization.axistitleface}
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54 #else:
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55 --axistitlesize=12
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56 --axistitlecolor=black
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57 --axistitleface=plain
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58 #end if
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59
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60 #if str( $axistextcustomization.axistextcust ) == "Defined":
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61 --axistextsize ${axistextcustomization.axistextsize}
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62 --axistextcolor ${axistextcustomization.axistextcolor}
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63 --axistextface ${axistextcustomization.axistextface}
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64 #else:
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65 --axistextsize=12
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66 --axistextcolor=black
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67 --axistextface=plain
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68 #end if
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69
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70 #if str( $plottitlecustomization.plottitlecust ) == "Defined":
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71 --plottitlesize ${plottitlecustomization.plottitlesize}
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72 --plottitlecolor ${plottitlecustomization.plottitlecolor}
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73 --plottitleface ${plottitlecustomization.plottitleface}
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74 #else:
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75 --plottitlesize=12
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76 --plottitlecolor=black
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77 --plottitleface=plain
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78 #end if
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79
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80 #if str( $dimensions.plotdim ) == "Defined":
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81 --woutputdim ${dimensions.woutputdim}
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82 --houtputdim ${dimensions.houtputdim}
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83 #else:
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84 --woutputdim=7
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85 --houtputdim=7
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86 #end if
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87
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88 ]]></command>
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89 <inputs>
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90 <param name="input1" type="data" format="tabular" label="Input (tabular format)" />
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91 <param name="xplot" type="integer" value="8" label="Column to plot on x-axis" />
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92 <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" />
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93 <param name="title" size="30" type="text" value="plot title" label="Title of plot" />
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94 <param name="xlab" size="30" type="text" value="title of x-axis" label="Label for x-axis"/>
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95 <param name="ylab" size="30" type="text" value="title of y-axis" label="Label for y-axis"/>
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96 <conditional name="points">
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97 <param name="pointoptions" type="select" label="Advanced - data point options">
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98 <option value="Default" selected="True">Default</option>
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99 <option value="Defined">User defined point options</option>
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100 </param>
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101 <when value="Default">
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102 <!--Do nothing here -->
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103 </when>
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104 <when value="Defined">
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105 <param name="size" size="4" type="float" value="1" label="relative size of points" />
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106 <param name="alpha" size="4" type="float" value="1" label="Transparency of points (On a scale of 0-1; 0=transparent, 1=default)" />
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107 <param name="pointcolor" type="select" label="Color of data points" >
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108 <option value="black">Black (default)</option>
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109 <option value="red">Red</option>
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110 <option value="white">White</option>
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111 <option value="blue">Blue</option>
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112 <option value="orange">Orange</option>
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113 <option value="yellow">Yellow</option>
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114 <option value="green">Green</option>
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115 <option value="purple">Purple</option>
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116 <option value="magenta">Magenta</option>
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117 <option value="cyan">Cyan</option>
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118 <option value="grey">Grey</option>
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119 <option value="gold">Gold</option>
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120 </param>
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121 </when>
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122 </conditional>
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123 <conditional name="factor">
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124 <param name="factoring" type="select" label="Advanced - plotting multiple groups" >
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125 <option value="Default" selected="True">No thanks - just plot the data as one group</option>
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126 <option value="Single">Plot multiple groups of data on one plot</option>
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127 <option value="Multiple">Plot multiple groups of data on individual plots</option>
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128 </param>
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129 <when value="Default">
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130 <!--Do nothing here -->
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131 </when>
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132 <when value="Single">
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133 <param name="factorcol" size="4" type="integer" value="1" label="column differentiating the different groups" />
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134 <param name="colors" type="select" label="Color schemes to differentiate your groups" >
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135 <option value="Default">Default color scheme</option>
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136 <option value="YlOrRd">Yellow to orange to red (discrete, max=9 colors)</option>
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137 <option value="YlOrBr">Yellow to orange to brown (discrete, max=9 colors)</option>
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138 <option value="YlGnBu">Yellow to green to blue (discrete, max=9 colors)</option>
