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1 <tool id="nwdisplay" name="Newick Display" version="1.6">
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2 <description>Display a phylogenetic tree as SVG</description>
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3 <edam_operations>
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4 <edam_operation>operation_0567</edam_operation>
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5 </edam_operations>
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6 <requirements>
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7 <requirement type="package" version="1.6">newick_utils</requirement>
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8 </requirements>
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9 <command>
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10 nw_display
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11 -s
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12 $scalebar
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13 -u "$legend"
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14 -I 'r'
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15 -i
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16 #if $condbranchsupport.branchsupport == "true":
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17 "fill:$condbranchsupport.supcolor;
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18 font-size:$condbranchsupport.supfontsize;
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19 transform:$condbranchsupport.suptransform;"
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20 #else:
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21 "visibility:hidden;"
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22 #end if
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23 -b
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24 #if $condbranchlength.branchlength == "true":
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25 "fill:$condbranchlength.lencolor;
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26 font-size:$condbranchlength.lenfontsize;
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27 transform:$condbranchlength.lentransform;"
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28 #else:
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29 "visibility:hidden;"
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30 #end if
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31
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32 -l "font-family:$leafFont;font-size:$leafSize;"
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33 -d "stroke:grey;fill:none;stroke-width:2;stoke-linecap:round;"
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34 -w $width
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35 $radial
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36
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37 $fileNewick > $output
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38
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39 </command>
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40 <inputs>
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41 <param name="fileNewick" format="txt,nw,nwk,nhx" type="data" label="Newick file" />
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42 <param name="scalebar" type="boolean" truevalue="" falsevalue="-S" checked="True" label="Display scale bar" />
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43 <param name="legend" type="text" value="" label="Unit name scale" />
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44 <param name="leafFont" type="text" value="sans-serif" label="Leaf font" />
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45 <param name="leafSize" type="text" value="10px" label="Leaf font-size" />
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46 <conditional name="condbranchsupport">
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47 <param name="branchsupport" type="select" label="Branch support">
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48 <option value="true">Display branch support</option>
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49 <option value="false" selected="true">Hide branch support</option>
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50 </param>
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51 <when value="true">
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52 <param name="supcolor" type="color" value="red" label="color" />
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53 <param name="supfontsize" type="text" value="10px" label="font-size" />
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54 <param name="suptransform" type="text" value="translateY(1.5em)" label="move" />
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55 </when>
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56 <when value="false" />
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57 </conditional>
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58 <conditional name="condbranchlength">
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59 <param name="branchlength" type="select" label="Branch length">
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60 <option value="true">Display branch length</option>
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61 <option value="false" selected="true">Hide branch length</option>
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62 </param>
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63 <when value="true">
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64 <param name="lencolor" type="color" value="blue" label="color" />
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65 <param name="lenfontsize" type="text" value="10px" label="font-size" />
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66 <param name="lentransform" type="text" value="translate(-1.5em,0em)" label="move" />
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67 </when>
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68 <when value="false" />
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69 </conditional>
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70 <param name="width" type="integer" value="800" label="SVG Tree width (px)" />
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71 <param name="radial" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Draw a radial tree" />
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72 </inputs>
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73 <outputs>
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74 <data name="output" format="svg" label="${fileNewick.name}.svg" />
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75 </outputs>
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76 <tests>
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77 <test>
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78 <param name="fileNewick" value="tree.nwk"/>
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79 <param name="width" value="400"/>
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80 <param name="leafFont" value="courier"/>
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81 <output name="output" file="tree.svg" lines_diff="2"/>
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82 </test>
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83 <test>
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84 <param name="fileNewick" value="tree.nwk"/>
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85 <param name="radial" value="-r"/>
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86 <param name="branchlength" value="true"/>
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87 <output name="output" file="tree2.svg" lines_diff="2"/>
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88 </test>
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89 </tests>
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90 <help>
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91 <![CDATA[
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92 **Displays a tree as a graph, as text or SVG.**
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93
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94
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95 Synopsis
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96 --------
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97
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98 nw_display [options] <tree filename|->
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99
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100 Input
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101 -----
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102
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103 Argument is the name of the file containing one or more trees,
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104 or '-' (in which case the tree is read on stdin).
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105
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106 Output
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107 ------
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108
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109 Outputs a graph representing the tree, either as text (default) or
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110 as SVG (option -s). Underscores in labels are replaced with spaces.
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111 Trees with no branch lengths are taken to be cladograms and are
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112 drawn with leaves aligned. Otherwise, the tree is assumed to be a
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113 phylogram: branch lengths are honored and a scale bar is drawn.
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114
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115 SVG graphics can be converted to other formats with converters
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116 such as Inkscape (e.g. to PDF) or ImageMagick (e.g. to PNG or JPEG).
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117 Inkscape is available from www.inkscape.org and ImageMagick from
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118 www.imagemagick.org.
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119
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120 Options
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121 -------
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122
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123 -a <number>: rotate all labels by this amount (radians, default: 0)
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124 [only SVG radial]
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125 -A <number>: rotate left-side labels by this amount (radians,
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126 default: 0.0349 (=~ 2°)) [only SVG radial]
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127 -b <string>: CSS for branch length labels. [only SVG]
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128 Default: 'font-size:small;font-family:sans'.
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129 setting 'opacity:0' disables printing of branch lengths.
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130 -c <filename>: use specified file as CSS map [only SVG]. A CSS map
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131 is a text file which specifies a style (CSS) for a clade.
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132 Each line has the following structure:
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133 <CSS> <flag> <label>+
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134 <CSS> is a valid CSS style specification (no spaces allowed)
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135 e.g. 'font-size:small;font-family:italics;stroke:green'.
