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1 <tool id="XY_Plot_1_multiformat" name="Plotting tool" version="1.0.1">
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2 <description>for multiple series and graph types and multiple output types</description>
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3 <requirements>
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4 <requirement type="package" version="3.2.1">R</requirement>
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5 <requirement type="package" version="2.11.1">fontconfig</requirement>
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6 </requirements>
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7 <command interpreter="bash">r_wrapper.sh $script_file</command>
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8
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9 <inputs>
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10 <param name="main" type="text" value="" label="Plot Title"/>
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11 <param name="xlab" type="text" value="" label="Label for x axis"/>
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12 <param name="ylab" type="text" value="" label="Label for y axis"/>
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13 <param name="ftype" type="select" label="File Type">
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14 <option value="pdf">PDF</option>
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15 <option value="png">PNG</option>
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16 <option value="jpeg">JPEG</option>
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17 <option value="bmp">BMP</option>
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18 <option value="tiff">TIFF</option>
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19 </param>
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20 <repeat name="series" title="Series">
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21 <param name="input" type="data" format="tabular" label="Dataset"/>
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22 <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/>
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23 <param name="ycol" type="data_column" data_ref="input" label="Column for y axis"/>
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24 <conditional name="series_type">
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25 <param name="type" type="select" label="Series Type">
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26 <option value="line" selected="true">Line</option>
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27 <option value="points">Points</option>
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28 </param>
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29 <when value="line">
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30 <param name="lty" type="select" label="Line Type">
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31 <option value="1">Solid</option>
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32 <option value="2">Dashed</option>
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33 <option value="3">Dotted</option>
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34 </param>
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35 <param name="col" type="select" label="Line Color">
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36 <option value="1">Black</option>
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37 <option value="2">Red</option>
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38 <option value="3">Green</option>
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39 <option value="4">Blue</option>
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40 <option value="5">Cyan</option>
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41 <option value="6">Magenta</option>
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42 <option value="7">Yellow</option>
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43 <option value="8">Gray</option>
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44 </param>
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45 <param name="lwd" type="float" label="Line Width" value="1.0"/>
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46 </when>
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47 <when value="points">
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48 <param name="pch" type="select" label="Point Type">
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49 <option value="1">Circle (hollow)</option>
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50 <option value="2">Triangle (hollow)</option>
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51 <option value="3">Cross</option>
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52 <option value="4">Diamond (hollow)</option>
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53 <option value="15">Square (filled)</option>
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54 <option value="16">Circle (filled)</option>
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55 <option value="17">Triangle (filled)</option>
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56 </param>
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57 <param name="col" type="select" label="Point Color">
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58 <option value="1">Black</option>
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59 <option value="2">Red</option>
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60 <option value="3">Green</option>
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61 <option value="4">Blue</option>
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62 <option value="5">Cyan</option>
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63 <option value="6">Magenta</option>
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64 <option value="7">Yellow</option>
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65 <option value="8">Gray</option>
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66 </param>
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67 <param name="cex" type="float" label="Point Scale" value="1.0"/>
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68 </when>
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69 </conditional>
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70 </repeat>
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71 </inputs>
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72
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73 <configfiles>
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74 <configfile name="script_file">
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75 ## Setup R error handling to go to stderr
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76 options( show.error.messages=F,
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77 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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78 ## Determine range of all series in the plot
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79 xrange = c( NULL, NULL )
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80 yrange = c( NULL, NULL )
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81 #for $i, $s in enumerate( $series )
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82 s${i} = read.table( "${s.input.file_name}" )
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83 x${i} = s${i}[,${s.xcol}]
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84 y${i} = s${i}[,${s.ycol}]
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85 xrange = range( x${i}, xrange )
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86 yrange = range( y${i}, yrange )
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87 #end for
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88 ## Open output PDF file
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89 #if $ftype.value == "pdf"
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90 pdf("outfile.pdf")
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91 #else
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92 "${ftype}"( "outfile.${ftype}" , type="cairo")
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93 #end if
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94 ## Dummy plot for axis / labels
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95 plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" )
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96 ## Plot each series
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97 #for $i, $s in enumerate( $series )
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98 #if $s.series_type['type'] == "line"
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99 lines( x${i}, y${i}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col} )
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100 #elif $s.series_type.type == "points"
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101 points( x${i}, y${i}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col} )
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102 #end if
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103 #end for
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104 ## Close the PDF file
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105 devname = dev.off()
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106 </configfile>
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107 </configfiles>
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108
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109 <outputs>
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110 <data format="pdf" name="out_file1" from_work_dir="outfile.pdf" >
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111 <filter>(ftype == 'pdf') </filter>
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112 </data>
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113 <data format="png" name="out_file2" from_work_dir="outfile.png">