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139 <option value="YlGn">Yellow to green (discrete, max=9 colors)</option>
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140 <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option>
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141 <option value="RdPu">Red to purple (discrete, max=9 colors)</option>
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142 <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option>
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143 <option value="PuRd">Purple to red (discrete, max=9 colors)</option>
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144 <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option>
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145 <option value="PuBu">Purple to blue(discrete, max=9 colors)</option>
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146 <option value="OrRd">Orange to red (discrete, max=9 colors)</option>
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147 <option value="Oranges">Shades of orange from light to dark (discrete, max=9 colors)</option>
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148 <option value="Greys">Shades of grey from light to dark (discrete, max=9 colors)</option>
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149 <option value="Greens">Shades of greens from light to dark (discrete, max=9 colors)</option>
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150 <option value="GnBu">Green to blue (discrete, max=9 colors)</option>
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151 <option value="BuPu">Blue to purple (discrete, max=9 colors)</option>
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152 <option value="BuGn">Blue to green (discrete, max=9 colors)</option>
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153 <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option>
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154 <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option>
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155 <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option>
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156 <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option>
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157 <option value="Pastel1">Pastel 1 - predefined pastel color pallete (discrete, max=9 colors)</option>
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158 <option value="Pastel2">Pastel 2 - predefined pastel color pallete (discrete, max=8 colors)</option>
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159 <option value="Paired">Paired - predefined color pallete (discrete, max=12 colors)</option>
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160 <option value="Dark2">Dark 2 - predefined color pallete (discrete, max=12 colors)</option>
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161 <option value="Accent">Accent - predefined color pallete (discrete, max=12 colors)</option>
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162 <option value="Spectral">Spectral - Red to yellow to purple (discrete, max=11 colors)</option>
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163 <option value="RdYlGn">Red to yellow to green (discrete, max=11 colors)</option>
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164 <option value="RdYlBu">Red to yellow to blue (discrete, max=11 colors)</option>
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165 <option value="RdGy">Red to grey (discrete, max=11 colors)</option>
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166 <option value="RdBu">Red to blue (discrete, max=11 colors)</option>
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167 <option value="PuOr">Purple to orange (discrete, max=11 colors)</option>
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168 <option value="PRGn">Purple to green (discrete, max=11 colors)</option>
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169 <option value="BrBG">Brown to teal (discrete, max=11 colors)</option>
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170 </param>
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171 <param name="colororder" type="select" label="Reverse color scheme" >
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172 <option value="1">Default order of color scheme</option>
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173 <option value="-1">Reverse the order of my color scheme</option>
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174 </param>
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175 </when>
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176 <when value="Multiple">
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177 <param name="factorcol" size="4" type="integer" value="1" label="column differentiating the different groups" />
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178 </when>
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179 </conditional>
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180 <conditional name="transformation">
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181 <param name="transform" type="select" label="Advanced - log transformation">
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182 <option value="none">Plot the data as it is</option>
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183 <option value="log2">Log2(value) transform my data</option>
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184 <option value="log2plus1">Log2(value+1) transform my data</option>
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185 <option value="log10">Log10(value) transform my data</option>
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186 <option value="log10plus1">Log10(value+1) transform my data</option>
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187 </param>
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188 <when value="none">
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189 <!--Do nothing here -->
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190 </when>
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191 <when value="log2">
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192 <!--Do nothing here -->
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193 </when>
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194 <when value="log2plus1">
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195 <!--Do nothing here -->
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196 </when>
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197 <when value="log10">
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198 <!--Do nothing here -->
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199 </when>
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200 <when value="log10plus1">
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201 <!--Do nothing here -->
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202 </when>
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203 </conditional>
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204 <conditional name="scaling">
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205 <param name="Plot_scaling" type="select" label="Advanced - axis scaling">
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206 <option value="Automatic" selected="True">Automatic axis scaling</option>
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207 <option value="Defined">User defined axis scales</option>
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208 </param>
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209 <when value="Automatic">
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210 <!--Do nothing here -->
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211 </when>
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212 <when value="Defined">
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213 <param name="xaxismin" size="4" type="integer" value="0" label="minimal range of x-axis" />
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214 <param name="xaxismax" size="4" type="integer" value="3" label="maximal range of x-axis" />
