Mercurial > repos > iuc > jbrowse
annotate jbrowse.py @ 20:558d652cd681 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75a0a1c7b26cac156f76e8266a0e2e3d81be7f02
| author | iuc |
|---|---|
| date | Thu, 30 Aug 2018 11:43:59 -0400 |
| parents | ff11d442feed |
| children | 1c718d8b3532 |
| rev | line source |
|---|---|
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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diff
changeset
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1 #!/usr/bin/env python |
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8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
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2 import argparse |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
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3 import binascii |
| 3 | 4 import copy |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
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5 import datetime |
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0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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6 import hashlib |
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8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
5
diff
changeset
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7 import json |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
5
diff
changeset
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8 import logging |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
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9 import os |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
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10 import shutil |
| 3 | 11 import struct |
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8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
5
diff
changeset
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12 import subprocess |
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1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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changeset
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13 import tempfile |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
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14 import xml.etree.ElementTree as ET |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
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15 from collections import defaultdict |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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16 |
| 3 | 17 from Bio.Data import CodonTable |
| 18 logging.basicConfig(level=logging.INFO) | |
| 19 log = logging.getLogger('jbrowse') | |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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20 TODAY = datetime.datetime.now().strftime("%Y-%m-%d") |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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21 GALAXY_INFRASTRUCTURE_URL = None |
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1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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changeset
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22 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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23 |
| 3 | 24 class ColorScaling(object): |
| 25 | |
| 26 COLOR_FUNCTION_TEMPLATE = """ | |
| 27 function(feature, variableName, glyphObject, track) {{ | |
| 28 var score = {score}; | |
| 29 {opacity} | |
| 30 return 'rgba({red}, {green}, {blue}, ' + opacity + ')'; | |
| 31 }} | |
| 32 """ | |
| 33 | |
| 34 COLOR_FUNCTION_TEMPLATE_QUAL = """ | |
| 35 function(feature, variableName, glyphObject, track) {{ | |
| 36 var search_up = function self(sf, attr){{ | |
| 37 if(sf.get(attr) !== undefined){{ | |
| 38 return sf.get(attr); | |
| 39 }} | |
| 40 if(sf.parent() === undefined) {{ | |
| 41 return; | |
| 42 }}else{{ | |
| 43 return self(sf.parent(), attr); | |
| 44 }} | |
| 45 }}; | |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
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46 |
| 3 | 47 var search_down = function self(sf, attr){{ |
| 48 if(sf.get(attr) !== undefined){{ | |
| 49 return sf.get(attr); | |
| 50 }} | |
| 51 if(sf.children() === undefined) {{ | |
| 52 return; | |
| 53 }}else{{ | |
| 54 var kids = sf.children(); | |
| 55 for(var child_idx in kids){{ | |
| 56 var x = self(kids[child_idx], attr); | |
| 57 if(x !== undefined){{ | |
| 58 return x; | |
| 59 }} | |
| 60 }} | |
| 61 return; | |
| 62 }} | |
| 63 }}; | |
| 64 | |
| 65 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color}); | |
| 66 var score = (search_up(feature, 'score') || search_down(feature, 'score')); | |
| 67 {opacity} | |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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changeset
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68 if(score === undefined){{ opacity = 1; }} |
| 3 | 69 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color); |
| 70 var red = parseInt(result[1], 16); | |
| 71 var green = parseInt(result[2], 16); | |
| 72 var blue = parseInt(result[3], 16); | |
| 73 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }} | |
| 74 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')'; | |
| 75 }} | |
| 76 """ | |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
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changeset
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77 |
| 3 | 78 OPACITY_MATH = { |
| 79 'linear': """ | |
| 80 var opacity = (score - ({min})) / (({max}) - ({min})); | |
| 81 """, | |
| 82 'logarithmic': """ | |
| 83 var opacity = (score - ({min})) / (({max}) - ({min})); | |
| 84 opacity = Math.log10(opacity) + Math.log10({max}); | |
| 85 """, | |
| 86 'blast': """ | |
| 87 var opacity = 0; | |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
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88 if(score == 0.0) {{ |
| 3 | 89 opacity = 1; |
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17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
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90 }} else {{ |
| 3 | 91 opacity = (20 - Math.log10(score)) / 180; |
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17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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changeset
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92 }} |
| 3 | 93 """ |
| 94 } | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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changeset
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95 |
| 3 | 96 BREWER_COLOUR_IDX = 0 |
| 97 BREWER_COLOUR_SCHEMES = [ | |
