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comparison test-data/gff3/test.xml @ 40:d5e8d72c432a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 7be399c9ee10ecd4b076cc1df775f585c3eb0eeb
author iuc
date Wed, 01 Mar 2017 23:06:18 -0500
parents 6bfd32bd1000
children c1451868f8d4
comparison
equal deleted inserted replaced
39:e62d1a610b2c 40:d5e8d72c432a
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>20</trackPadding> 10 <trackPadding>40</trackPadding>
11
12 <shareLink>true</shareLink> 11 <shareLink>true</shareLink>
13 <aboutDescription></aboutDescription> 12 <aboutDescription></aboutDescription>
14 <show_tracklist>true</show_tracklist> 13 <show_tracklist>true</show_tracklist>
15 <show_nav>true</show_nav> 14 <show_nav>true</show_nav>
16 <show_overview>true</show_overview> 15 <show_overview>false</show_overview>
17 <show_menu>true</show_menu> 16 <show_menu>true</show_menu>
18 <hideGenomeOptions>false</hideGenomeOptions> 17 <hideGenomeOptions>false</hideGenomeOptions>
19 </general> 18 </general>
20 </metadata> 19 </metadata>
21 <tracks> 20 <tracks>
22 <track cat="Auto Coloured" format="gene_calls" visibility="default_off"> 21 <track cat="#date# / Auto Coloured" format="gene_calls" visibility="default_on">
23 <files> 22 <files>
24 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/> 23 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/>
25 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/> 24 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/>
26 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/> 25 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/>
27 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/> 26 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/>
28 </files> 27 </files>
29 28
30 <options> 29 <options>
31 <style> 30 <style>
32 <className>feature</className> 31 <className>feature</className>
33 <description>note,description</description> 32 <description>feature</description>
34 <label>name,id</label> 33 <label>name,id</label>
35 <height>100px</height> 34 <height>100px</height>
36 </style> 35 </style>
37 <scaling> 36 <gff>
38 <method>ignore</method> 37 </gff>
39 <scheme> 38 <scaling>
40 <color>__auto__</color> 39 <method>ignore</method>
41 </scheme> 40 <scheme>
42 </scaling> 41 <color>__auto__</color>
43 <menus> 42 </scheme>
44 </menus> 43 </scaling>
45 44 </options>
46 <gff> 45 </track>
47 <trackType>JBrowse/View/Track/CanvasFeatures</trackType> 46 <track cat="Ignore Scale" format="gene_calls">
48 <index>false</index> 47 <files>
49 </gff> 48 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/>
50 </options> 49 </files>
51 </track> 50
52 <track cat="Ignore Scale" format="gene_calls" visibility="default_off"> 51 <options>
53 <files> 52 <style>
54 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/> 53 <className>feature</className>
55 </files> 54 <description>feature</description>
56 55 <label>name,id</label>
57 <options> 56 <height>100px</height>
58 <style> 57 </style>
59 <className>feature</className> 58 <gff>
60 <description>note,description</description> 59 </gff>
61 <label>name,id</label> 60 <scaling>
62 <height>100px</height> 61 <method>ignore</method>
63 </style> 62 <scheme>
64 <scaling> 63 <color>#ff00ff</color>
65 <method>ignore</method> 64 </scheme>
66 <scheme> 65 </scaling>
67 <color>#ff00ff</color> 66 </options>
68 </scheme> 67 </track>
69 </scaling> 68 <track cat="Scaled Colour" format="gene_calls">
70 <menus> 69 <files>
71 </menus> 70 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/>
72 71 </files>
73 <gff> 72
74 <trackType>JBrowse/View/Track/CanvasFeatures</trackType> 73 <options>
75 <index>false</index> 74 <style>
76 </gff> 75 <className>feature</className>
77 </options> 76 <description>feature</description>
78 </track> 77 <label>name,id</label>
79 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 78 <height>100px</height>
80 <files> 79 </style>
81 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/> 80 <gff>
82 </files> 81 </gff>
83 82 <scaling>
84 <options> 83 <method>score</method>
85 <style> 84 <algo>linear</algo>
86 <className>feature</className> 85 <scales>
87 <description>note,description</description> 86 <type>__auto__</type>
88 <label>name,id</label> 87 </scales>
89 <height>100px</height> 88 <scheme>
90 </style> 89 <type>opacity</type>
91 <scaling> 90 <color>__auto__</color>
92 <method>score</method> 91 </scheme>
93 <algo>linear</algo> 92 </scaling>
94 <scales> 93 </options>
95 <type>automatic</type> 94 </track>
96 95 <track cat="Scaled Colour" format="gene_calls">
97 </scales> 96 <files>
98 <scheme> 97 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/>
99 <type>opacity</type> 98 </files>
100 <color>__auto__</color> 99
101 </scheme> 100 <options>
102 </scaling> 101 <style>
103 <menus> 102 <className>feature</className>
104 </menus> 103 <description>feature</description>
105 104 <label>name,id</label>
106 <gff> 105 <height>100px</height>
107 <trackType>JBrowse/View/Track/CanvasFeatures</trackType> 106 </style>
108 <index>false</index> 107 <gff>
