Mercurial > repos > iuc > ggplot2_point

annotate ggplot_point.xml @ 15:f87634b12749 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
author iuc
date Thu, 15 May 2025 13:02:15 +0000
parents 5298e06f14f9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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15
f87634b12749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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1 <tool id="ggplot2_point" name="Scatterplot with ggplot2" version="@TOOL_VERSION@+galaxy2" profile="23.0">
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2 <macros>
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3 <import>macros.xml</import>
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4 <token name="@SIMPLE_GGLINE@">gg_line = geom_line(size=1, alpha=1, gg_factor)</token>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements">
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8 <requirement type="package" version="2.1.0">r-svglite</requirement>
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9 </expand>
0
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10 <command detect_errors="exit_code"><![CDATA[
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11 cat '$script' &&
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12 Rscript '$script'
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13 ]]></command>
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14 <configfiles>
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15 <configfile name="script"><![CDATA[
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16 @R_INIT@
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18 ## Import library
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19 library(ggplot2)
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21 @XY_SCALING@
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22
2
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23 @THEME@
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24
2
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25 @LEGEND@
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27 input <- read.csv('$input1', sep='\t')
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29 ## renaming columns so ggplot can use them
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30 names(input)[$xplot] <- "xcol"
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31 names(input)[$yplot] <- "ycol"
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32
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33 ## choosing whether to plot data as multiple groups on one plot(factoring) OR multiple groups on different plots
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34 #if $adv.factor.factoring == "Multiple"
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35 gg_facet = facet_wrap( ~ factor)
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36 gg_factor = NULL
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37 color_scale = NULL
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38 #if $adv.type_conditional.type_options == "lines":
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39 @SIMPLE_GGLINE@
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40 #elif $adv.type_conditional.points.pointoptions == "default"
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41 gg_point = geom_point(size=1, alpha=1, gg_factor)
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42 @SIMPLE_GGLINE@
0
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43 #else
10
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44 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape'))
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45 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape'))
0
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46 #end if
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47
2
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48 names(input)[$adv.factor.factorcol] <- "factor"
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49
2
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50 #elif $adv.factor.factoring == "Single"
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51 gg_facet = NULL
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52 gg_factor = aes(colour=factor(factor))
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53
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54 #if $adv.type_conditional.type_options == "lines":
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55 @SIMPLE_GGLINE@
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56 #elif $adv.type_conditional.points.pointoptions == "default"
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57 gg_point = geom_point(size=1, alpha=1, gg_factor)
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58 @SIMPLE_GGLINE@
2
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59 #else
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60 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, gg_factor, shape=as.numeric('$adv.type_conditional.points.shape'))
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61 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, gg_factor, shape=as.numeric('$adv.type_conditional.points.shape'))
2
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62 #end if
0
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63
4
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64 #if $adv.factor.colororder == 1
2
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65 color_scale = scale_colour_hue(direction='$adv.factor.colororder')
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66 #else
4
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67 color_scale = scale_color_brewer(palette='$adv.factor.colors', direction='$adv.factor.colororder')
2
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68 #end if
0
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69
2
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70 names(input)[$adv.factor.factorcol] <- "factor"
0
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71 #else
2
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72 gg_facet = NULL
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73 gg_factor = NULL
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74 color_scale = NULL
0
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75
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76 #if $adv.type_conditional.type_options == "lines":
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77 @SIMPLE_GGLINE@
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78 #elif $adv.type_conditional.points.pointoptions == "default"
2
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79 gg_point = geom_point(size=1, alpha=1, gg_factor)
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80 @SIMPLE_GGLINE@
2
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81 #else
10
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82 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape'))
299307abd804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
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83 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape'))
2
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84 #end if
0
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85 #end if
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86
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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87 @TRANSFORM@
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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 ##axis label custization
2
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90 #if $adv.axis_title_customization.axis_customization == "default"
0
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91 gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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92 #else
9
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93 gg_axistitle = theme(axis.title = element_text(color = '$adv.axis_text_customization.color', size = $adv.axis_text_customization.size, face = '$adv.axis_text_customization.face'))
0
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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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 ##axis text(tick) custization
2
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97 #if $adv.axis_text_customization.axis_customization == "default"
0
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98 gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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99 #else
9
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100 gg_axistext = theme(axis.text = element_text(color = '$adv.axis_text_customization.color', size = $adv.axis_text_customization.size, face = '$adv.axis_text_customization.face'))
0
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101 #end if
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102
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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103 ##plot title custimization
2
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104 #if $adv.plot_title_customization.axis_customization == "default"
0
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105 gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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106 #else
9
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107 gg_plottitle = theme(plot.title = element_text(color='$adv.axis_text_customization.color', size=$adv.axis_text_customization.size, face='$adv.axis_text_customization.face'))
0
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108 #end if
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109
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110 ## grid line customization
2
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111 #if $adv.gridlinecust == "default"
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112 gg_gridline = NULL
2
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113 #elif $adv.gridlinecust == "hidemajor"
0
