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comparison test-data/gff3/test.xml @ 34:6bfd32bd1000 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 78b61c12f3ee0bc7952d70e7e288d14592ce1ade
author iuc
date Tue, 15 Nov 2016 05:25:16 -0500
parents 12d5699f92e9
children d5e8d72c432a
comparison
equal deleted inserted replaced
33:3444b3f25a08 34:6bfd32bd1000
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <root> 2 <root>
3 <metadata> 3 <metadata>
4 <gencode>11</gencode> 4 <gencode>11</gencode>
5 <genomes> 5 <genomes>
6 <genome>test-data/merlin.fa</genome> 6 <genome>test-data/merlin.fa</genome>
7 </genomes> 7 </genomes>
8 <general> 8 <general>
9 <defaultLocation></defaultLocation> 9 <defaultLocation></defaultLocation>
10 <trackPadding>40</trackPadding> 10 <trackPadding>20</trackPadding>
11
11 <shareLink>true</shareLink> 12 <shareLink>true</shareLink>
12 <aboutDescription></aboutDescription> 13 <aboutDescription></aboutDescription>
13 <show_tracklist>true</show_tracklist> 14 <show_tracklist>true</show_tracklist>
14 <show_nav>true</show_nav> 15 <show_nav>true</show_nav>
15 <show_overview>false</show_overview> 16 <show_overview>true</show_overview>
16 <show_menu>true</show_menu> 17 <show_menu>true</show_menu>
17 <hideGenomeOptions>false</hideGenomeOptions> 18 <hideGenomeOptions>false</hideGenomeOptions>
18 </general> 19 </general>
19 </metadata> 20 </metadata>
20 <tracks> 21 <tracks>
21 <track cat="Auto Coloured" format="gene_calls" visibility="default_on"> 22 <track cat="Auto Coloured" format="gene_calls" visibility="default_off">
22 <files> 23 <files>
23 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/> 24 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/>
24 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/> 25 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/>
25 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/> 26 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/>
26 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/> 27 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/>
27 </files> 28 </files>
28 29
29 <options> 30 <options>
30 <style> 31 <style>
31 <className>feature</className> 32 <className>feature</className>
32 <description>feature</description> 33 <description>note,description</description>
33 <label>name,id</label> 34 <label>name,id</label>
34 <height>100px</height> 35 <height>100px</height>
35 </style> 36 </style>
36 <gff> 37 <scaling>
37 </gff> 38 <method>ignore</method>
38 <scaling> 39 <scheme>
39 <method>ignore</method> 40 <color>__auto__</color>
40 <scheme> 41 </scheme>
41 <color>__auto__</color> 42 </scaling>
42 </scheme> 43 <menus>
43 </scaling> 44 </menus>
44 </options> 45
45 </track> 46 <gff>
46 <track cat="Ignore Scale" format="gene_calls"> 47 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
47 <files> 48 <index>false</index>
48 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/> 49 </gff>
49 </files> 50 </options>
50 51 </track>
51 <options> 52 <track cat="Ignore Scale" format="gene_calls" visibility="default_off">
52 <style> 53 <files>
53 <className>feature</className> 54 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/>
54 <description>feature</description> 55 </files>
55 <label>name,id</label> 56
56 <height>100px</height> 57 <options>
57 </style> 58 <style>
58 <gff> 59 <className>feature</className>
59 </gff> 60 <description>note,description</description>
60 <scaling> 61 <label>name,id</label>
61 <method>ignore</method> 62 <height>100px</height>
62 <scheme> 63 </style>
63 <color>#ff00ff</color> 64 <scaling>
64 </scheme> 65 <method>ignore</method>
65 </scaling> 66 <scheme>
66 </options> 67 <color>#ff00ff</color>
67 </track> 68 </scheme>
68 <track cat="Scaled Colour" format="gene_calls"> 69 </scaling>
69 <files> 70 <menus>
70 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/> 71 </menus>
71 </files> 72
72 73 <gff>
73 <options> 74 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
74 <style> 75 <index>false</index>
75 <className>feature</className> 76 </gff>
76 <description>feature</description> 77 </options>
77 <label>name,id</label> 78 </track>
78 <height>100px</height> 79 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
79 </style> 80 <files>
80 <gff> 81 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/>
81 </gff> 82 </files>
82 <scaling> 83
83 <method>score</method> 84 <options>
84 <algo>linear</algo> 85 <style>
85 <scales> 86 <className>feature</className>
86 <type>__auto__</type> 87 <description>note,description</description>
87 </scales> 88 <label>name,id</label>
88 <scheme> 89 <height>100px</height>
89 <type>opacity</type> 90 </style>
90 <color>__auto__</color> 91 <scaling>
91 </scheme> 92 <method>score</method>
92 </scaling> 93 <algo>linear</algo>
93 </options> 94 <scales>
94 </track> 95 <type>automatic</type>
95 <track cat="Scaled Colour" format="gene_calls"> 96
96 <files> 97 </scales>
97 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/> 98 <scheme>
98 </files> 99 <type>opacity</type>
99 100 <color>__auto__</color>
100 <options> 101 </scheme>
101 <style> 102 </scaling>
102 <className>feature</className> 103 <menus>
103 <description>feature</description> 104 </menus>
104 <label>name,id</label> 105
105 <height>100px</height> 106 <gff>
106 </style> 107 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
107 <gff> 108 <index>false</index>
108 </gff> 109 </gff>
109 <scaling> 110 </options>
110 <method>score</method> 111 </track>
111 <algo>linear</algo> 112 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
112 <scales> 113 <files>
113 <type>__auto__</type> 114 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/>
114 </scales> 115 </files>
