Mercurial > repos > iuc > ggplot2_point

annotate ggplot_point.xml @ 4:52b8083a6159 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
author iuc
date Sun, 24 Mar 2019 13:21:18 -0400
parents 9a482995958c
children 9cec81e1b90e
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1 <tool id="ggplot2_point" name="Scatterplot w ggplot2" version="@VERSION@+galaxy1">
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <expand macro="requirements">
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6 <requirement type="package" version="1.2.1">r-svglite</requirement>
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7 </expand>
0
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8 <command detect_errors="exit_code"><![CDATA[
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9 cat '$script' &&
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10 Rscript '$script'
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11 ]]></command>
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12 <configfiles>
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13 <configfile name="script"><![CDATA[
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14 @R_INIT@
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16 ## Import library
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17 library(ggplot2)
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19 @XY_SCALING@
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20
2
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21 @THEME@
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22
2
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23 @LEGEND@
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25 input <- read.csv('$input1', sep='\t', header=TRUE)
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27 ## renaming columns so ggplot can use them
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28 names(input)[$xplot] <- "xcol"
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29 names(input)[$yplot] <- "ycol"
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30
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31 ## choosing whether to plot data as multiple groups on one plot(factoring) OR multiple groups on different plots
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32 #if $adv.factor.factoring == "Multiple"
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33 gg_facet = facet_wrap( ~ factor)
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34 gg_factor = NULL
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35 color_scale = NULL
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36 #if $adv.points.pointoptions == "Default"
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37 gg_point = geom_point(size=1, alpha=1, gg_factor)
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38 gg_line = geom_line(size=1, alpha=1, gg_factor)
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39 #else
2
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40 gg_point = geom_point(size='$adv.points.size', alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
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41 gg_line = geom_line(size='$adv.points.size', alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
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42 #end if
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43
2
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44 names(input)[$adv.factor.factorcol] <- "factor"
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45
2
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46 #elif $adv.factor.factoring == "Single"
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47 gg_facet = NULL
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48 gg_factor = aes(colour=factor(factor))
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49
2
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50 #if $adv.points.pointoptions == "default"
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51 gg_point = geom_point(size=1, alpha=1, gg_factor)
4
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52 gg_line = geom_line(size=1, alpha=1, gg_factor)
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53 #else
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54 gg_point = geom_point(size=$adv.points.size, alpha='$adv.points.alpha', gg_factor)
4
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55 gg_line = geom_line(size=$adv.points.size, alpha='$adv.points.alpha', gg_factor)
2
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56 #end if
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57
4
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58 #if $adv.factor.colororder == 1
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59 color_scale = scale_colour_hue(direction='$adv.factor.colororder')
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60 #else
4
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61 color_scale = scale_color_brewer(palette='$adv.factor.colors', direction='$adv.factor.colororder')
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62 #end if
0
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63
2
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64 names(input)[$adv.factor.factorcol] <- "factor"
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65 #else
2
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66 gg_facet = NULL
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67 gg_factor = NULL
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68 color_scale = NULL
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69
2
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70 #if $adv.points.pointoptions == "default"
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71 gg_point = geom_point(size=1, alpha=1, gg_factor)
4
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72 gg_line = geom_line(size=1, alpha=1, gg_factor)
2
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73 #else
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74 gg_point = geom_point(size=$adv.points.size, alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
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75 gg_line = geom_line(size=$adv.points.size, alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
2
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76 #end if
0
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77 #end if
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78
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79 @TRANSFORM@
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80
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81 ##axis label custization
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82 #if $adv.axis_title_customization.axis_customization == "default"
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83 gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
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84 #else
2
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85 gg_axistitle = theme(axis.title = element_text(color = '$adv.color', size = '$adv.size', face = '$adv.face'))
0
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86 #end if
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87
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88 ##axis text(tick) custization
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89 #if $adv.axis_text_customization.axis_customization == "default"
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90 gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
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91 #else
2
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92 gg_axistext = theme(axis.text = element_text(color = '$adv.color', size = '$adv.size', face = '$adv.face'))
0
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93 #end if
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94
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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95 ##plot title custimization
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96 #if $adv.plot_title_customization.axis_customization == "default"
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97 gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
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98 #else
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99 gg_plottitle = theme(plot.title = element_text(color='$adv.color', size='$adv.size', face='$adv.face'))
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100 #end if
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101
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102 ## grid line customization
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103 #if $adv.gridlinecust == "default"
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104 gg_gridline = NULL
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105 #elif $adv.gridlinecust == "hidemajor"
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106 gg_gridline = theme(panel.grid.major = element_blank())
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107 #elif $adv.gridlinecust == "hideminor"
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108 gg_gridline = theme(panel.grid.minor = element_blank())
2
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109 #elif $adv.gridlinecust == "hideboth"
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110 gg_gridline = theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank())
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111 #end if
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112
4
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113 ## choose between graph types (points/lines/both)
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114 #if $adv.type == "points"
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115 gg_line = NULL
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116 #elif $adv.type == "lines"
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117 gg_point = NULL
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118 #end if
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119
0
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120 #this is the actual ggplot command to make the final plot(s)
4
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121 plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
2
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122 gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('$title') + xlab('$xlab') + ylab('$ylab')+
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123 gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
