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comparison tools/mytools/dreme_out/dreme.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <?xml version='1.0' encoding='UTF-8' standalone='yes'?>
2 <!DOCTYPE dreme[
3 <!ELEMENT dreme (model, motifs, run_time)>
4 <!ATTLIST dreme version CDATA #REQUIRED release CDATA #REQUIRED>
5 <!ELEMENT model
6 (command_line, positives, negatives, background, stop, ngen, add_pv_thresh,
7 seed, host, when, description?)>
8 <!ELEMENT command_line (#PCDATA)>
9 <!ELEMENT positives EMPTY>
10 <!ATTLIST positives
11 name CDATA #REQUIRED count CDATA #REQUIRED file CDATA #REQUIRED
12 last_mod_date CDATA #REQUIRED>
13 <!--
14 negatives must have a file and last_mod_date specified when the from
15 attribute is file.
16 -->
17 <!ELEMENT negatives EMPTY>
18 <!ATTLIST negatives
19 name CDATA #REQUIRED count CDATA #REQUIRED from (shuffled|file) #REQUIRED
20 file CDATA #IMPLIED last_mod_date CDATA #IMPLIED>
21 <!--
22 background allows DNA and RNA (AA is not going to be supported with DREME)
23 however currently only DNA is implemented. Note that when type is dna the
24 value for T must be supplied and when the type is rna the value for U must
25 be supplied. The sum of the frequencies must be 1 (with a small error).
26 -->
27 <!ELEMENT background EMPTY>
28 <!ATTLIST background
29 type (dna|rna) #REQUIRED
30 A CDATA #REQUIRED C CDATA #REQUIRED G CDATA #REQUIRED
31 T CDATA #IMPLIED U CDATA #IMPLIED
32 from (dataset|file) #REQUIRED
33 file CDATA #IMPLIED last_mod_date CDATA #IMPLIED>
34 <!ELEMENT stop EMPTY>
35 <!ATTLIST stop
36 evalue CDATA #IMPLIED count CDATA #IMPLIED time CDATA #IMPLIED>
37 <!ELEMENT ngen (#PCDATA)>
38 <!ELEMENT seed (#PCDATA)>
39 <!ELEMENT add_pv_thresh (#PCDATA)>
40 <!ELEMENT host (#PCDATA)>
41 <!ELEMENT when (#PCDATA)>
42 <!ELEMENT description (#PCDATA)>
43 <!ELEMENT motifs (motif+)>
44 <!ELEMENT motif (pos+, match+)>
45 <!ATTLIST motif
46 id CDATA #REQUIRED seq CDATA #REQUIRED length CDATA #REQUIRED
47 nsites CDATA #REQUIRED p CDATA #REQUIRED n CDATA #REQUIRED
48 pvalue CDATA #REQUIRED evalue CDATA #REQUIRED unerased_evalue CDATA #REQUIRED>
49 <!--
50 pos allows DNA and RNA (AA is not going to be supported with DREME)
51 however current only DNA is implemented. When the type in the background
52 is 'dna' pos must have a T attribute and when it is 'rna' pos must have a
53 U attribute
54 -->
55 <!ELEMENT pos EMPTY>
56 <!ATTLIST pos
57 i CDATA #REQUIRED A CDATA #REQUIRED C CDATA #REQUIRED G CDATA #REQUIRED
58 T CDATA #IMPLIED U CDATA #IMPLIED>
59 <!ELEMENT match EMPTY>
60 <!ATTLIST match
61 seq CDATA #REQUIRED p CDATA #REQUIRED n CDATA #REQUIRED
62 pvalue CDATA #REQUIRED evalue CDATA #REQUIRED>
63 <!ELEMENT run_time EMPTY>
64 <!ATTLIST run_time
65 cpu CDATA #REQUIRED real CDATA #REQUIRED stop (evalue|count|time) #REQUIRED>
66 ]>
67 <dreme version="4.7.0" release="Wed Sep 28 17:30:10 EST 2011">
68 <model>
69 <command_line>dreme -p test.fa -desc xxxx</command_line>
70 <positives name="test" count="3" file="test.fa" last_mod_date="Sat Dec 10 12:52:18 EST 2011" />
71 <negatives name="shuffled positive sequences" count="3" from="shuffled"/>
72 <background type="dna" A="0.243" C="0.270" G="0.243" T="0.243" from="dataset"/>
73 <stop evalue="0.05"/>
74 <ngen>100</ngen>
75 <add_pv_thresh>0.01</add_pv_thresh>
76 <seed>1</seed>
77 <host>SHARPLAB.MIT.EDU</host>
78 <when>Sun Dec 11 09:26:43 EST 2011</when>
79 <description>xxxx</description>
80 </model>
81 <motifs>
82 </motifs>
83 <run_time cpu="0.01" real="0.01" stop="evalue"/>
84 </dreme>