Mercurial > repos > iuc > meme_fimo

comparison test-data/fimo_output_test2.xml @ 15:0c5239d1aa65 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
author iuc
date Wed, 11 Dec 2019 18:05:35 -0500
parents 4eb02864e5df
children c5209f38700d
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14:c1a9a297ba8b 15:0c5239d1aa65
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <!-- Begin document body --> 2 <!-- Begin document body -->
3 <fimo version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700"> 3 <fimo version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700">
4 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 4 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
5 xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" 5 xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
6 > 6 >
7 <command-line>fimo -oc fimo_test2_out --bgfile fimo_background_probs_hsa_chrM.txt dreme_fimo_input_1.xml hsa_chrM.fa</command-line>
8 <settings> 7 <settings>
9 <setting name="output directory">fimo_test2_out</setting> 8 <setting name="allow clobber">false</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">fimo_background_probs_hsa_chrM.txt</setting>
13 <setting name="allow clobber">true</setting>
14 <setting name="compute q-values">true</setting> 9 <setting name="compute q-values">true</setting>
15 <setting name="parse genomic coord.">false</setting> 10 <setting name="parse genomic coord.">false</setting>
16 <setting name="text only">false</setting> 11 <setting name="text only">false</setting>
17 <setting name="scan both strands">true</setting> 12 <setting name="scan both strands">true</setting>
18 <setting name="output threshold">0.0001</setting> 13 <setting name="output threshold">0.0001</setting>
43 <motif name="YTAACA" alt="DREME-2" width="6" best-possible-match="TTAACA"/> 38 <motif name="YTAACA" alt="DREME-2" width="6" best-possible-match="TTAACA"/>
44 <motif name="TCTGT" alt="DREME-3" width="5" best-possible-match="TCTGT"/> 39 <motif name="TCTGT" alt="DREME-3" width="5" best-possible-match="TCTGT"/>
45 <motif name="SCCAGG" alt="DREME-4" width="6" best-possible-match="CCCAGG"/> 40 <motif name="SCCAGG" alt="DREME-4" width="6" best-possible-match="CCCAGG"/>
46 <motif name="CCAGCAY" alt="DREME-5" width="7" best-possible-match="CCAGCAC"/> 41 <motif name="CCAGCAY" alt="DREME-5" width="7" best-possible-match="CCAGCAC"/>
47 <motif name="GMATGT" alt="DREME-6" width="6" best-possible-match="GAATGT"/> 42 <motif name="GMATGT" alt="DREME-6" width="6" best-possible-match="GAATGT"/>
48 <background source="fimo_background_probs_hsa_chrM.txt">
49 <value letter="A">0.278</value> 43 <value letter="A">0.278</value>
50 <value letter="C">0.222</value> 44 <value letter="C">0.222</value>
51 <value letter="G">0.222</value> 45 <value letter="G">0.222</value>
52 <value letter="T">0.278</value> 46 <value letter="T">0.278</value>
53 </background> 47 </background>