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comparison test-data/gff3/test.xml @ 3:7342f467507b draft

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Uploaded v0.4 of JBrowse
author iuc
date Thu, 31 Dec 2015 13:58:43 -0500
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children ae9382cfb6ac
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2:b6a0e126dbee 3:7342f467507b
1 <?xml version="1.0"?>
2 <root>
3 <metadata>
4 <gencode>11</gencode>
5 <genomes>
6 <genome>test-data/merlin.fa</genome>
7 </genomes>
8 </metadata>
9 <tracks>
10 <track cat="Auto Coloured" format="gene_calls">
11 <files>
12 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/>
13 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/>
14 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/>
15 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/>
16 </files>
17
18 <options>
19 <style>
20 <className>feature</className>
21 <description>feature</description>
22 <label>name,id</label>
23 <height>100px</height>
24 </style>
25 <gff>
26 </gff>
27 <scaling>
28 <method>ignore</method>
29 <scheme>
30 <color>__auto__</color>
31 </scheme>
32 </scaling>
33 </options>
34 </track>
35 <track cat="Ignore Scale" format="gene_calls">
36 <files>
37 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/>
38 </files>
39
40 <options>
41 <style>
42 <className>feature</className>
43 <description>feature</description>
44 <label>name,id</label>
45 <height>100px</height>
46 </style>
47 <gff>
48 </gff>
49 <scaling>
50 <method>ignore</method>
51 <scheme>
52 <color>#ff00ff</color>
53 </scheme>
54 </scaling>
55 </options>
56 </track>
57 <track cat="Scaled Colour" format="gene_calls">
58 <files>
59 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/>
60 </files>
61
62 <options>
63 <style>
64 <className>feature</className>
65 <description>feature</description>
66 <label>name,id</label>
67 <height>100px</height>
68 </style>
69 <gff>
70 </gff>
71 <scaling>
72 <method>score</method>
73 <algo>linear</algo>
74 <scales>
75 <type>__auto__</type>
76 </scales>
77 <scheme>
78 <type>opacity</type>
79 <color>__auto__</color>
80 </scheme>
81 </scaling>
82 </options>
83 </track>
84 <track cat="Scaled Colour" format="gene_calls">
85 <files>
86 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/>
87 </files>
88
89 <options>
90 <style>
91 <className>feature</className>
92 <description>feature</description>
93 <label>name,id</label>
94 <height>100px</height>
95 </style>
96 <gff>
97 </gff>
98 <scaling>
99 <method>score</method>
100 <algo>linear</algo>
101 <scales>
102 <type>__auto__</type>
103 </scales>
104 <scheme>
105 <type>opacity</type>
106 <color>#0000ff</color>
107 </scheme>
108 </scaling>
109 </options>
110 </track>
111 <track cat="Scaled Colour" format="gene_calls">
112 <files>
113 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/>
114 </files>
115
116 <options>
117 <style>
118 <className>feature</className>
119 <description>feature</description>
120 <label>name,id</label>
121 <height>100px</height>
122 </style>
123 <gff>
124 </gff>
125 <scaling>
126 <method>score</method>
127 <algo>linear</algo>
128 <scales>
129 <type>manual</type>
130 <min>0</min>
131 <max>1000</max>
132 </scales>
133 <scheme>
134 <type>opacity</type>
135 <color>__auto__</color>
136 </scheme>
137 </scaling>
138 </options>
139 </track>
140 <track cat="Scaled Colour" format="gene_calls">
141 <files>
142 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/>
143 </files>
144
145 <options>
146 <style>
147 <className>feature</className>
148 <description>feature</description>
149 <label>name,id</label>
150 <height>100px</height>
151 </style>
152 <gff>
153 </gff>
154 <scaling>
155 <method>score</method>
156 <algo>linear</algo>
157 <scales>
158 <type>manual</type>
159 <min>0</min>
160 <max>1000</max>
161 </scales>
162 <scheme>
163 <type>opacity</type>
164 <color>#ff0000</color>
165 </scheme>
166 </scaling>
167 </options>
168 </track>
169
170
171 <track cat="Realistic" format="gene_calls">
172 <files>
173 <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>
174 </files>
175
176 <options>
177 <style>
178 <className>feature</className>
179 <description>feature</description>
180 <label>name,id</label>
181 <height>100px</height>
182 </style>
183 <gff>
184 </gff>
185 <scaling>
186 <method>ignore</method>
187 <scheme>
188 <color>__auto__</color>
189 </scheme>
190 </scaling>
191 </options>
192 </track>
193 <track cat="Realistic" format="gene_calls">
194 <files>
195 <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>
196 </files>
197
198 <options>
199 <style>
200 <className>feature</className>
201 <description>feature</description>
202 <label>name,id</label>
203 <height>100px</height>
204 </style>
205 <gff>
206 <match>cDNA_match</match>
207 </gff>
208 <scaling>
209 <method>ignore</method>
210 <scheme>
211 <type>opacity</type>
212 <color>__auto__</color>
213 </scheme>
214 </scaling>
215 </options>
216 </track>
217 </tracks>
218 </root>