Mercurial > repos > iuc > meme_psp_gen
comparison test-data/meme_output_custom.html @ 8:8436beac5eed draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
| author | iuc |
|---|---|
| date | Mon, 14 Jul 2025 21:32:53 +0000 |
| parents | |
| children |
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| 7:47e7ae719765 | 8:8436beac5eed |
|---|---|
| 1 "options": { | |
| 2 "mod": "zoops", | |
| 3 "revcomp": false, | |
| 4 "nmotifs": 1, | |
| 5 "objfun": "E-value of product of p-values", | |
| 6 "spfun": "E-value of product of p-values", | |
| 7 "minw": 8, | |
| 8 "maxw": 50, | |
| 9 "minsites": 2, | |
| 10 "maxsites": 30, | |
| 11 "wnsites": 0.8, | |
| 12 "spmap": "uni", | |
| 13 "spfuzz": 0.5, | |
| 14 "searchsize": 1500, | |
| 15 "maxsize": 1000000, | |
| 16 "norand": "no", | |
| 17 "csites": 1000, | |
| 18 "hsfrac": 0, | |
| 19 "prior": "dirichlet", | |
| 20 "b": 0.01, | |
| 21 "maxiter": 50, | |
| 22 "distance": 0.001, | |
| 23 "wg": 11, | |
| 24 "ws": 1, | |
| 25 "noendgaps": false, | |
| 26 "substring": true, | |
| 27 "seed": 0, | |
| 28 "brief": 1000 | |
| 29 }, | |
| 30 "alphabet": { | |
| 31 "name": "DNA with covalent modifications", | |
| 32 "like": "dna", | |
| 33 "ncore": 16, | |
| 34 "symbols": [ | |
| 35 { | |
| 36 "symbol": "A", | |
| 37 "name": "Adenine", | |
| 38 "colour": "8510A8", | |
| 39 "complement": "T" | |
| 40 }, { | |
| 41 "symbol": "C", | |
| 42 "name": "Cytosine", | |
| 43 "colour": "A50026", | |
| 44 "complement": "G" | |
| 45 }, { | |
| 46 "symbol": "G", | |
| 47 "name": "Guanine", | |
| 48 "colour": "313695", | |
| 49 "complement": "C" | |
| 50 }, { | |
| 51 "symbol": "T", | |
| 52 "name": "Thymine", | |
| 53 "colour": "A89610", | |
| 54 "complement": "A" | |
| 55 }, { | |
| 56 "symbol": "a", | |
| 57 "name": "N6-methyladenine", | |
| 58 "colour": "8510A8", | |
| 59 "complement": "t" | |
| 60 }, { | |
| 61 "symbol": "c", | |
| 62 "name": "5-Carboxylcytosine", | |
| 63 "colour": "FEE090", | |
| 64 "complement": "4" | |
| 65 }, { | |
| 66 "symbol": "f", | |
| 67 "name": "5-Formylcytosine", | |
| 68 "colour": "FDAE61", | |
| 69 "complement": "3" | |
| 70 }, { | |
| 71 "symbol": "g", | |
| 72 "name": "modified_g", | |
| 73 "colour": "00897B", | |
| 74 "complement": "5" | |
| 75 }, { | |
| 76 "symbol": "h", | |
| 77 "name": "5-Hydroxymethylcytosine", | |
| 78 "colour": "F46D43", | |
| 79 "complement": "2" | |
| 80 }, { | |
| 81 "symbol": "m", | |
| 82 "name": "5-Methylcytosine", | |
| 83 "colour": "D73027", | |
| 84 "complement": "1" | |
| 85 }, { | |
| 86 "symbol": "t", | |
| 87 "name": "Thymine_lowercase", | |
| 88 "colour": "756BB1", | |
| 89 "complement": "a" | |
| 90 }, { | |
| 91 "symbol": "1", | |
| 92 "name": "Guanine:5-Methylcytosine", | |
| 93 "colour": "4575B4", | |
| 94 "complement": "m" | |
| 95 }, { | |
| 96 "symbol": "2", | |
| 97 "name": "Guanine:5-Hydroxymethylcytosine", | |
| 98 "colour": "74ADD1", | |
| 99 "complement": "h" | |
| 100 }, { | |
| 101 "symbol": "3", | |
| 102 "name": "Guanine:5-Formylcytosine", | |
| 103 "colour": "ABD9E9", | |
| 104 "complement": "f" | |
| 105 }, { | |
| 106 "symbol": "4", | |
| 107 "name": "Guanine:5-Carboxylcytosine", | |
| 108 "colour": "E0F3F8", | |
| 109 "complement": "c" | |
| 110 }, { | |
| 111 "symbol": "5", | |
| 112 "name": "cytosine_lowercase", | |
| 113 "colour": "53698A", | |
| 114 "complement": "g" | |
| 115 }, { | |
| 116 "symbol": "?", | |
| 117 "equals": "ACGTacfghmt12345" | |
| 118 } | |
| 119 ] | |
| 120 }, | |
| 121 "background": { | |
| 122 "source": "--sequences--", | |
| 123 "order": 0, | |
| 124 "freqs": [ | |
| 125 0.263, 0.2, 0.249, 0.189, 0.0297, 0.027, 0.00066, 0.00726, | |
| 126 0.00066, 0.00396, 0.0277, 0.00066, 0.00066, 0.00066, 0.00066, | |
| 127 0.00066 | |
| 128 ] | |
| 129 }, | |
| 130 "sequence_db": { | |
| 131 "primary_source": "Galaxy_FASTA_Input", | |
| 132 "primary_count": 30, | |
| 133 "primary_positions": 1500, | |
| 134 "control_source": "--none--", | |
| 135 "control_count": 0, | |
| 136 "control_positions": 0, | |
| 137 "freqs": [ | |
| 138 0.265, 0.201, 0.251, 0.19, 0.0293, 0.0267, 0, 0.00667, 0, 0.00333, | |
| 139 0.0273, 0, 0, 0, 0, 0 | |
| 140 ], | |
| 141 "sequences": [ | |
| 142 { | |
| 143 "name": "chr21_19617074_19617124_+", | |
| 144 "length": 50, | |
| 145 "weight": 1.000000 | |
| 146 }, { | |
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| 215 "name": "chr21_45705687_45705737_+", | |
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| 219 "name": "chr21_45971413_45971463_-", | |
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| 235 "name": "chr21_46031920_46031970_+", | |
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| 238 }, { | |
| 239 "name": "chr21_46046964_46047014_+", | |
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| 262 } | |
| 263 ] | |
| 264 }, | |
| 265 "motifs": [ | |
| 266 { | |
| 267 "db": 0, | |
| 268 "id": "taCaaACAGtataactctcac", | |
| 269 "alt": "MEME-1", | |
| 270 "len": 21, | |
| 271 "nsites": 5, | |
| 272 "evalue": "4.6e-028", | |
| 273 "ic": 55.7, | |
| 274 "re": 68.0, | |
| 275 "llr": 236, | |
| 276 "bt": 7.73664, |
