Mercurial > repos > iuc > meme_meme
annotate test-data/fimo_output_test3.xml @ 16:3c2ac7c3f0b8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
author | iuc |
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date | Sat, 27 Nov 2021 09:45:12 +0000 |
parents | 3f0dd362b755 |
children | 19237efe98d1 |
rev | line source |
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13
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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2 <!-- Begin document body --> |
14
3f0dd362b755
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
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3 <fimo version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700"> |
13
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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4 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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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
iuc
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6 > |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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7 <settings> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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8 <setting name="background file name">--uniform--</setting> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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9 <setting name="allow clobber">false</setting> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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10 <setting name="compute q-values">true</setting> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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11 <setting name="parse genomic coord.">false</setting> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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12 <setting name="text only">false</setting> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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13 <setting name="scan both strands">true</setting> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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14 <setting name="output threshold">0.01</setting> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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15 <setting name="threshold type">p-value</setting> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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16 <setting name="max stored scores">100000</setting> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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17 <setting name="pseudocount">0.1</setting> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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18 <setting name="verbosity">2</setting> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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19 <setting name="selected motif">ACTAAYH</setting> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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20 </settings> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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21 <sequence-data num-sequences="1" num-residues="16569" /> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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22 <alphabet name="DNA" like="dna"> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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23 <letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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24 <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
iuc
parents:
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25 <letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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26 <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
iuc
parents:
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27 <letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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28 <letter id="V" symbol="V" equals="ACG" name="Not T"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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29 <letter id="H" symbol="H" equals="ACT" name="Not G"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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30 <letter id="D" symbol="D" equals="AGT" name="Not C"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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31 <letter id="B" symbol="B" equals="CGT" name="Not A"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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32 <letter id="M" symbol="M" equals="AC" name="Amino"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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33 <letter id="R" symbol="R" equals="AG" name="Purine"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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34 <letter id="W" symbol="W" equals="AT" name="Weak"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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35 <letter id="S" symbol="S" equals="CG" name="Strong"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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36 <letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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37 <letter id="K" symbol="K" equals="GT" name="Keto"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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38 </alphabet> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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39 <motif name="ACTAAYH" alt="DREME-1" width="7" best-possible-match="ACTAACA"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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40 <motif name="YTAACA" alt="DREME-2" width="6" best-possible-match="TTAACA"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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41 <motif name="TCTGT" alt="DREME-3" width="5" best-possible-match="TCTGT"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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42 <motif name="SCCAGG" alt="DREME-4" width="6" best-possible-match="CCCAGG"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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43 <motif name="CCAGCAY" alt="DREME-5" width="7" best-possible-match="CCAGCAC"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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44 <motif name="GMATGT" alt="DREME-6" width="6" best-possible-match="GAATGT"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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45 <background source="--uniform--"> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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46 <value letter="A">0.250</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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47 <value letter="C">0.250</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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48 <value letter="G">0.250</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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49 <value letter="T">0.250</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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50 </background> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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51 <cisml-file>cisml.xml</cisml-file> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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52 </fimo> |