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215 <param name="yaxismin" size="4" type="integer" value="0" label="minimal range of y-axis" />
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216 <param name="yaxismax" size="4" type="integer" value="3" label="maximal range of y-axis" />
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217 </when>
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218 </conditional>
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219 <conditional name="theme">
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220 <param name="theme_selector" type="select" label="Advanced - backgound theme for plot">
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221 <option value="bw">Black and white</option>
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222 <option value="Default">Default (grey)</option>
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223 </param>
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224 <when value="bw"/>
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225 <when value="Default"></when>
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226 </conditional>
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227 <conditional name="axistitlecustomization">
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228 <param name="axistitlecust" type="select" label="Advanced - axis label options">
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229 <option value="Default" selected="True">Default</option>
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230 <option value="Defined">User defined label options</option>
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231 </param>
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232 <when value="Default">
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233 <!--Do nothing here -->
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234 </when>
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235 <when value="Defined">
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236 <param name="axistitlesize" size="4" type="float" value="12" label="Axis label size (default = 12)"/>
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237 <param name="axistitlecolor" type="select" label="Color of axis label">
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238 <option value="black">Black (default)</option>
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239 <option value="red">Red</option>
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240 <option value="white">White</option>
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241 <option value="blue">Blue</option>
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242 <option value="orange">Orange</option>
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243 <option value="yellow">Yellow</option>
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244 <option value="green">Green</option>
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245 <option value="purple">Purple</option>
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246 <option value="magenta">Magenta</option>
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247 <option value="cyan">Cyan</option>
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248 <option value="grey">Grey</option>
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249 <option value="gold">Gold</option>
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250 </param>
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251 <param name="axistitleface" size="4" type="select" label="Font effect of axis label">
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252 <option value="plain">Normal (default)</option>
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253 <option value="bold">Bold</option>
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254 <option value="italic">Italic</option>
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255 </param>
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256 </when>
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257 </conditional>
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258 <conditional name="axistextcustomization">
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259 <param name="axistextcust" type="select" label="Advanced - axis text options">
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260 <option value="Default" selected="True">Default</option>
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261 <option value="Defined">User defined axis text options</option>
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262 </param>
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263 <when value="Default">
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264 <!--Do nothing here -->
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265 </when>
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266 <when value="Defined">
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267 <param name="axistextsize" size="4" type="float" value="12" label="Axis text size (default = 12)"/>
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268 <param name="axistextcolor" type="select" label="Color of axis text">
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269 <option value="black">Black (default)</option>
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270 <option value="red">Red</option>
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271 <option value="white">White</option>
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272 <option value="blue">Blue</option>
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273 <option value="orange">Orange</option>
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274 <option value="yellow">Yellow</option>
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275 <option value="green">Green</option>
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276 <option value="purple">Purple</option>
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277 <option value="magenta">Magenta</option>
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278 <option value="cyan">Cyan</option>
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279 <option value="grey">Grey</option>
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280 <option value="gold">Gold</option>
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281 </param>
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282 <param name="axistextface" size="4" type="select" label="Font effect of axis text">
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283 <option value="plain">Normal (default)</option>
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284 <option value="bold">Bold</option>
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285 <option value="italic">Italic</option>
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286 </param>
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287 </when>
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288 </conditional>
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289 <conditional name="plottitlecustomization">
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290 <param name="plottitlecust" type="select" label="Advanced - Plot title options">
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291 <option value="Default" selected="True">Default</option>
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292 <option value="Defined">User defined plot title options</option>
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293 </param>
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294 <when value="Default">
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295 <!--Do nothing here -->
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296 </when>
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297 <when value="Defined">
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298 <param name="plottitlesize" size="4" type="float" value="12" label="Plot title size (default = 12)"/>
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299 <param name="plottitlecolor" type="select" label="Color of plot title">