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136 <flag> is either 'Individual' or 'Clade' (case is not important, can
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137 be abbreviated down to 'I' or 'C'). If set to 'Clade', the style is
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138 applied to the clade defined by the labels. If 'Individual', the
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139 style is applied to each node individually.
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140 <label>+ is a nonempty, whitespace-separated list of Newick labels
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141 (spaces are allowed IFF the label is enclosed in ''). If a label
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142 matches more than one node, all matching nodes are used.
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143 Default: no CSS map, whole tree is black (unless specified otherwise
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144 via option -d).
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145 <CSS>, <flag>, and <labels>+ are separated by whitespace.
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146 The following specifies red stroke for a clade defined by A, B and C;
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147 and 2-pixel wide, blue stroke for individual nodes D, E, and F:
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148 stroke:red Clade A B C
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149 stroke:blue;stroke-width:2 I D E F
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150 If no colormap is specified, the default is (but see option -d):
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151 stroke:black;fill:none;stroke-width:1;stroke-linecap:round
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152 -d <string>: CSS for 'plain' tree nodes (i.e., unless overridden by -c)
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153 [only SVG]
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154 Default: stroke:black;fill:none;stroke-width:1;stroke-linecap:round
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155
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156 -h: prints this message and exits
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157
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158 -i <string>: CSS for inner node labels. [only SVG]
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159 Default: 'font-size:small;font-family:sans'.
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160
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161 setting 'visibility:hidden' disables printing of inner node labels.
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162 -I <char> sets the position of the inner node label. Valid options are
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163 'l' (near the leaves), 'm' (middle) or 'r' (near the root). Default
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164 is 'l'.
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165
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166 -l <string>: CSS for leaf node labels. [only SVG]
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167 Default: 'font-size:medium;font-family:sans'.
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168 setting 'visibility:hidden' disables printing of leaf node labels.
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169 Note: if you change this, you will probably need to adjust the
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170 space allocated to leaf labels - see option -W.
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171 -n <number> add this number of pixels to the horizontal position of
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172 node labels. [SVG only]
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173
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174 -o <filename>: use specified file as ornament map. Works like the CSS
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175 map (see option -c), except that it specifies arbitrary SVG snippets
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176 instead of CSS styles. For example, the following
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177 "<circle style='fill:red' r='5'>" Clade A B C
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178 will draw a red circle of radius 5 at the root of the clade defined
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179 by nodes A, B, and C. Keyword 'Individual' is also accepted and
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180 works like for CSS.
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181
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182 -R <integer>: use that many pixels for the root [only SVG]
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183
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184 -r: draw a radial tree (default: orthogonal) [only SVG]
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185
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186 -s: output graph as SVG (default: ASCII graphics). All output is on
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187 stdout, so if there is more than one tree, stdout will be a
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188 concatenation of SVG documents. These can be split into individual
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189 files with the csplit(1) command:
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190
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191 $ nw_display -s many_trees.nw > multiple_svg
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192 $ csplit -zs -f tree\_ -b '%02d.svg' multiple_svg '/<?xml/' {*}
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193
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194 will generate as many SVG files as there are Newick trees in
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195 many_trees.nw. The files will be named tree_01.svg, tree_02.svg, etc.
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196
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197 -S: suppress scale bar (ignored for cladograms)
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198
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199 -t: set the zero of the scale at the maximum depth instead of the root.
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200 This is useful when the branch lengths are in time units: zero marks
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201 the present, and the scale shows the age of the ancestral nodes.
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202 -u <string>: string is used as unit name for scale bar (ignored
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203 if no scale bar is drawn).
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204 -U <URL_filename>: use specified URL map [only SVG]. A URL map
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205 is a text file which specifies a URL for a label.
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206 Each line has the following structure:
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207 <label> <URL>
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208 Clicking on a label will follow the link (if any).
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209 -v <number>: number of pixels between leaves (default: 40) [only SVG
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210 orthogonal]
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211 -w <number>: graph should be no wider than <number>, measured in
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212 characters for text and pixels for SVG. Defaults: 80 (text),
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213 300 (SVG)
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214 -W <number>: use this as an estimate of the width of a leaf label
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215 character (in pixels) [only SVG]. This affects the space left for
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216 the tree nodes. Default: 5.0 You will probably need this if you
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217 change the leaf label font properties (option -l), especially size.
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218 You will probably need trial and error to find the right value.
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219
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220 LibXML
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221 ......
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222
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223 If LibXML is being used, the handling of ornaments (-o) is more elaborate.
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224 See the tutorial, section 2.2 (displaying) for details.
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225 This executable uses LibXML2.
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226
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227 Examples
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228 --------
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229
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230 # display tree as ASCII::
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231
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232 $ nw_display data/catarrhini
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233
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234 # display tree as SVG, using a color map::
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235
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236 $ nw_display -s -c data/color.map data/catarrhini
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237
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238 # ditto, convert to other graphics formats::
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239
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240 $ nw_display -s -c data/color.map data/catarrhini > catarrhini.svg
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241 $ convert catarrhini.svg catarrhini.png # PNG, with ImageMagick
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242 $ convert catarrhini.svg catarrhini.jpeg # JPEG, with ImageMagick
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243 $ inkscape -z -f catarrhini.svg -A catarrhini.pdf # PDF, with Inkscape
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244
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245 # the same; no branch lengths::
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246
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247 $ nw_display -s -b 'visibility:hidden' -c data/color.map data/catarrhini
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248
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249 # radial tree, leaf labels in italics::
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250
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251 $ nw_display -s -r -l 'font-style:italics' data/catarrhini
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252
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253 ]]>
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254 </help>
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255 <citations>
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256 <citation type="doi">10.1186/1748-7188-3-7</citation>
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257 </citations>
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258 </tool>
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