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comparison test-data/fimo_output_xml_2.xml @ 0:315f05ef7d49 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
author iuc
date Wed, 25 Apr 2018 12:12:03 -0400
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-1:000000000000 0:315f05ef7d49
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <!-- Begin document body -->
3 <settings>
4 <setting name="allow clobber">false</setting>
5 <setting name="compute q-values">false</setting>
6 <setting name="text only">false</setting>
7 <setting name="scan both strands">false</setting>
8 <setting name="output threshold">0.0001</setting>
9 <setting name="threshold type">p-value</setting>
10 <setting name="max stored scores">100000</setting>
11 <setting name="pseudocount">0.1</setting>
12 <setting name="verbosity">1</setting>
13 </settings>
14 <sequence-data num-sequences="1" num-residues="5386" />
15 <alphabet name="Protein" like="protein">
16 <letter id="A" symbol="A" name="Alanine" colour="0000CC"/>
17 <letter id="C" symbol="C" name="Cysteine" colour="0000CC"/>
18 <letter id="D" symbol="D" name="Aspartic acid" colour="FF00FF"/>
19 <letter id="E" symbol="E" name="Glutamic acid" colour="FF00FF"/>
20 <letter id="F" symbol="F" name="Phenylalanine" colour="0000CC"/>
21 <letter id="G" symbol="G" name="Glycine" colour="FFB300"/>
22 <letter id="H" symbol="H" name="Histidine" colour="FFCCCC"/>
23 <letter id="I" symbol="I" name="Isoleucine" colour="0000CC"/>
24 <letter id="K" symbol="K" name="Lysine" colour="CC0000"/>
25 <letter id="L" symbol="L" name="Leucine" colour="0000CC"/>
26 <letter id="M" symbol="M" name="Methionine" colour="0000CC"/>
27 <letter id="N" symbol="N" name="Asparagine" colour="008000"/>
28 <letter id="P" symbol="P" name="Proline" colour="FFFF00"/>
29 <letter id="Q" symbol="Q" name="Glutamine" colour="008000"/>
30 <letter id="R" symbol="R" name="Arginine" colour="CC0000"/>
31 <letter id="S" symbol="S" name="Serine" colour="008000"/>
32 <letter id="T" symbol="T" name="Threonine" colour="008000"/>
33 <letter id="V" symbol="V" name="Valine" colour="0000CC"/>
34 <letter id="W" symbol="W" name="Tryptophan" colour="0000CC"/>
35 <letter id="Y" symbol="Y" name="Tyrosine" colour="33E6CC"/>
36 <letter id="X" symbol="X" aliases="*." equals="ACDEFGHIKLMNPQRSTVWY" name="Any amino acid"/>
37 <letter id="B" symbol="B" equals="DN" name="Asparagine or Aspartic acid"/>
38 <letter id="Z" symbol="Z" equals="EQ" name="Glutamine or Glutamic acid"/>
39 <letter id="J" symbol="J" equals="IL" name="Leucine or Isoleucine"/>
40 </alphabet>
41 <motif name="1" width="11" best-possible-match="GGGGTATAAAA"/>
42 <background source="non-redundant database">
43 <value letter="A">0.073</value>
44 <value letter="C">0.018</value>
45 <value letter="D">0.052</value>
46 <value letter="E">0.062</value>
47 <value letter="F">0.040</value>
48 <value letter="G">0.069</value>
49 <value letter="H">0.022</value>
50 <value letter="I">0.056</value>
51 <value letter="K">0.058</value>
52 <value letter="L">0.092</value>
53 <value letter="M">0.023</value>
54 <value letter="N">0.046</value>
55 <value letter="P">0.051</value>
56 <value letter="Q">0.041</value>
57 <value letter="R">0.052</value>
58 <value letter="S">0.074</value>
59 <value letter="T">0.059</value>
60 <value letter="V">0.064</value>
61 <value letter="W">0.013</value>
62 <value letter="Y">0.033</value>
63 </background>
64 <cisml-file>cisml.xml</cisml-file>
65 </fimo>