Mercurial > repos > cafletezbrant > kmersvm
annotate kmersvm/kmertopwm.xml @ 7:fd740d515502 draft default tip
Uploaded revised kmer-SVM to include modules from kmer-visual.
author | cafletezbrant |
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date | Sun, 16 Jun 2013 18:06:14 -0400 |
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fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
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1 <tool id="kmer2meme" name="Kmer To MEME"> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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2 <description>Convert kmers to MEME format for motif finding by Tomtom</description> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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3 <command interpreter="perl">kmer2meme.pl |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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4 $weights $N |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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5 </command> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
diff
changeset
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6 |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
diff
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7 <inputs> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
diff
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8 <param format="tabular" name="weights" type="data" label="Kmer Weights"/> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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changeset
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9 <param type="integer" name="N" value="10" label="Kmer Number"> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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10 <validator type="in_range" message="Kmer number must be in range 1 - 50" min="1" max="50"/> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
diff
changeset
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11 </param> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
diff
changeset
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12 </inputs> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
diff
changeset
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13 |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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14 <outputs> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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15 <data format="txt" from_work_dir="kmer2meme.meme" name="MEME for Kmers" label="${tool.name} on ${on_string}: MEME"/> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
diff
changeset
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16 </outputs> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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17 |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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18 <help> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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19 This is a utility function that creates PWMs in MEME format for use with Tomtom. |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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20 |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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21 'Kmer Weights' is the weight file generated by 'Train SVM'. |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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22 |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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23 'Kmer Number' is the number of most positive and most negative kmers to be processed. |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
diff
changeset
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24 </help> |
fd740d515502
Uploaded revised kmer-SVM to include modules from kmer-visual.
cafletezbrant
parents:
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25 </tool> |