| 98 (166, 206, 227), | |
| 99 (31, 120, 180), | |
| 100 (178, 223, 138), | |
| 101 (51, 160, 44), | |
| 102 (251, 154, 153), | |
| 103 (227, 26, 28), | |
| 104 (253, 191, 111), | |
| 105 (255, 127, 0), | |
| 106 (202, 178, 214), | |
| 107 (106, 61, 154), | |
| 108 (255, 255, 153), | |
| 109 (177, 89, 40), | |
| 110 (228, 26, 28), | |
| 111 (55, 126, 184), | |
| 112 (77, 175, 74), | |
| 113 (152, 78, 163), | |
| 114 (255, 127, 0), | |
| 115 ] | |
| 116 | |
| 117 BREWER_DIVERGING_PALLETES = { | |
| 118 'BrBg': ("#543005", "#003c30"), | |
| 119 'PiYg': ("#8e0152", "#276419"), | |
| 120 'PRGn': ("#40004b", "#00441b"), | |
| 121 'PuOr': ("#7f3b08", "#2d004b"), | |
| 122 'RdBu': ("#67001f", "#053061"), | |
| 123 'RdGy': ("#67001f", "#1a1a1a"), | |
| 124 'RdYlBu': ("#a50026", "#313695"), | |
| 125 'RdYlGn': ("#a50026", "#006837"), | |
| 126 'Spectral': ("#9e0142", "#5e4fa2"), | |
| 127 } | |
| 128 | |
| 129 def __init__(self): | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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130 self.brewer_colour_idx = 0 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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131 |
| 3 | 132 def rgb_from_hex(self, hexstr): |
| 133 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back | |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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134 return struct.unpack('BBB', binascii.unhexlify(hexstr)) |
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1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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135 |
| 3 | 136 def min_max_gff(self, gff_file): |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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137 min_val = None |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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138 max_val = None |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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139 with open(gff_file, 'r') as handle: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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140 for line in handle: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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141 try: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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142 value = float(line.split('\t')[5]) |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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143 min_val = min(value, (min_val or value)) |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
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144 max_val = max(value, (max_val or value)) |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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145 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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146 if value < min_val: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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147 min_val = value |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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148 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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149 if value > max_val: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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150 max_val = value |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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151 except Exception: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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152 pass |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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153 return min_val, max_val |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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154 |
| 3 | 155 def hex_from_rgb(self, r, g, b): |
| 156 return '#%02x%02x%02x' % (r, g, b) | |
| 157 | |
| 158 def _get_colours(self): | |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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159 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)] |
| 3 | 160 self.brewer_colour_idx += 1 |
| 161 return r, g, b | |
| 162 | |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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163 def parse_menus(self, track): |
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db5fe5a3176a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
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164 trackConfig = {'menuTemplate': [{}, {}, {}, {}]} |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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165 |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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166 if 'menu' in track['menus']: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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167 menu_list = [track['menus']['menu']] |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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168 if isinstance(track['menus']['menu'], list): |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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169 menu_list = track['menus']['menu'] |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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170 |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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171 for m in menu_list: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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172 tpl = { |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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173 'action': m['action'], |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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174 'label': m.get('label', '{name}'), |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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175 'iconClass': m.get('iconClass', 'dijitIconBookmark'), |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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176 } |
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177 if 'url' in m: |
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178 tpl['url'] = m['url'] |
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179 if 'content' in m: |
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180 tpl['content'] = m['content'] |
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181 if 'title' in m: |
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182 tpl['title'] = m['title'] |
