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annotate xy_plot.xml @ 4:d449deb33159 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit d792f43f02cd0d6ab74411c21e0897937cb075aa
author devteam
date Sun, 17 Dec 2017 12:37:27 -0500
parents 2d28f96a309a
children
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2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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1 <tool id="XY_Plot_1" name="Plotting tool" version="1.0.2">
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2 <description>for multiple series and graph types</description>
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3 <requirements>
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4 <requirement type="package" version="3.4.2">r-base</requirement>
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5 </requirements>
4
d449deb33159 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit d792f43f02cd0d6ab74411c21e0897937cb075aa
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6 <command>Rscript $script_file</command>
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7 <configfiles>
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8 <configfile name="script_file">
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9 ## Setup R error handling to go to stderr
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10 options( show.error.messages=F,
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11 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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12 ## Determine range of all series in the plot
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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13 xrange = c( NULL, NULL )
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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14 yrange = c( NULL, NULL )
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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15 #for $i, $s in enumerate( $series )
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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16 s${i} = read.table( "${s.input.file_name}", h=${s.header} )
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17 x${i} = s${i}[,${s.xcol}]
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18 yrange = 0
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19 #for $column in str($s.ycol).split(','):
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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20 y${i}${column} = s${i}[,${column}]
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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21 yrange = range(y${i}${column}, yrange, na.rm=TRUE )
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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22 #end for
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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23 xrange = range( x${i}, xrange, na.rm=TRUE )
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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24 #end for
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25 ## Open output PDF file
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26 #if $outftype.value == "pdf"
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27 pdf("outfile.pdf")
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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28 #else
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29 "${outftype}"( "outfile.${outftype}" , type="cairo")
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30 #end if
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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31 ## Dummy plot for axis / labels
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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32 plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" )
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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33 ## Plot each series
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34 #for $i, $s in enumerate( $series )
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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35 #if $s.series_type['type'] == "line"
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36 #for $column in str($s.ycol).split(','):
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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37 lines( x${i}, y${i}${column}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col} )
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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38 #end for
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39 #elif $s.series_type.type == "points"
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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40 #for $column in str($s.ycol).split(','):
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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41 points( x${i}, y${i}${column}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col} )
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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42 #end for
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43 #end if
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44 #end for
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45 ## Close the PDF file
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46 devname = dev.off()
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47 </configfile>
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48 </configfiles>
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49
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50 <inputs>
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51 <param name="main" type="text" value="" label="Plot Title"/>
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52 <param name="xlab" type="text" value="" label="Label for x axis"/>
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53 <param name="ylab" type="text" value="" label="Label for y axis"/>
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54 <param name="outftype" type="select" label="Output File Type">
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55 <option value="pdf">PDF</option>
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56 <option value="png">PNG</option>
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57 </param>
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58 <repeat name="series" title="Series">
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59 <param name="input" type="data" format="tabular" label="Dataset"/>
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60 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?"/>
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61 <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/>
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62 <param name="ycol" type="data_column" data_ref="input" multiple="true" label="Column for y axis"/>
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63 <conditional name="series_type">
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64 <param name="type" type="select" label="Series Type">
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65 <option value="line" selected="true">Line</option>
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66 <option value="points">Points</option>
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67 </param>
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68 <when value="line">
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69 <param name="lty" type="select" label="Line Type">
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70 <option value="1">Solid</option>
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71 <option value="2">Dashed</option>
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72 <option value="3">Dotted</option>
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73 </param>
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74 <param name="col" type="select" label="Line Color">
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75 <option value="1">Black</option>
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76 <option value="2">Red</option>
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77 <option value="3">Green</option>
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78 <option value="4">Blue</option>
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79 <option value="5">Cyan</option>
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80 <option value="6">Magenta</option>
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81 <option value="7">Yellow</option>
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82 <option value="8">Gray</option>
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83 </param>
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84 <param name="lwd" type="float" label="Line Width" value="1.0"/>
