Mercurial > repos > iuc > ggplot2_point

annotate ggplot_point.xml @ 2:9a482995958c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
author iuc
date Mon, 11 Jun 2018 16:04:40 -0400
parents 1bff6682e780
children 52b8083a6159
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9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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1 <tool id="ggplot2_point" name="Scatterplot w ggplot2" version="@VERSION@+galaxy0">
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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>
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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7 </expand>
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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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1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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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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2
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23 @LEGEND@
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1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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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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1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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33 gg_facet = facet_wrap( ~ factor)
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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34 gg_factor = NULL
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35 color_scale = NULL
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36 #if $adv.points.pointoptions == "Default"
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37 gg_point = geom_point(size=1, alpha=1, gg_factor)
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38 #else
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39 gg_point = geom_point(size='$adv.points.size', alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
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40 #end if
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41
2
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42 names(input)[$adv.factor.factorcol] <- "factor"
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43
2
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44 #elif $adv.factor.factoring == "Single"
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45 gg_facet = NULL
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46 gg_factor = aes(colour=factor(factor))
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47
2
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48 #if $adv.points.pointoptions == "default"
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49 gg_point = geom_point(size=1, alpha=1, gg_factor)
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50 #else
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51 gg_point = geom_point(size=$adv.points.size, alpha='$adv.points.alpha', gg_factor)
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52 #end if
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53
2
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54 #if $adv.colors == "Default"
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55 color_scale = scale_colour_hue(direction='$adv.factor.colororder')
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56 #else
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57 color_scale = scale_color_brewer(palette='$adv.colors', direction='$adv.factor.colororder')
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58 #end if
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59
2
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60 names(input)[$adv.factor.factorcol] <- "factor"
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61 #else
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62 gg_facet = NULL
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63 gg_factor = NULL
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64 color_scale = NULL
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65
2
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66 #if $adv.points.pointoptions == "default"
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67 gg_point = geom_point(size=1, alpha=1, gg_factor)
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68 #else
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69 gg_point = geom_point(size=$adv.points.size, alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
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70 #end if
0
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71 #end if
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73 @TRANSFORM@
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75 ##axis label custization
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76 #if $adv.axis_title_customization.axis_customization == "default"
0
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77 gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
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78 #else
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79 gg_axistitle = theme(axis.title = element_text(color = '$adv.color', size = '$adv.size', face = '$adv.face'))
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80 #end if
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81
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82 ##axis text(tick) custization
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83 #if $adv.axis_text_customization.axis_customization == "default"
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84 gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
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85 #else
2
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86 gg_axistext = theme(axis.text = element_text(color = '$adv.color', size = '$adv.size', face = '$adv.face'))
0
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87 #end if
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88
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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89 ##plot title custimization
2
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90 #if $adv.plot_title_customization.axis_customization == "default"
0
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91 gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
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92 #else
2
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93 gg_plottitle = theme(plot.title = element_text(color='$adv.color', size='$adv.size', face='$adv.face'))
0
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94 #end if
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95
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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96 ## grid line customization
2
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97 #if $adv.gridlinecust == "default"
0
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98 gg_gridline = NULL
2
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99 #elif $adv.gridlinecust == "hidemajor"
0
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100 gg_gridline = theme(panel.grid.major = element_blank())
2
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101 #elif $adv.gridlinecust == "hideminor"
0
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102 gg_gridline = theme(panel.grid.minor = element_blank())
2
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103 #elif $adv.gridlinecust == "hideboth"
0
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104 gg_gridline = theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank())
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105 #end if
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106
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107 #this is the actual ggplot command to make the final plot(s)
2
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108 plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_facet +
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109 gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('$title') + xlab('$xlab') + ylab('$ylab')+
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110 gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
0
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111
2
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112 @SAVE_OUTPUT@
0
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113 ]]></configfile>
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114 </configfiles>
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115 <inputs>
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116 <param name="input1" type="data" format="tabular" label="Input in tabular format" />
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117 <param name="xplot" type="integer" value="8" label="Column to plot on x-axis" />
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118 <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" />
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119
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120 <expand macro="title" />
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121 <expand macro="xy_lab" />