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183 |
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184 trackConfig['menuTemplate'].append(tpl) |
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185 |
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186 return trackConfig |
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187 |
| 3 | 188 def parse_colours(self, track, trackFormat, gff3=None): |
| 189 # Wiggle tracks have a bicolor pallete | |
| 190 trackConfig = {'style': {}} | |
| 191 if trackFormat == 'wiggle': | |
| 192 | |
| 193 trackConfig['style']['pos_color'] = track['wiggle']['color_pos'] | |
| 194 trackConfig['style']['neg_color'] = track['wiggle']['color_neg'] | |
| 195 | |
| 196 if trackConfig['style']['pos_color'] == '__auto__': | |
| 197 trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours()) | |
| 198 trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours()) | |
| 199 | |
| 200 # Wiggle tracks can change colour at a specified place | |
| 201 bc_pivot = track['wiggle']['bicolor_pivot'] | |
| 202 if bc_pivot not in ('mean', 'zero'): | |
| 203 # The values are either one of those two strings | |
| 204 # or a number | |
| 205 bc_pivot = float(bc_pivot) | |
| 206 trackConfig['bicolor_pivot'] = bc_pivot | |
| 207 elif 'scaling' in track: | |
| 208 if track['scaling']['method'] == 'ignore': | |
| 209 if track['scaling']['scheme']['color'] != '__auto__': | |
| 210 trackConfig['style']['color'] = track['scaling']['scheme']['color'] | |
| 211 else: | |
| 212 trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours()) | |
| 213 else: | |
| 214 # Scored method | |
| 215 algo = track['scaling']['algo'] | |
| 216 # linear, logarithmic, blast | |
| 217 scales = track['scaling']['scales'] | |
| 218 # type __auto__, manual (min, max) | |
| 219 scheme = track['scaling']['scheme'] | |
| 220 # scheme -> (type (opacity), color) | |
| 221 # ================================== | |
| 222 # GENE CALLS OR BLAST | |
| 223 # ================================== | |
| 224 if trackFormat == 'blast': | |
| 225 red, green, blue = self._get_colours() | |
| 226 color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{ | |
| 227 'score': "feature._parent.get('score')", | |
| 228 'opacity': self.OPACITY_MATH['blast'], | |
| 229 'red': red, | |
| 230 'green': green, | |
| 231 'blue': blue, | |
| 232 }) | |
| 233 trackConfig['style']['color'] = color_function.replace('\n', '') | |
| 234 elif trackFormat == 'gene_calls': | |
| 235 # Default values, based on GFF3 spec | |
| 236 min_val = 0 | |
| 237 max_val = 1000 | |
| 238 # Get min/max and build a scoring function since JBrowse doesn't | |
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239 if scales['type'] == 'automatic' or scales['type'] == '__auto__': |
| 3 | 240 min_val, max_val = self.min_max_gff(gff3) |
| 241 else: | |
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242 min_val = scales.get('min', 0) |
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243 max_val = scales.get('max', 1000) |
| 3 | 244 |
| 245 if scheme['color'] == '__auto__': | |
| 246 user_color = 'undefined' | |
| 247 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) | |
| 248 elif scheme['color'].startswith('#'): | |
| 249 user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:])) | |
| 250 auto_color = 'undefined' | |
| 251 else: | |
| 252 user_color = 'undefined' | |
| 253 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) | |
| 254 | |
| 255 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{ | |
|
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256 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val, 'min': min_val}), |
| 3 | 257 'user_spec_color': user_color, |
| 258 'auto_gen_color': auto_color, | |
| 259 }) | |
| 260 | |
| 261 trackConfig['style']['color'] = color_function.replace('\n', '') | |
| 262 return trackConfig | |
| 263 | |
| 264 | |
| 265 def etree_to_dict(t): | |
| 266 d = {t.tag: {} if t.attrib else None} | |
| 267 children = list(t) | |
| 268 if children: | |
| 269 dd = defaultdict(list) | |
| 270 for dc in map(etree_to_dict, children): | |
|
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271 for k, v in dc.items(): |
| 3 | 272 dd[k].append(v) |
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273 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}} |
| 3 | 274 if t.attrib: |
|
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275 d[t.tag].update(('@' + k, v) for k, v in t.attrib.items()) |
| 3 | 276 if t.text: |
| 277 text = t.text.strip() | |
| 278 if children or t.attrib: | |
| 279 if text: | |
|
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280 d[t.tag]['#text'] = text |
| 3 | 281 else: |
| 282 d[t.tag] = text | |
| 283 return d | |
| 284 | |
| 285 | |
| 286 # score comes from feature._parent.get('score') or feature.get('score') | |
| 287 | |
| 288 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__)) | |
| 289 | |
| 290 | |
|
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291 def metadata_from_node(node): |
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292 metadata = {} |
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293 try: |
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294 if len(node.findall('dataset')) != 1: |
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295 # exit early |
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296 return metadata |
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297 except Exception: |
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298 return {} |
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299 |
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300 for (key, value) in node.findall('dataset')[0].attrib.items(): |
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301 metadata['dataset_%s' % key] = value |
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302 |
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303 for (key, value) in node.findall('history')[0].attrib.items(): |
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304 metadata['history_%s' % key] = value |
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305 |
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306 for (key, value) in node.findall('metadata')[0].attrib.items(): |
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307 metadata['metadata_%s' % key] = value |
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308 |
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309 for (key, value) in node.findall('tool')[0].attrib.items(): |
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310 metadata['tool_%s' % key] = value |
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311 |