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300 <option value="black">Black (default)</option>
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301 <option value="red">Red</option>
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302 <option value="white">White</option>
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303 <option value="blue">Blue</option>
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304 <option value="orange">Orange</option>
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305 <option value="yellow">Yellow</option>
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306 <option value="green">Green</option>
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307 <option value="purple">Purple</option>
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308 <option value="magenta">Magenta</option>
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309 <option value="cyan">Cyan</option>
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310 <option value="grey">Grey</option>
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311 <option value="gold">Gold</option>
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312 </param>
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313 <param name="plottitleface" size="4" type="select" label="Font effect of plot title">
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314 <option value="plain">Normal (default)</option>
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315 <option value="bold">Bold</option>
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316 <option value="italic">Italic</option>
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317 </param>
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318 </when>
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319 </conditional>
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320 <conditional name="gridlinecustomization">
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321 <param name="gridlinecust" type="select" label="Advanced - grid lines">
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322 <option value="Default">Default grid lines</option>
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323 <option value="hidemajor">Hide major grid lines</option>
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324 <option value="hideminor">Hide minor grid lines</option>
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325 <option value="hideboth">Hide major and minor grid lines</option>
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326 </param>
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327 <when value="Default">
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328 <!--Do nothing here -->
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329 </when>
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330 <when value="hidemajor">
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331 <!--Do nothing here -->
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332 </when>
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333 <when value="hideminor">
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334 <!--Do nothing here -->
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335 </when>
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336 <when value="hideboth">
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337 <!--Do nothing here -->
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338 </when>
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339 </conditional>
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340 <conditional name="dimensions">
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341 <param name="plotdim" type="select" label="Advanced - output dimensions">
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342 <option value="Default" selected="True">Default</option>
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343 <option value="Defined">User defined output dimensions</option>
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344 </param>
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345 <when value="Default">
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346 <!--Do nothing here -->
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347 </when>
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348 <when value="Defined">
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349 <param name="woutputdim" size="4" type="float" value="7" label="width of output (inches)" />
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350 <param name="houtputdim" size="4" type="float" value="7" label="height of output (inches)" />
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351 </when>
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352 </conditional>
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353 </inputs>
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354 <outputs>
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355 <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/> -->
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356 <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/>
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357 </outputs>
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358 <tests>
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359 <test>
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360 <param name="input1" value="input.txt"/>
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361 <output name="output1" file="Rplot.pdf"/>
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362 </test>
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363 </tests>
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364 <help><![CDATA[
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365 This tool will generate a scatterplot representing data from two groups/conditions.
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366
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367 The input data should be in tabular format and the user can determine which groups (columns) to plot.
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368
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369 Multiple groups can be plotted on the same or multiple plots by providing a column with a group identifier under "Advanced - plotting multiple groups".
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370
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371 Feel free to explore the (many) advanced options to customize your plot. Galaxy makes this type optimization easy for the user!
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372
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373 The ouput is a pdf file with your scatterplot. The dimensions of this file can be modified under "Advanced - output dimensions"
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374
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375
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376
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377
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378 Please report issues at: https://github.com/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot
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379 ]]></help>
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380 <citations>
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381 <citation type="bibtex">
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382 @misc{renameTODO,
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383 author = {8.5.2016, FirstTODO},
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384 year = {TODO},
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385 title = {TODO},
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386 url = {http://docs.ggplot2.org/current/geom_point.html},
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387 }</citation>
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388 </citations>
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389 </tool>
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390
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