Mercurial > repos > iuc > meme_meme

annotate test-data/fimo_output_test2.xml @ 13:57e5d9382f36 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 14:10:48 -0400
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children 3f0dd362b755
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13
57e5d9382f36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <!-- Begin document body -->
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3 <fimo version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700">
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4 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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5 xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
57e5d9382f36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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6 >
57e5d9382f36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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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>
57e5d9382f36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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8 <settings>
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9 <setting name="output directory">fimo_test2_out</setting>
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10 <setting name="MEME file name">dreme_fimo_input_1.xml</setting>
57e5d9382f36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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11 <setting name="sequence file name">hsa_chrM.fa</setting>
57e5d9382f36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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12 <setting name="background file name">fimo_background_probs_hsa_chrM.txt</setting>
57e5d9382f36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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13 <setting name="allow clobber">true</setting>
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14 <setting name="compute q-values">true</setting>
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15 <setting name="parse genomic coord.">false</setting>
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16 <setting name="text only">false</setting>
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17 <setting name="scan both strands">true</setting>
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18 <setting name="output threshold">0.0001</setting>
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19 <setting name="threshold type">p-value</setting>
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20 <setting name="max stored scores">100000</setting>
57e5d9382f36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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21 <setting name="pseudocount">0.1</setting>
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22 <setting name="verbosity">2</setting>
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23 </settings>
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24 <sequence-data num-sequences="1" num-residues="16569" />
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25 <alphabet name="DNA" like="dna">
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26 <letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
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27 <letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/>
57e5d9382f36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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28 <letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/>
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29 <letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/>
57e5d9382f36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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30 <letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/>
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31 <letter id="V" symbol="V" equals="ACG" name="Not T"/>
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32 <letter id="H" symbol="H" equals="ACT" name="Not G"/>
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33 <letter id="D" symbol="D" equals="AGT" name="Not C"/>
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34 <letter id="B" symbol="B" equals="CGT" name="Not A"/>
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35 <letter id="M" symbol="M" equals="AC" name="Amino"/>
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36 <letter id="R" symbol="R" equals="AG" name="Purine"/>
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37 <letter id="W" symbol="W" equals="AT" name="Weak"/>
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38 <letter id="S" symbol="S" equals="CG" name="Strong"/>
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39 <letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/>
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40 <letter id="K" symbol="K" equals="GT" name="Keto"/>
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41 </alphabet>
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42 <motif name="ACTAAYH" alt="DREME-1" width="7" best-possible-match="ACTAACA"/>
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43 <motif name="YTAACA" alt="DREME-2" width="6" best-possible-match="TTAACA"/>
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44 <motif name="TCTGT" alt="DREME-3" width="5" best-possible-match="TCTGT"/>
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45 <motif name="SCCAGG" alt="DREME-4" width="6" best-possible-match="CCCAGG"/>
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46 <motif name="CCAGCAY" alt="DREME-5" width="7" best-possible-match="CCAGCAC"/>
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47 <motif name="GMATGT" alt="DREME-6" width="6" best-possible-match="GAATGT"/>
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48 <background source="fimo_background_probs_hsa_chrM.txt">
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49 <value letter="A">0.278</value>
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50 <value letter="C">0.222</value>
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51 <value letter="G">0.222</value>
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52 <value letter="T">0.278</value>
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53 </background>
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54 <cisml-file>cisml.xml</cisml-file>
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55 </fimo>