109 </gff> 108 </gff>
110 </options> 109 <scaling>
111 </track> 110 <method>score</method>
112 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 111 <algo>linear</algo>
113 <files> 112 <scales>
114 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/> 113 <type>__auto__</type>
115 </files> 114 </scales>
116 115 <scheme>
117 <options> 116 <type>opacity</type>
118 <style> 117 <color>#0000ff</color>
119 <className>feature</className> 118 </scheme>
120 <description>note,description</description> 119 </scaling>
121 <label>name,id</label> 120 </options>
122 <height>100px</height> 121 </track>
123 </style> 122 <track cat="Scaled Colour" format="gene_calls">
124 <scaling> 123 <files>
125 <method>score</method> 124 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/>
126 <algo>linear</algo> 125 </files>
127 <scales> 126
128 <type>automatic</type> 127 <options>
129 128 <style>
130 </scales> 129 <className>feature</className>
131 <scheme> 130 <description>feature</description>
132 <type>opacity</type> 131 <label>name,id</label>
133 <color>#0000ff</color> 132 <height>100px</height>
134 </scheme> 133 </style>
135 </scaling> 134 <gff>
136 <menus> 135 </gff>
137 </menus> 136 <scaling>
138 137 <method>score</method>
139 <gff> 138 <algo>linear</algo>
140 <trackType>JBrowse/View/Track/CanvasFeatures</trackType> 139 <scales>
141 <index>false</index> 140 <type>manual</type>
142 </gff> 141 <min>0</min>
143 </options> 142 <max>1000</max>
144 </track> 143 </scales>
145 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 144 <scheme>
146 <files> 145 <type>opacity</type>
147 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/> 146 <color>__auto__</color>
148 </files> 147 </scheme>
149 148 </scaling>
150 <options> 149 </options>
151 <style> 150 </track>
152 <className>feature</className> 151 <track cat="Scaled Colour" format="gene_calls">
153 <description>note,description</description> 152 <files>
154 <label>name,id</label> 153 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/>
155 <height>100px</height> 154 </files>
156 </style> 155
157 <scaling> 156 <options>
158 <method>score</method> 157 <style>
159 <algo>linear</algo> 158 <className>feature</className>
160 <scales> 159 <description>feature</description>
161 <type>manual</type> 160 <label>name,id</label>
162 161 <height>100px</height>
163 <min>0</min> 162 </style>
164 <max>1000</max> 163 <gff>
165 </scales> 164 </gff>
166 <scheme> 165 <scaling>
167 <type>opacity</type> 166 <method>score</method>
168 <color>__auto__</color> 167 <algo>linear</algo>
169 </scheme> 168 <scales>
170 </scaling> 169 <type>manual</type>
171 <menus> 170 <min>0</min>
172 </menus> 171 <max>1000</max>
173 172 </scales>
174 <gff> 173 <scheme>
175 <trackType>JBrowse/View/Track/CanvasFeatures</trackType> 174 <type>opacity</type>
176 <index>false</index> 175 <color>#ff0000</color>
177 </gff> 176 </scheme>
178 </options> 177 </scaling>
179 </track> 178 </options>
180 <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> 179 </track>
181 <files> 180
182 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/> 181
183 </files> 182 <track cat="Realistic" format="gene_calls">
184 183 <files>
185 <options> 184 <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>
186 <style> 185 </files>
187 <className>feature</className> 186
188 <description>note,description</description> 187 <options>
189 <label>name,id</label> 188 <style>
190 <height>100px</height> 189 <className>feature</className>
191 </style> 190 <description>feature</description>
192 <scaling> 191 <label>name,id</label>
193 <method>score</method> 192 <height>100px</height>
194 <algo>linear</algo> 193 </style>
195 <scales> 194 <gff>
196 <type>manual</type> 195 </gff>
197 196 <scaling>
198 <min>0</min> 197 <method>ignore</method>
199 <max>1000</max> 198 <scheme>
200 </scales> 199 <color>__auto__</color>
201 <scheme> 200 </scheme>
202 <type>opacity</type> 201 </scaling>
203 <color>#ff0000</color> 202 </options>
204 </scheme> 203 </track>
205 </scaling> 204 <track cat="Realistic" format="gene_calls">
206 <menus> 205 <files>
207 </menus> 206 <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>
208 207 </files>
209 <gff> 208
210 <trackType>JBrowse/View/Track/CanvasFeatures</trackType> 209 <options>
211 <index>false</index> 210 <style>
212 </gff> 211 <className>feature</className>
213 </options> 212 <description>feature</description>
214 </track> 213 <label>name,id</label>
215 <track cat="Realistic" format="gene_calls" visibility="default_off"> 214 <height>100px</height>
216 <files> 215 </style>
217 <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/> 216 <gff>
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>
265 <match>cDNA_match</match> 217 <match>cDNA_match</match>
266 <index>false</index> 218 </gff>
267 </gff> 219 <scaling>
220 <method>ignore</method>
221 <scheme>
222 <type>opacity</type>
223 <color>__auto__</color>
224 </scheme>
225 </scaling>
268 </options> 226 </options>
269 </track> 227 </track>
270 </tracks> 228 </tracks>
271 </root> 229 </root>