Mercurial > repos > iuc > meme_fimo

comparison test-data/fimo_output_xml_2.xml @ 0:27c742760a84 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
author iuc
date Tue, 22 Dec 2015 16:59:48 -0500
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children 8d8905e040cf
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-1:000000000000 0:27c742760a84
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <!-- Begin document body -->
3 <fimo version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000">
4 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
5 xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
6 >
7 <command-line>fimo --alpha 1.000000 --max-stored-scores 100000 --motif-pseudo 0.100000 --no-qvalue --thresh 0.000100 --o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1978/dataset_2738_files --verbosity 1 /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</command-line>
8 <settings>
9 <setting name="output directory">/Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1978/dataset_2738_files</setting>
10 <setting name="MEME file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat</setting>
11 <setting name="sequence file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</setting>
12 <setting name="allow clobber">false</setting>
13 <setting name="compute q-values">false</setting>
14 <setting name="parse genomic coord.">false</setting>
15 <setting name="text only">false</setting>
16 <setting name="scan both strands">false</setting>
17 <setting name="output threshold">0.0001</setting>
18 <setting name="threshold type">p-value</setting>
19 <setting name="max stored scores">100000</setting>
20 <setting name="pseudocount">0.1</setting>
21 <setting name="verbosity">1</setting>
22 </settings>
23 <sequence-data num-sequences="1" num-residues="5386" />
24 <alphabet name="Protein" like="protein">
25 <letter id="A" symbol="A" name="Alanine" colour="0000CC"/>
26 <letter id="C" symbol="C" name="Cysteine" colour="0000CC"/>
27 <letter id="D" symbol="D" name="Aspartic acid" colour="FF00FF"/>
28 <letter id="E" symbol="E" name="Glutamic acid" colour="FF00FF"/>
29 <letter id="F" symbol="F" name="Phenylalanine" colour="0000CC"/>
30 <letter id="G" symbol="G" name="Glycine" colour="FFB300"/>
31 <letter id="H" symbol="H" name="Histidine" colour="FFCCCC"/>
32 <letter id="I" symbol="I" name="Isoleucine" colour="0000CC"/>
33 <letter id="K" symbol="K" name="Lysine" colour="CC0000"/>
34 <letter id="L" symbol="L" name="Leucine" colour="0000CC"/>
35 <letter id="M" symbol="M" name="Methionine" colour="0000CC"/>
36 <letter id="N" symbol="N" name="Asparagine" colour="008000"/>
37 <letter id="P" symbol="P" name="Proline" colour="FFFF00"/>
38 <letter id="Q" symbol="Q" name="Glutamine" colour="008000"/>
39 <letter id="R" symbol="R" name="Arginine" colour="CC0000"/>
40 <letter id="S" symbol="S" name="Serine" colour="008000"/>
41 <letter id="T" symbol="T" name="Threonine" colour="008000"/>
42 <letter id="V" symbol="V" name="Valine" colour="0000CC"/>
43 <letter id="W" symbol="W" name="Tryptophan" colour="0000CC"/>
44 <letter id="Y" symbol="Y" name="Tyrosine" colour="33E6CC"/>
45 <letter id="X" symbol="X" aliases="*." equals="ACDEFGHIKLMNPQRSTVWY" name="Any amino acid"/>
46 <letter id="B" symbol="B" equals="DN" name="Asparagine or Aspartic acid"/>
47 <letter id="Z" symbol="Z" equals="EQ" name="Glutamine or Glutamic acid"/>
48 <letter id="J" symbol="J" equals="IL" name="Leucine or Isoleucine"/>
49 </alphabet>
50 <motif name="1" width="11" best-possible-match="GGGGTATAAAA"/>
51 <background source="non-redundant database">
52 <value letter="A">0.073</value>
53 <value letter="C">0.018</value>
54 <value letter="D">0.052</value>
55 <value letter="E">0.062</value>
56 <value letter="F">0.040</value>
57 <value letter="G">0.069</value>
58 <value letter="H">0.022</value>
59 <value letter="I">0.056</value>
60 <value letter="K">0.058</value>
61 <value letter="L">0.092</value>
62 <value letter="M">0.023</value>
63 <value letter="N">0.046</value>
64 <value letter="P">0.051</value>
65 <value letter="Q">0.041</value>
66 <value letter="R">0.052</value>
67 <value letter="S">0.074</value>
68 <value letter="T">0.059</value>
69 <value letter="V">0.064</value>
70 <value letter="W">0.013</value>
71 <value letter="Y">0.033</value>
72 </background>
73 <cisml-file>cisml.xml</cisml-file>
74 </fimo>