Mercurial > repos > iuc > meme_psp_gen
annotate test-data/fimo_output_test1.xml @ 4:e24560178fad draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
author | iuc |
---|---|
date | Sat, 27 Nov 2021 09:44:44 +0000 |
parents | ff2f53a32d0e |
children | 5f95d385a33c |
rev | line source |
---|---|
2
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
2 <!-- Begin document body --> |
3
ff2f53a32d0e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents:
2
diff
changeset
|
3 <fimo version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700"> |
2
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
4 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
5 xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
6 > |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
7 <settings> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
8 <setting name="background file name">--nrdb--</setting> |
3
ff2f53a32d0e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents:
2
diff
changeset
|
9 <setting name="allow clobber">false</setting> |
2
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
10 <setting name="compute q-values">true</setting> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
11 <setting name="parse genomic coord.">false</setting> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
12 <setting name="text only">false</setting> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
13 <setting name="scan both strands">true</setting> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
14 <setting name="output threshold">0.0001</setting> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
15 <setting name="threshold type">p-value</setting> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
16 <setting name="max stored scores">100000</setting> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
17 <setting name="pseudocount">0.1</setting> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
18 <setting name="verbosity">2</setting> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
19 </settings> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
20 <sequence-data num-sequences="1" num-residues="16569" /> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
21 <alphabet name="DNA" like="dna"> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
22 <letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
23 <letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
24 <letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
25 <letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
26 <letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
27 <letter id="V" symbol="V" equals="ACG" name="Not T"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
28 <letter id="H" symbol="H" equals="ACT" name="Not G"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
29 <letter id="D" symbol="D" equals="AGT" name="Not C"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
30 <letter id="B" symbol="B" equals="CGT" name="Not A"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
31 <letter id="M" symbol="M" equals="AC" name="Amino"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
32 <letter id="R" symbol="R" equals="AG" name="Purine"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
33 <letter id="W" symbol="W" equals="AT" name="Weak"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
34 <letter id="S" symbol="S" equals="CG" name="Strong"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
35 <letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
36 <letter id="K" symbol="K" equals="GT" name="Keto"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
37 </alphabet> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
38 <motif name="TACTAAYM" alt="MEME-1" width="8" best-possible-match="TACTAACA"/> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
39 <background source="--nrdb--"> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
40 <value letter="A">0.275</value> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
41 <value letter="C">0.225</value> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
42 <value letter="G">0.225</value> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
43 <value letter="T">0.275</value> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
44 </background> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
45 <cisml-file>cisml.xml</cisml-file> |
b48e673af4e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
|
46 </fimo> |