Mercurial > repos > iuc > jbrowse

annotate test-data/gff3/test.xml @ 8:ad4b9d7eae6a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
author iuc
date Tue, 29 Nov 2016 10:55:30 -0500
parents ae9382cfb6ac
children ff11d442feed
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1 <?xml version="1.0"?>
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2 <root>
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3 <metadata>
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4 <gencode>11</gencode>
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5 <genomes>
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6 <genome>test-data/merlin.fa</genome>
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7 </genomes>
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8 <general>
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9 <defaultLocation></defaultLocation>
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10 <trackPadding>20</trackPadding>
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11
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12 <shareLink>true</shareLink>
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13 <aboutDescription></aboutDescription>
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14 <show_tracklist>true</show_tracklist>
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15 <show_nav>true</show_nav>
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16 <show_overview>true</show_overview>
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17 <show_menu>true</show_menu>
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18 <hideGenomeOptions>false</hideGenomeOptions>
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19 </general>
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20 </metadata>
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21 <tracks>
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22 <track cat="Auto Coloured" format="gene_calls" visibility="default_off">
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23 <files>
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24 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/>
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25 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/>
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26 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/>
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27 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/>
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28 </files>
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29
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30 <options>
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31 <style>
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32 <className>feature</className>
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33 <description>note,description</description>
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34 <label>name,id</label>
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35 <height>100px</height>
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36 </style>
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37 <scaling>
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38 <method>ignore</method>
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39 <scheme>
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40 <color>__auto__</color>
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41 </scheme>
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42 </scaling>
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43 <menus>
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44 </menus>
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45
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46 <gff>
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47 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
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48 <index>false</index>
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49 </gff>
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50 </options>
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51 </track>
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52 <track cat="Ignore Scale" format="gene_calls" visibility="default_off">
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53 <files>
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54 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/>
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55 </files>
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57 <options>
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58 <style>
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59 <className>feature</className>
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60 <description>note,description</description>
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61 <label>name,id</label>
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62 <height>100px</height>
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63 </style>
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64 <scaling>
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65 <method>ignore</method>
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66 <scheme>
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67 <color>#ff00ff</color>
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68 </scheme>
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69 </scaling>
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70 <menus>
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71 </menus>
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73 <gff>
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74 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
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75 <index>false</index>
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76 </gff>
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77 </options>
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78 </track>
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79 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
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80 <files>
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81 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/>
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82 </files>
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84 <options>
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85 <style>
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86 <className>feature</className>
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87 <description>note,description</description>
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88 <label>name,id</label>
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89 <height>100px</height>
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90 </style>
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91 <scaling>
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92 <method>score</method>
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93 <algo>linear</algo>
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94 <scales>
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95 <type>automatic</type>
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97 </scales>
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98 <scheme>
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99 <type>opacity</type>
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100 <color>__auto__</color>
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101 </scheme>
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102 </scaling>
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103 <menus>
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104 </menus>
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106 <gff>
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107 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
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108 <index>false</index>
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109 </gff>
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110 </options>
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111 </track>
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112 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
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parents:
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113 <files>
8
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parents: 5
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114 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/>
3
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115 </files>
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iuc
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116
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iuc
parents:
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117 <options>
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iuc
parents:
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118 <style>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
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119 <className>feature</className>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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120 <description>note,description</description>
3
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iuc
parents:
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121 <label>name,id</label>
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iuc
parents:
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122 <height>100px</height>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
123 </style>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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124 <scaling>
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iuc
parents: 5
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125 <method>score</method>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
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126 <algo>linear</algo>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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127 <scales>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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128 <type>automatic</type>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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129
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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130 </scales>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
131 <scheme>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
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132 <type>opacity</type>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
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133 <color>#0000ff</color>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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134 </scheme>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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135 </scaling>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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136 <menus>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
137 </menus>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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138
3
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139 <gff>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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140 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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141 <index>false</index>
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parents:
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142 </gff>
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parents:
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143 </options>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
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144 </track>
8
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parents: 5
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145 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
3
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parents:
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146 <files>
8
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parents: 5