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312 # Additional Mappings applied: |
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313 metadata['dataset_edam_format'] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format(metadata['dataset_edam_format'], metadata['dataset_file_ext']) |
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314 metadata['history_user_email'] = '<a href="mailto:{0}">{0}</a>'.format(metadata['history_user_email']) |
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315 metadata['history_display_name'] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format( |
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316 galaxy=GALAXY_INFRASTRUCTURE_URL, |
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317 encoded_hist_id=metadata['history_id'], |
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318 hist_name=metadata['history_display_name'] |
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319 ) |
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320 metadata['tool_tool'] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format( |
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321 galaxy=GALAXY_INFRASTRUCTURE_URL, |
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322 encoded_id=metadata['dataset_id'], |
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323 tool_id=metadata['tool_tool_id'], |
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324 tool_version=metadata['tool_tool_version'], |
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325 ) |
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326 return metadata |
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327 |
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328 |
| 3 | 329 class JbrowseConnector(object): |
| 330 | |
| 331 def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1): | |
| 332 self.TN_TABLE = { | |
| 333 'gff3': '--gff', | |
| 334 'gff': '--gff', | |
| 335 'bed': '--bed', | |
| 336 'genbank': '--gbk', | |
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337 } |
| 3 | 338 |
| 339 self.cs = ColorScaling() | |
| 340 self.jbrowse = jbrowse | |
| 341 self.outdir = outdir | |
| 342 self.genome_paths = genomes | |
| 343 self.standalone = standalone | |
| 344 self.gencode = gencode | |
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345 self.tracksToIndex = [] |
| 3 | 346 |
| 347 if standalone: | |
| 348 self.clone_jbrowse(self.jbrowse, self.outdir) | |
| 349 else: | |
| 350 try: | |
| 351 os.makedirs(self.outdir) | |
| 352 except OSError: | |
| 353 # Ignore if the folder exists | |
| 354 pass | |
| 355 | |
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356 try: |
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357 os.makedirs(os.path.join(self.outdir, 'data', 'raw')) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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358 except OSError: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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359 # Ignore if the folder exists |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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360 pass |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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361 |
| 3 | 362 self.process_genomes() |
| 363 self.update_gencode() | |
| 364 | |
| 365 def update_gencode(self): | |
| 366 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)] | |
| 367 trackList = os.path.join(self.outdir, 'data', 'trackList.json') | |
| 368 with open(trackList, 'r') as handle: | |
| 369 trackListData = json.load(handle) | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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370 |
| 3 | 371 trackListData['tracks'][0].update({ |
| 372 'codonStarts': table.start_codons, | |
| 373 'codonStops': table.stop_codons, | |
| 374 'codonTable': table.forward_table, | |
| 375 }) | |
| 376 | |
| 377 with open(trackList, 'w') as handle: | |
| 378 json.dump(trackListData, handle, indent=2) | |
| 379 | |
| 380 def subprocess_check_call(self, command): | |
| 381 log.debug('cd %s && %s', self.outdir, ' '.join(command)) | |
| 382 subprocess.check_call(command, cwd=self.outdir) | |
| 383 | |
| 384 def _jbrowse_bin(self, command): | |
| 385 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command)) | |
| 386 | |
| 387 def process_genomes(self): | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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388 for genome_node in self.genome_paths: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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389 # TODO: Waiting on https://github.com/GMOD/jbrowse/pull/884 |
| 3 | 390 self.subprocess_check_call([ |
| 391 'perl', self._jbrowse_bin('prepare-refseqs.pl'), | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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392 '--fasta', genome_node['path']]) |
| 3 | 393 |
|
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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394 def generate_names(self): |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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395 # Generate names |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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396 args = [ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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397 'perl', self._jbrowse_bin('generate-names.pl'), |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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398 '--hashBits', '16' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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399 ] |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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400 |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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401 tracks = ','.join(self.tracksToIndex) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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402 if tracks: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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403 args += ['--tracks', tracks] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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404 else: |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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405 # No tracks to index, index only the refseq |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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406 args += ['--tracks', 'DNA'] |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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407 |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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408 self.subprocess_check_call(args) |