115 <scheme> 116
116 <type>opacity</type> 117 <options>
117 <color>#0000ff</color> 118 <style>
118 </scheme> 119 <className>feature</className>
119 </scaling> 120 <description>note,description</description>
120 </options> 121 <label>name,id</label>
121 </track> 122 <height>100px</height>
122 <track cat="Scaled Colour" format="gene_calls"> 123 </style>
123 <files> 124 <scaling>
124 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/> 125 <method>score</method>
125 </files> 126 <algo>linear</algo>
126 127 <scales>
127 <options> 128 <type>automatic</type>
128 <style> 129
129 <className>feature</className> 130 </scales>
130 <description>feature</description> 131 <scheme>
131 <label>name,id</label> 132 <type>opacity</type>
132 <height>100px</height> 133 <color>#0000ff</color>
133 </style> 134 </scheme>
134 <gff> 135 </scaling>
135 </gff> 136 <menus>
136 <scaling> 137 </menus>
137 <method>score</method> 138
138 <algo>linear</algo> 139 <gff>
139 <scales> 140 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
140 <type>manual</type> 141 <index>false</index>
141 <min>0</min> 142 </gff>
142 <max>1000</max> 143 </options>
143 </scales> 144 </track>
144 <scheme> 145 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
145 <type>opacity</type> 146 <files>
146 <color>__auto__</color> 147 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/>
147 </scheme> 148 </files>
148 </scaling> 149
149 </options> 150 <options>
150 </track> 151 <style>
151 <track cat="Scaled Colour" format="gene_calls"> 152 <className>feature</className>
152 <files> 153 <description>note,description</description>
153 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/> 154 <label>name,id</label>
154 </files> 155 <height>100px</height>
155 156 </style>
156 <options> 157 <scaling>
157 <style> 158 <method>score</method>
158 <className>feature</className> 159 <algo>linear</algo>
159 <description>feature</description> 160 <scales>
160 <label>name,id</label> 161 <type>manual</type>
161 <height>100px</height> 162
162 </style> 163 <min>0</min>
163 <gff> 164 <max>1000</max>
164 </gff> 165 </scales>
165 <scaling> 166 <scheme>
166 <method>score</method> 167 <type>opacity</type>
167 <algo>linear</algo> 168 <color>__auto__</color>
168 <scales> 169 </scheme>
169 <type>manual</type> 170 </scaling>
170 <min>0</min> 171 <menus>
171 <max>1000</max> 172 </menus>
172 </scales> 173
173 <scheme> 174 <gff>
174 <type>opacity</type> 175 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
175 <color>#ff0000</color> 176 <index>false</index>
176 </scheme> 177 </gff>
177 </scaling> 178 </options>
178 </options> 179 </track>
179 </track> 180 <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
180 181 <files>
181 182 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/>
182 <track cat="Realistic" format="gene_calls"> 183 </files>
183 <files> 184
184 <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/> 185 <options>
185 </files> 186 <style>
186 187 <className>feature</className>
187 <options> 188 <description>note,description</description>
188 <style> 189 <label>name,id</label>
189 <className>feature</className> 190 <height>100px</height>
190 <description>feature</description> 191 </style>
191 <label>name,id</label> 192 <scaling>
192 <height>100px</height> 193 <method>score</method>
193 </style> 194 <algo>linear</algo>
194 <gff> 195 <scales>
195 </gff> 196 <type>manual</type>
196 <scaling> 197
197 <method>ignore</method> 198 <min>0</min>
198 <scheme> 199 <max>1000</max>
199 <color>__auto__</color> 200 </scales>
200 </scheme> 201 <scheme>
201 </scaling> 202 <type>opacity</type>
202 </options> 203 <color>#ff0000</color>
203 </track> 204 </scheme>
204 <track cat="Realistic" format="gene_calls"> 205 </scaling>
205 <files> 206 <menus>
206 <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/> 207 </menus>
207 </files> 208
208 209 <gff>
209 <options> 210 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
210 <style> 211 <index>false</index>
211 <className>feature</className> 212 </gff>
212 <description>feature</description> 213 </options>
213 <label>name,id</label> 214 </track>
214 <height>100px</height> 215 <track cat="Realistic" format="gene_calls" visibility="default_off">
215 </style> 216 <files>
216 <gff> 217 <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>
218 </files>
219
220 <options>
221 <style>
222 <className>feature</className>
223 <description>note,description</description>
224 <label>name,id</label>
225 <height>100px</height>
226 </style>
227 <scaling>
228 <method>ignore</method>
229 <scheme>
230 <color>__auto__</color>
231 </scheme>
232 </scaling>
233 <menus>
234 </menus>
235
236 <gff>
237 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
238 <index>false</index>
239 </gff>
240 </options>
241 </track>
242 <track cat="Realistic" format="gene_calls" visibility="default_off">
243 <files>
244 <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>
245 </files>
246
247 <options>
248 <style>
249 <className>feature</className>
250 <description>note,description</description>
251 <label>name,id</label>
252 <height>100px</height>
253 </style>
254 <scaling>
255 <method>ignore</method>
256 <scheme>
257 <color>__auto__</color>
258 </scheme>
259 </scaling>
260 <menus>
261 </menus>
262
263 <gff>
264 <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
217 <match>cDNA_match</match> 265 <match>cDNA_match</match>
218 </gff> 266 <index>false</index>
219 <scaling> 267 </gff>
220 <method>ignore</method>
221 <scheme>
222 <type>opacity</type>
223 <color>__auto__</color>
224 </scheme>
225 </scaling>
226 </options> 268 </options>
227 </track> 269 </track>
228 </tracks> 270 </tracks>
229 </root> 271 </root>