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147 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/>
3
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148 </files>
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iuc
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149
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parents:
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150 <options>
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iuc
parents:
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151 <style>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
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152 <className>feature</className>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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153 <description>note,description</description>
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iuc
parents:
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154 <label>name,id</label>
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iuc
parents:
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155 <height>100px</height>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
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156 </style>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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157 <scaling>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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158 <method>score</method>
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parents: 5
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159 <algo>linear</algo>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
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160 <scales>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
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161 <type>manual</type>
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parents: 5
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162
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
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163 <min>0</min>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
164 <max>1000</max>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
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165 </scales>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
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166 <scheme>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
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167 <type>opacity</type>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
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168 <color>__auto__</color>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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169 </scheme>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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170 </scaling>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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171 <menus>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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172 </menus>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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173
3
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174 <gff>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
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175 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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176 <index>false</index>
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parents:
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177 </gff>
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parents:
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178 </options>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
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179 </track>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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180 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
3
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parents:
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181 <files>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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182 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/>
3
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183 </files>
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parents:
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184
7342f467507b Uploaded v0.4 of JBrowse
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parents:
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185 <options>
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iuc
parents:
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186 <style>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
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187 <className>feature</className>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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188 <description>note,description</description>
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iuc
parents:
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189 <label>name,id</label>
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iuc
parents:
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190 <height>100px</height>
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iuc
parents:
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191 </style>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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192 <scaling>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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193 <method>score</method>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
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194 <algo>linear</algo>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
195 <scales>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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196 <type>manual</type>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
197
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
198 <min>0</min>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
199 <max>1000</max>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
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200 </scales>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
201 <scheme>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
202 <type>opacity</type>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
203 <color>#ff0000</color>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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204 </scheme>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
205 </scaling>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
206 <menus>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
207 </menus>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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208
3
7342f467507b Uploaded v0.4 of JBrowse
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parents:
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209 <gff>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
210 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
211 <index>false</index>
3
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iuc
parents:
diff changeset
212 </gff>
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iuc
parents:
diff changeset
213 </options>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
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214 </track>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
215 <track cat="Realistic" format="gene_calls" visibility="default_off">
3
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parents:
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216 <files>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
217 <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>
3
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parents:
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218 </files>
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iuc
parents:
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219
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
220 <options>
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iuc
parents:
diff changeset
221 <style>
7342f467507b Uploaded v0.4 of JBrowse
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parents:
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222 <className>feature</className>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
223 <description>note,description</description>
3
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iuc
parents:
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224 <label>name,id</label>
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iuc
parents:
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225 <height>100px</height>
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iuc
parents:
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226 </style>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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227 <scaling>
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228 <method>ignore</method>
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229 <scheme>
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230 <color>__auto__</color>
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231 </scheme>
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232 </scaling>
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233 <menus>
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234 </menus>
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235
3
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236 <gff>
8
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237 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
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238 <index>false</index>
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239 </gff>
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240 </options>
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241 </track>
8
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242 <track cat="Realistic" format="gene_calls" visibility="default_off">
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243 <files>
8
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244 <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>
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245 </files>
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246
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247 <options>
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248 <style>
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249 <className>feature</className>
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250 <description>note,description</description>
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251 <label>name,id</label>
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252 <height>100px</height>
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253 </style>
8
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254 <scaling>
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255 <method>ignore</method>
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256 <scheme>
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257 <color>__auto__</color>
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258 </scheme>
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259 </scaling>
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260 <menus>
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261 </menus>
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262
3
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263 <gff>
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264 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
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265 <match>cDNA_match</match>
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266 <index>false</index>
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267 </gff>
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268 </options>
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269 </track>
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270 </tracks>
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271 </root>