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comparison test-data/blastxml/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 ff11d442feed
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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="Blah" format="blast">
11 <files>
12 <trackFile path="test-data/blastxml/blast.xml" ext="blastxml" label="BlastP"/>
13 </files>
14
15 <options>
16 <style>
17 <className>feature</className>
18 <description></description>
19 <label>Description</label>
20 <height>400px</height>
21 </style>
22 <blast>
23 <parent>test-data/blastxml/merlin.gff</parent>
24 <protein>true</protein>
25 <min_gap>10</min_gap>
26 </blast>
27 <scaling>
28 <method>score</method>
29 <algo>blast</algo>
30 <scales>
31 <type>__auto__</type>
32 </scales>
33 <scheme>
34 <type>opacity</type>
35 <color>__auto__</color>
36 </scheme>
37 </scaling>
38 </options>
39 </track>
40 <track cat="Blah" format="blast">
41 <files>
42 <trackFile path="test-data/blastxml/blast.xml" ext="blastxml" label="BlastP, min_gap=3"/>
43 </files>
44
45 <options>
46 <style>
47 <className>feature</className>
48 <description></description>
49 <label>Description</label>
50 <height>400px</height>
51 </style>
52 <blast>
53 <parent>test-data/blastxml/merlin.gff</parent>
54 <protein>true</protein>
55 <min_gap>3</min_gap>
56 </blast>
57 <scaling>
58 <method>score</method>
59 <algo>blast</algo>
60 <scales>
61 <type>__auto__</type>
62 </scales>
63 <scheme>
64 <type>opacity</type>
65 <color>__auto__</color>
66 </scheme>
67 </scaling>
68 </options>
69 </track>
70
71 <track cat="Blah" format="blast">
72 <files>
73 <trackFile path="test-data/blastxml/blast-gene1.xml" ext="blastxml" label="Non protein match/matchpart"/>
74 </files>
75
76 <options>
77 <style>
78 <className>feature</className>
79 <description></description>
80 <label>Description</label>
81 <height>400px</height>
82 </style>
83 <blast>
84 <parent>test-data/blastxml/merlin.gff</parent>
85 <min_gap>3</min_gap>
86 </blast>
87 <scaling>
88 <method>ignore</method>
89 <algo>linear</algo>
90 <scheme>
91 <type>opacity</type>
92 <color>__auto__</color>
93 </scheme>
94 </scaling>
95 </options>
96 </track>
97
98 <track cat="Blah" format="blast">
99 <files>
100 <trackFile path="test-data/blastxml/blastn-gene1.xml" ext="blastxml" label="Non protein match/matchpart, no parent"/>
101 </files>
102
103 <options>
104 <style>
105 <className>feature</className>
106 <description></description>
107 <label>Description</label>
108 <height>400px</height>
109 </style>
110 <blast>
111 <min_gap>40</min_gap>
112 </blast>
113 <scaling>
114 <method>score</method>
115 <algo>blast</algo>
116 <scales>
117 <type>__auto__</type>
118 </scales>
119 <scheme>
120 <type>opacity</type>
121 <color>__auto__</color>
122 </scheme>
123 </scaling>
124 </options>
125 </track>
126
127 </tracks>
128 </root>