2
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122 <section name="adv" title="Advanced Options" expanded="false">
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123 <conditional name="points">
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124 <param name="pointoptions" type="select" label="Data point options">
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125 <option value="default" selected="true">Default</option>
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126 <option value="defined">User defined point options</option>
0
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127 </param>
2
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128 <when value="default">
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129 <!--Do nothing here -->
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130 </when>
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131 <when value="defined">
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132 <param name="size" type="float" value="1" label="relative size of points" />
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133 <param name="alpha" type="float" value="1" label="Transparency of points (On a scale of 0-1; 0=transparent, 1=default)" />
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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134 <param name="pointcolor" type="select" label="Color of data points" >
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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135 <option value="black">Black (default)</option>
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136 <option value="red">Red</option>
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137 <option value="white">White</option>
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138 <option value="blue">Blue</option>
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139 <option value="orange">Orange</option>
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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140 <option value="yellow">Yellow</option>
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141 <option value="green">Green</option>
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142 <option value="purple">Purple</option>
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143 <option value="magenta">Magenta</option>
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144 <option value="cyan">Cyan</option>
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145 <option value="grey">Grey</option>
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146 <option value="gold">Gold</option>
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147 </param>
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148 </when>
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149 </conditional>
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150 <conditional name="factor">
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151 <param name="factoring" type="select" label="Plotting multiple groups" >
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152 <option value="Default" selected="true">No thanks - just plot the data as one group</option>
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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153 <option value="Single">Plot multiple groups of data on one plot</option>
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154 <option value="Multiple">Plot multiple groups of data on individual plots</option>
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155 </param>
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156 <when value="Default">
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157 <!--Do nothing here -->
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158 </when>
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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159 <when value="Single">
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160 <param name="factorcol" type="integer" value="1" label="column differentiating the different groups" />
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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161 <expand macro="colors" />
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162 <param name="colororder" type="select" label="Reverse color scheme" >
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163 <option value="1">Default order of color scheme</option>
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164 <option value="-1">Reverse the order of my color scheme</option>
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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165 </param>
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166 </when>
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167 <when value="Multiple">
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168 <param name="factorcol" type="integer" value="1" label="column differentiating the different groups" />
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169 </when>
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170 </conditional>
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171 <conditional name="axis_title_customization">
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172 <expand macro="axis_customization" label="Axis title options" />
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173 </conditional>
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174 <conditional name="axis_text_customization">
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175 <expand macro="axis_customization" label="Axis text options" />
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176 </conditional>
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177 <conditional name="plot_title_customization">
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178 <expand macro="axis_customization" label="Plot title options" />
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179 </conditional>
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180 <param name="gridlinecust" type="select" label="Grid lines">
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181 <option value="default">Default grid lines</option>
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182 <option value="hidemajor">Hide major grid lines</option>
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183 <option value="hideminor">Hide minor grid lines</option>
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184 <option value="hideboth">Hide major and minor grid lines</option>
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185 </param>
2
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186 <expand macro="transform" />
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187 <expand macro="xy_scaling" />
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188 <expand macro="theme" />
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189 <expand macro="legend" />
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190 </section>
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191 <section name="out" title="Output Options" expanded="true">
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192 <expand macro="dimensions" />
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193 </section>
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194 </inputs>
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195 <outputs>
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196 <expand macro="additional_output" />
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197 </outputs>
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198 <tests>
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199 <test>
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200 <param name="input1" value="mtcars.txt" ftype="tabular" />
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201 <param name="additional_output_format" value="pdf" />
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202 <output name="output2" file="ggplot_point_result1.pdf" compare="sim_size" />
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203 </test>
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204 </tests>
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205 <help><![CDATA[
2
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206 This tool will generate a scatterplot representing data from two groups/conditions.
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207
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208 The input data should be in tabular format and the user can determine which groups (columns) to plot.
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209
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210 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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211
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212 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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213
2
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214 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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215 ]]></help>
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216 <expand macro="citations"/>
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217 </tool>