Mercurial > repos > iuc > meme_fimo

comparison test-data/fimo_output_test3.xml @ 13:4eb02864e5df draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
author iuc
date Thu, 17 May 2018 14:11:00 -0400
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children 0c5239d1aa65
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12:02f6ad791bbf 13:4eb02864e5df
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <!-- Begin document body -->
3 <fimo version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700">
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 -o ./fimo_test4_out --thresh 0.01 --bgfile --uniform-- --max-stored-scores 100000 --motif ACTAAYH --motif-pseudo 0.1 dreme_fimo_input_1.xml hsa_chrM.fa</command-line>
8 <settings>
9 <setting name="output directory">./fimo_test4_out</setting>
10 <setting name="MEME file name">dreme_fimo_input_1.xml</setting>
11 <setting name="sequence file name">hsa_chrM.fa</setting>
12 <setting name="background file name">--uniform--</setting>
13 <setting name="allow clobber">false</setting>
14 <setting name="compute q-values">true</setting>
15 <setting name="parse genomic coord.">false</setting>
16 <setting name="text only">false</setting>
17 <setting name="scan both strands">true</setting>
18 <setting name="output threshold">0.01</setting>
19 <setting name="threshold type">p-value</setting>
20 <setting name="max stored scores">100000</setting>
21 <setting name="pseudocount">0.1</setting>
22 <setting name="verbosity">2</setting>
23 <setting name="selected motif">ACTAAYH</setting>
24 </settings>
25 <sequence-data num-sequences="1" num-residues="16569" />
26 <alphabet name="DNA" like="dna">
27 <letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
28 <letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/>
29 <letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/>
30 <letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/>
31 <letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/>
32 <letter id="V" symbol="V" equals="ACG" name="Not T"/>
33 <letter id="H" symbol="H" equals="ACT" name="Not G"/>
34 <letter id="D" symbol="D" equals="AGT" name="Not C"/>
35 <letter id="B" symbol="B" equals="CGT" name="Not A"/>
36 <letter id="M" symbol="M" equals="AC" name="Amino"/>
37 <letter id="R" symbol="R" equals="AG" name="Purine"/>
38 <letter id="W" symbol="W" equals="AT" name="Weak"/>
39 <letter id="S" symbol="S" equals="CG" name="Strong"/>
40 <letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/>
41 <letter id="K" symbol="K" equals="GT" name="Keto"/>
42 </alphabet>
43 <motif name="ACTAAYH" alt="DREME-1" width="7" best-possible-match="ACTAACA"/>
44 <motif name="YTAACA" alt="DREME-2" width="6" best-possible-match="TTAACA"/>
45 <motif name="TCTGT" alt="DREME-3" width="5" best-possible-match="TCTGT"/>
46 <motif name="SCCAGG" alt="DREME-4" width="6" best-possible-match="CCCAGG"/>
47 <motif name="CCAGCAY" alt="DREME-5" width="7" best-possible-match="CCAGCAC"/>
48 <motif name="GMATGT" alt="DREME-6" width="6" best-possible-match="GAATGT"/>
49 <background source="--uniform--">
50 <value letter="A">0.250</value>
51 <value letter="C">0.250</value>
52 <value letter="G">0.250</value>
53 <value letter="T">0.250</value>
54 </background>
55 <cisml-file>cisml.xml</cisml-file>
56 </fimo>