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114 gg_gridline = theme(panel.grid.major = element_blank())
2
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115 #elif $adv.gridlinecust == "hideminor"
0
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116 gg_gridline = theme(panel.grid.minor = element_blank())
2
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117 #elif $adv.gridlinecust == "hideboth"
0
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118 gg_gridline = theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank())
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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119 #end if
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120
4
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121 ## choose between graph types (points/lines/both)
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122 #if $adv.type_conditional.type_options == "points"
4
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123 gg_line = NULL
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124 #elif $adv.type_conditional.type_options == "lines"
4
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125 gg_point = NULL
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126 #end if
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127
0
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128 #this is the actual ggplot command to make the final plot(s)
15
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129 plot_out <- ggplot(input, aes_string(x=names(input)[$xplot], y=names(input)[$yplot])) + gg_point + gg_line + gg_facet +
2
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130 gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('$title') + xlab('$xlab') + ylab('$ylab')+
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131 gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
0
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132
2
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133 @SAVE_OUTPUT@
0
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134 ]]></configfile>
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135 </configfiles>
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136 <inputs>
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137 <param name="input1" type="data" format="tabular" label="Input in tabular format" />
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138
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139 <conditional name="cols">
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140 <param name="header" type="select" label="Does the dataset have a header?" help="If the table has a header, columns can be selected based on the name.">
f87634b12749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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141 <option value="yes" selected="true">yes</option>
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142 <option value="no">no</option>
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143 </param>
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144 <when value="yes">
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145 <param name="xplot" type="data_column" data_ref="input1" use_header_names="true" label="Column to plot on x-axis" />
f87634b12749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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146 <param name="yplot" type="data_column" data_ref="input1" use_header_names="true" label="Column to plot on y-axis" />
f87634b12749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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147 </when>
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148 <when value="no">
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149 <param name="xplot" type="data_column" data_ref="input1" label="Column to plot on x-axis" />
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150 <param name="yplot" type="data_column" data_ref="input1" label="Column to plot on y-axis" />
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151 </when>
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152 </conditional>
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153
0
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154
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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155 <expand macro="title" />
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156 <expand macro="xy_lab" />
9
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157 <section name="adv" title="Advanced options">
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158 <conditional name="type_conditional">
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159 <param name="type_options" type="select" label="Type of plot" >
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160 <option value="points">Points only (default)</option>
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161 <option value="lines">Lines only </option>
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162 <option value="pointslines">Points and Lines</option>
0
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163 </param>
9
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164 <when value ="points">
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165 <expand macro="points_options"/>
2
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166 </when>
9
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167 <when value="pointslines">
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168 <expand macro="points_options"/>
2
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169 </when>
9
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170 <when value="lines"/>
2
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171 </conditional>
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172 <conditional name="factor">
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173 <param name="factoring" type="select" label="Plotting multiple groups" >
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174 <option value="Default" selected="true">No thanks - just plot the data as one group</option>
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175 <option value="Single">Plot multiple groups of data on one plot</option>
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176 <option value="Multiple">Plot multiple groups of data on individual plots</option>
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177 </param>
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178 <when value="Default">
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179 <!--Do nothing here -->
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180 </when>
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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181 <when value="Single">
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182 <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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183 <expand macro="colors" />
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184 <param name="colororder" type="select" label="Reverse color scheme" >
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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185 <option value="1">Default order of color scheme</option>
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186 <option value="-1">Reverse the order of my color scheme</option>
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187 </param>
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188 </when>
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189 <when value="Multiple">
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190 <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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191 </when>
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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192 </conditional>
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193 <conditional name="axis_title_customization">
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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194 <expand macro="axis_customization" label="Axis title options" />
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195 </conditional>
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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196 <conditional name="axis_text_customization">
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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197 <expand macro="axis_customization" label="Axis text options" />
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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198 </conditional>
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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199 <conditional name="plot_title_customization">
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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200 <expand macro="axis_customization" label="Plot title options" />
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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201 </conditional>
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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202 <param name="gridlinecust" type="select" label="Grid lines">
9
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203 <option value="default">Default grid lines</option>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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204 <option value="hidemajor">Hide major grid lines</option>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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205 <option value="hideminor">Hide minor grid lines</option>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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206 <option value="hideboth">Hide major and minor grid lines</option>
0
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207 </param>
2
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208 <expand macro="transform" />
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209 <expand macro="xy_scaling" />