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124
2
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125 @SAVE_OUTPUT@
0
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126 ]]></configfile>
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127 </configfiles>
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128 <inputs>
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129 <param name="input1" type="data" format="tabular" label="Input in tabular format" />
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130 <param name="xplot" type="integer" value="8" label="Column to plot on x-axis" />
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131 <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" />
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132
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133 <expand macro="title" />
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134 <expand macro="xy_lab" />
2
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135 <section name="adv" title="Advanced Options" expanded="false">
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136 <param name="type" type="select" label="Type of plot" >
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137 <option value="points">Points only (default)</option>
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138 <option value="lines">Lines only </option>
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139 <option value="pointslines">Points and Lines</option>
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140 </param>
2
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141 <conditional name="points">
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142 <param name="pointoptions" type="select" label="Data point options">
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143 <option value="default" selected="true">Default</option>
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144 <option value="defined">User defined point options</option>
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145 </param>
2
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146 <when value="default">
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147 <!--Do nothing here -->
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148 </when>
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149 <when value="defined">
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150 <param name="size" type="float" value="1" label="relative size of points" />
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151 <param name="alpha" type="float" value="1" label="Transparency of points (On a scale of 0-1; 0=transparent, 1=default)" />
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152 <param name="pointcolor" type="select" label="Color of data points" >
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153 <option value="black">Black (default)</option>
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154 <option value="red">Red</option>
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155 <option value="white">White</option>
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156 <option value="blue">Blue</option>
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157 <option value="orange">Orange</option>
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158 <option value="yellow">Yellow</option>
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159 <option value="green">Green</option>
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160 <option value="purple">Purple</option>
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161 <option value="magenta">Magenta</option>
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162 <option value="cyan">Cyan</option>
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163 <option value="grey">Grey</option>
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164 <option value="gold">Gold</option>
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165 </param>
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166 </when>
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167 </conditional>
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168 <conditional name="factor">
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169 <param name="factoring" type="select" label="Plotting multiple groups" >
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170 <option value="Default" selected="true">No thanks - just plot the data as one group</option>
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171 <option value="Single">Plot multiple groups of data on one plot</option>
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172 <option value="Multiple">Plot multiple groups of data on individual plots</option>
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173 </param>
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174 <when value="Default">
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175 <!--Do nothing here -->
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176 </when>
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177 <when value="Single">
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178 <param name="factorcol" type="integer" value="1" label="column differentiating the different groups" />
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179 <expand macro="colors" />
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180 <param name="colororder" type="select" label="Reverse color scheme" >
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181 <option value="1">Default order of color scheme</option>
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182 <option value="-1">Reverse the order of my color scheme</option>
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183 </param>
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184 </when>
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185 <when value="Multiple">
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186 <param name="factorcol" type="integer" value="1" label="column differentiating the different groups" />
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187 </when>
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188 </conditional>
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189 <conditional name="axis_title_customization">
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190 <expand macro="axis_customization" label="Axis title options" />
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191 </conditional>
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192 <conditional name="axis_text_customization">
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193 <expand macro="axis_customization" label="Axis text options" />
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194 </conditional>
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195 <conditional name="plot_title_customization">
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196 <expand macro="axis_customization" label="Plot title options" />
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197 </conditional>
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198 <param name="gridlinecust" type="select" label="Grid lines">
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199 <option value="default">Default grid lines</option>
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200 <option value="hidemajor">Hide major grid lines</option>
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201 <option value="hideminor">Hide minor grid lines</option>
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202 <option value="hideboth">Hide major and minor grid lines</option>
0
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203 </param>
2
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204 <expand macro="transform" />
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205 <expand macro="xy_scaling" />
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206 <expand macro="theme" />
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207 <expand macro="legend" />
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208 </section>
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209 <section name="out" title="Output Options" expanded="true">
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210 <expand macro="dimensions" />
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211 </section>
0
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212 </inputs>
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213 <outputs>
2
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214 <expand macro="additional_output" />
0
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215 </outputs>
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216 <tests>
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217 <test>
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218 <param name="input1" value="mtcars.txt" ftype="tabular" />
2
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219 <param name="additional_output_format" value="pdf" />
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220 <output name="output2" file="ggplot_point_result1.pdf" compare="sim_size" />
0
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221 </test>
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222 </tests>
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223 <help><![CDATA[
2
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224 This tool will generate a scatterplot representing data from two groups/conditions.
0
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225
2
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226 The input data should be in tabular format and the user can determine which groups (columns) to plot.
0
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227
2
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228 Multiple groups can be plotted on the same or multiple plots by providing a column with a group identifier under "Advanced - plotting multiple groups".
0
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229
2
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230 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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231
2
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232 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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233 ]]></help>
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234 <expand macro="citations"/>
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235 </tool>