Mercurial > repos > iuc > funannotate_annotate
annotate test-data/funannotate_db/trained_species/fly/augustus/fly_metapars.utr.cfg @ 6:582fd74dc2a1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 2c4f8172c3f452e1119b3d528c97da382750adeb
author | iuc |
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date | Tue, 25 Apr 2023 18:29:19 +0000 |
parents | a5baa4ff168d |
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a5baa4ff168d
"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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1 # This file contains the list of meta parameters for the Untranslated Regions (UTRs), which are subject to optimization. |
a5baa4ff168d
"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
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2 # All other parameters are chosen as given in the species parameter file. The order |
a5baa4ff168d
"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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3 # of the parameters determines the order in the optimization process. |
a5baa4ff168d
"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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4 # Basically, different values for these meta parameters are tried out and the ones |
a5baa4ff168d
"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
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5 # giving best performance in a cross-validation on the training set are chosen. |
a5baa4ff168d
"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
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6 # For each parameter the range of possible values is specified after the parameter |
a5baa4ff168d
"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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7 # name and at least one white space. |
a5baa4ff168d
"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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8 # 3 cases are possible for the range: |
a5baa4ff168d
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9 # - an explicit list is given, e.g. protein "on" "off" |
a5baa4ff168d
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10 # - it is an integer range, e.g. window_size "1"-"5" |
a5baa4ff168d
"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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11 # - it is a range of floating point numbers, e.g. pseudocount "0.3"_"1.8" |
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12 # |
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13 # |
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14 # Mario Stanke, 9.5.2008 |
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15 # |
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16 |
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17 /UtrModel/prob_polya "0.0"_"1.0" |
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18 /UtrModel/d_polya_cleavage_min "6"-"14" |
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19 /UtrModel/d_polya_cleavage_max "17"-"27" |
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20 /UtrModel/tss_start "0"-"12" |
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21 /UtrModel/tss_end "0"-"8" |
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22 /UtrModel/tts_motif_memory "0"-"2" |
a5baa4ff168d
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23 /UtrModel/utr5patternweight "0.1"_"1.0" |
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24 /UtrModel/utr3patternweight "0.1"_"1.0" |
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25 /UtrModel/patpseudocount "1"_"3" |
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26 /UtrModel/tssup_k "0"-"2" |
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27 /UtrModel/slope_of_bandwidth "0.2"_"0.4" |
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28 /UtrModel/minwindowcount "1"-"4" |
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29 #/UtrModel/k "2"-"4" |
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