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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210 <expand macro="theme" />
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211 <expand macro="legend" />
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212 </section>
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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213 <section name="out" title="Output Options" expanded="true">
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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214 <expand macro="dimensions" />
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215 </section>
0
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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216 </inputs>
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217 <outputs>
2
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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218 <expand macro="additional_output" />
0
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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219 </outputs>
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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220 <tests>
14
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221 <test expect_num_outputs="2">
0
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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222 <param name="input1" value="mtcars.txt" ftype="tabular" />
2
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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223 <param name="additional_output_format" value="pdf" />
15
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diff changeset
224 <param name="xplot" value="8"/>
f87634b12749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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225 <param name="yplot" value="9"/>
2
9a482995958c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents: 0
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226 <output name="output2" file="ggplot_point_result1.pdf" compare="sim_size" />
0
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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227 </test>
9
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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228 <!-- Test text options-->
14
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229 <test expect_num_outputs="2">
9
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230 <param name="input1" value="mtcars.txt" ftype="tabular" />
15
f87634b12749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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231 <conditional name="cols">
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232 <param name="header" value="no"/>
f87634b12749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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233 </conditional>
f87634b12749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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234 <param name="xplot" value="8"/>
f87634b12749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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235 <param name="yplot" value="9"/>
9
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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diff changeset
236 <section name="adv">
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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diff changeset
237 <conditional name="type_conditional">
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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diff changeset
238 <param name="type_options" value="points"/>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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239 <conditional name="points">
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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240 <param name="pointoptions" value="default"/>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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241 </conditional>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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242 </conditional>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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diff changeset
243 <conditional name="axis_text_customization">
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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diff changeset
244 <param name="axis_customization" value="defined"/>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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diff changeset
245 <param name="color" value="red"/>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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246 </conditional>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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247 </section>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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248 <param name="additional_output_format" value="pdf" />
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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249 <output name="output2" file="ggplot_point_result2.pdf" compare="sim_size" />
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
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250 </test>
11
d0fc8b746d57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
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parents: 10
diff changeset
251 <!-- Test lines option -->
14
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diff changeset
252 <test expect_num_outputs="2">
11
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253 <param name="input1" value="mtcars.txt" ftype="tabular" />
15
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254 <param name="xplot" value="8"/>
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255 <param name="yplot" value="9"/>
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256 <section name="adv">
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257 <conditional name="type_conditional">
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258 <param name="type_options" value="lines"/>
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259 </conditional>
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260 </section>
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261 <param name="additional_output_format" value="pdf" />
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262 <output name="output2" file="ggplot_line_result1.pdf" compare="sim_size" />
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263 </test>
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264 <!-- Test defined point options options-->
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265 <test expect_num_outputs="2">
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266 <param name="input1" value="mtcars.txt" ftype="tabular" />
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267 <param name="xplot" value="8"/>
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268 <param name="yplot" value="9"/>
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269 <section name="adv">
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270 <conditional name="type_conditional">
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271 <param name="type_options" value="points"/>
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272 <conditional name="points">
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273 <param name="pointoptions" value="defined"/>
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274 <param name="size" value="2"/>
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275 <param name="alpha" value="0.5"/>
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276 <param name="pointcolor" value="gold"/>
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277 <param name="shape" value="6"/>
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278 </conditional>
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279 </conditional>
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280 <conditional name="axis_text_customization">
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281 <param name="axis_customization" value="defined"/>
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282 <param name="color" value="red"/>
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283 </conditional>
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284 </section>
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285 <param name="additional_output_format" value="pdf" />
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286 <output name="output2" file="ggplot_point_result3.pdf" ftype="pdf" compare="sim_size" />
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287 </test>
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288 </tests>
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289 <help><![CDATA[
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290 This tool will generate a scatterplot representing data from two groups/conditions.
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291
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292 The input data should be in tabular format and the user can determine which groups (columns) to plot.
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293
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294 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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295
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296 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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297
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298 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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299 ]]></help>
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300 <expand macro="citations"/>
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301 </tool>