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85 </when>
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86 <when value="points">
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87 <param name="pch" type="select" label="Point Type">
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88 <option value="1">Circle (hollow)</option>
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89 <option value="2">Triangle (hollow)</option>
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90 <option value="3">Cross</option>
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91 <option value="4">Diamond (hollow)</option>
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92 <option value="15">Square (filled)</option>
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93 <option value="16">Circle (filled)</option>
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94 <option value="17">Triangle (filled)</option>
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95 </param>
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96 <param name="col" type="select" label="Point Color">
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97 <option value="1">Black</option>
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98 <option value="2">Red</option>
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99 <option value="3">Green</option>
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100 <option value="4">Blue</option>
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101 <option value="5">Cyan</option>
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102 <option value="6">Magenta</option>
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103 <option value="7">Yellow</option>
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104 <option value="8">Gray</option>
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105 </param>
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106 <param name="cex" type="float" label="Point Scale" value="1.0"/>
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107 </when>
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108 </conditional>
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109 </repeat>
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110 </inputs>
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111 <outputs>
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112 <data format="pdf" name="out_file_pdf" from_work_dir="outfile.pdf" >
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113 <filter>(outftype == 'pdf')</filter>
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114 </data>
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115 <data format="png" name="out_file_png" from_work_dir="outfile.png">
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116 <filter>(outftype == 'png')</filter>
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117 </data>
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118 </outputs>
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119 <tests>
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120 <test>
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121 <param name="main" value="Example XY Plot"/>
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122 <param name="xlab" value="Column 1"/>
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123 <param name="ylab" value="Column 2"/>
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124 <param name="outftype" value="pdf"/>
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125 <param name="input" value="2.tabular" ftype="tabular"/>
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126 <param name="xcol" value="1"/>
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127 <param name="ycol" value="2"/>
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128 <param name="type" value="line"/>
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129 <param name="lty" value="2"/>
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130 <param name="col" value="2"/>
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131 <param name="lwd" value="1.0"/>
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132 <output name="out_file_pdf" file="XY_Plot_1_out.pdf" ftype="pdf" compare="sim_size" />
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133 </test>
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134 <test><!-- test with file with header line, NA values, multiple ycols and PNG output -->
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135 <param name="main" value="Example XY Plot PNG"/>
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136 <param name="xlab" value="xlab"/>
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137 <param name="ylab" value="ylab"/>
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138 <param name="outftype" value="png"/>
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139 <param name="series_0|input" value="testinput2.tsv" ftype="tabular"/>
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140 <param name="series_0|header" value="TRUE"/>
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141 <param name="series_0|xcol" value="1"/>
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142 <param name="series_0|ycol" value="2,3"/>
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143 <param name="series_0|type" value="points"/>
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144 <param name="series_0|pch" value="1"/>
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145 <param name="series_0|col" value="2"/>
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146 <param name="series_0|cex" value="1.0"/>
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147 <output name="out_file_png" ftype="png" file="testoutput.png" compare="sim_size" />
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148 </test>
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149 </tests>
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150 <help>
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151 .. class:: infomark
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152
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153 This tool allows you to plot values contained in columns of a dataset against each other and also allows you to have different series corresponding to the same or different datasets in one plot.
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154
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155 -----
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156
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157 .. class:: warningmark
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158
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159 This tool throws an error if the columns selected for plotting are absent or are not numeric and also if the lengths of these columns differ.
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160
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161 -----
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162
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163 **Example**
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164
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165 Input file::
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166
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167 1 68 4.1
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168 2 71 4.6
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169 3 62 3.8
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170 4 75 4.4
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171 5 58 3.2
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172 6 60 3.1
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173 7 67 3.8
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174 8 68 4.1
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175 9 71 4.3
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176 10 69 3.7
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177
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178 Create a two series XY plot on the above data:
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179
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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180 - Series 1: Red Dashed-Line plot between columns 1 and 2
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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181 - Series 2: Blue Circular-Point plot between columns 3 and 2
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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182
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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183 .. image:: xy_example.jpg
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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184 </help>
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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185 <citations/>
2d28f96a309a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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186 </tool>