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114 <filter>(ftype == 'png') </filter>
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115 </data>
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116 <data format="jpg" name="out_file3" from_work_dir="outfile.jpeg">
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117 <filter>(ftype == 'jpeg') </filter>
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118 </data>
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119 <data format="bmp" name="out_file4" from_work_dir="outfile.bmp">
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120 <filter>(ftype == 'bmp') </filter>
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121 </data>
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122 <data format="tiff" name="out_file5" from_work_dir="outfile.tiff">
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123 <filter>(ftype == 'tiff') </filter>
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124 </data>
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125 </outputs>
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126
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127 <tests>
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128 <test>
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129 <param name="main" value="Example XY Plot PDF"/>
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130 <param name="xlab" value="Column 1"/>
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131 <param name="ylab" value="Column 2"/>
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132 <param name="ftype" value="pdf"/>
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133 <param name="input" value="2.tabular" ftype="tabular"/>
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134 <param name="xcol" value="1"/>
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135 <param name="ycol" value="2"/>
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136 <param name="type" value="line"/>
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137 <param name="lty" value="2"/>
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138 <param name="col" value="2"/>
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139 <param name="lwd" value="1.0"/>
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140 <output name="out_file1" file="XY_Plot_1_multi_out.pdf" format="pdf" />
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141 </test>
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142 <test>
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143 <param name="main" value="Example XY Plot PNG"/>
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144 <param name="xlab" value="Column 1"/>
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145 <param name="ylab" value="Column 2"/>
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146 <param name="ftype" value="png"/>
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147 <param name="input" value="2.tabular" ftype="tabular"/>
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148 <param name="xcol" value="1"/>
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149 <param name="ycol" value="2"/>
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150 <param name="type" value="line"/>
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151 <param name="lty" value="2"/>
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152 <param name="col" value="2"/>
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153 <param name="lwd" value="1.0"/>
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154 <output name="out_file2" md5="c2762c725f80fe4419e35768cac5d11b" />
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155 </test>
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156 <test>
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157 <param name="main" value="Example XY Plot JPEG"/>
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158 <param name="xlab" value="Column 1"/>
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159 <param name="ylab" value="Column 2"/>
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160 <param name="ftype" value="jpeg"/>
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161 <param name="input" value="2.tabular" ftype="tabular"/>
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162 <param name="xcol" value="1"/>
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163 <param name="ycol" value="2"/>
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164 <param name="type" value="line"/>
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165 <param name="lty" value="2"/>
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166 <param name="col" value="2"/>
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167 <param name="lwd" value="1.0"/>
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168 <output name="out_file3" md5="5c89f4e87bb5f2a809877b471f9c2d69" />
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169 </test>
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170 <test>
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171 <param name="main" value="Example XY Plot BMP"/>
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172 <param name="xlab" value="Column 1"/>
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173 <param name="ylab" value="Column 2"/>
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174 <param name="ftype" value="bmp"/>
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175 <param name="input" value="2.tabular" ftype="tabular"/>
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176 <param name="xcol" value="1"/>
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177 <param name="ycol" value="2"/>
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178 <param name="type" value="line"/>
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179 <param name="lty" value="2"/>
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180 <param name="col" value="2"/>
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181 <param name="lwd" value="1.0"/>
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182 <output name="out_file4" md5="74ea4b29bd7de44c1b6377c6c26671e7"/>
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183 </test>
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184 <test>
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185 <param name="main" value="Example XY Plot TIFF"/>
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186 <param name="xlab" value="Column 1"/>
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187 <param name="ylab" value="Column 2"/>
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188 <param name="ftype" value="tiff"/>
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189 <param name="input" value="2.tabular" ftype="tabular"/>
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190 <param name="xcol" value="1"/>
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191 <param name="ycol" value="2"/>
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192 <param name="type" value="line"/>
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193 <param name="lty" value="2"/>
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194 <param name="col" value="2"/>
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195 <param name="lwd" value="1.0"/>
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196 <output name="out_file5" md5="7ebf7d201ad9cdf0fc6995639749ae7d"/>
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197 </test>
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198 </tests>
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199 <help>
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200 .. class:: infomark
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201
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202 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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203
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204 -----
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205
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206 .. class:: warningmark
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207
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208 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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209
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210 -----
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211
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212 **Example**
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213
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214 Input file::
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215
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216 1 68 4.1
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217 2 71 4.6
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218 3 62 3.8
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219 4 75 4.4
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220 5 58 3.2
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221 6 60 3.1
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222 7 67 3.8
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223 8 68 4.1
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224 9 71 4.3
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225 10 69 3.7
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226
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227 Create a two series XY plot on the above data:
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228
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229 - Series 1: Red Dashed-Line plot between columns 1 and 2
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230 - Series 2: Blue Circular-Point plot between columns 3 and 2
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231
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232 .. image:: xy_example.jpg
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233 </help>
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234 </tool>
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