| 3 | 409 |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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410 def _add_json(self, json_data): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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411 cmd = [ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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412 'perl', self._jbrowse_bin('add-json.pl'), |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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413 json.dumps(json_data), |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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414 os.path.join('data', 'trackList.json') |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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415 ] |
| 3 | 416 self.subprocess_check_call(cmd) |
|
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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417 |
| 3 | 418 def _add_track_json(self, json_data): |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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419 if len(json_data) == 0: |
| 3 | 420 return |
| 421 | |
| 422 tmp = tempfile.NamedTemporaryFile(delete=False) | |
| 423 tmp.write(json.dumps(json_data)) | |
| 424 tmp.close() | |
| 425 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name, | |
| 426 os.path.join('data', 'trackList.json')] | |
| 427 self.subprocess_check_call(cmd) | |
| 428 os.unlink(tmp.name) | |
| 429 | |
| 430 def _blastxml_to_gff3(self, xml, min_gap=10): | |
| 431 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False) | |
| 432 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'), | |
| 433 '--trim', '--trim_end', '--min_gap', str(min_gap), xml] | |
| 434 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name) | |
| 435 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased) | |
| 436 gff3_unrebased.close() | |
| 437 return gff3_unrebased.name | |
| 438 | |
| 439 def add_blastxml(self, data, trackData, blastOpts, **kwargs): | |
| 440 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap']) | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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441 |
|
5
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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442 if 'parent' in blastOpts and blastOpts['parent'] != 'None': |
| 3 | 443 gff3_rebased = tempfile.NamedTemporaryFile(delete=False) |
| 444 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')] | |
| 445 if blastOpts.get('protein', 'false') == 'true': | |
| 446 cmd.append('--protein2dna') | |
| 447 cmd.extend([os.path.realpath(blastOpts['parent']), gff3]) | |
| 448 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name) | |
| 449 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased) | |
| 450 gff3_rebased.close() | |
| 451 | |
| 452 # Replace original gff3 file | |
| 453 shutil.copy(gff3_rebased.name, gff3) | |
| 454 os.unlink(gff3_rebased.name) | |
| 455 | |
| 456 config = { | |
| 457 'glyph': 'JBrowse/View/FeatureGlyph/Segments', | |
| 458 "category": trackData['category'], | |
| 459 } | |
| 460 | |
| 461 clientConfig = trackData['style'] | |
| 462 | |
| 463 cmd = ['perl', self._jbrowse_bin('flatfile-to-json.pl'), | |
| 464 '--gff', gff3, | |
| 465 '--trackLabel', trackData['label'], | |
| 466 '--key', trackData['key'], | |
| 467 '--clientConfig', json.dumps(clientConfig), | |
| 468 '--config', json.dumps(config), | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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469 '--trackType', 'BlastView/View/Track/CanvasFeatures' |
| 3 | 470 ] |
| 471 | |
|
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472 # className in --clientConfig is ignored, it needs to be set with --className |
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473 if 'className' in trackData['style']: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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474 cmd += ['--className', trackData['style']['className']] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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475 |
| 3 | 476 self.subprocess_check_call(cmd) |
| 477 os.unlink(gff3) | |
| 478 | |
|
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479 if blastOpts.get('index', 'false') == 'true': |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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480 self.tracksToIndex.append("%s" % trackData['label']) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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481 |
| 3 | 482 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): |
| 483 dest = os.path.join('data', 'raw', trackData['label'] + '.bw') | |
|
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484 cmd = ['ln', '-s', data, dest] |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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485 self.subprocess_check_call(cmd) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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486 |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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487 url = os.path.join('raw', trackData['label'] + '.bw') |
| 3 | 488 trackData.update({ |
|
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489 "urlTemplate": url, |
| 3 | 490 "storeClass": "JBrowse/Store/SeqFeature/BigWig", |
| 491 "type": "JBrowse/View/Track/Wiggle/Density", | |
| 492 }) | |
| 493 | |
| 494 trackData['type'] = wiggleOpts['type'] | |
| 495 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False | |
| 496 | |
| 497 if 'min' in wiggleOpts and 'max' in wiggleOpts: | |
| 498 trackData['min_score'] = wiggleOpts['min'] | |
| 499 trackData['max_score'] = wiggleOpts['max'] | |
| 500 else: | |
| 501 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local') | |
| 502 | |
|
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503 trackData['scale'] = wiggleOpts['scale'] |
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504 |
| 3 | 505 self._add_track_json(trackData) |
| 506 | |
| 507 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): | |
| 508 dest = os.path.join('data', 'raw', trackData['label'] + '.bam') | |
| 509 cmd = ['ln', '-s', os.path.realpath(data), dest] | |
|
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510 self.subprocess_check_call(cmd) |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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511 |
| 3 | 512 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai'] |
| 513 self.subprocess_check_call(cmd) | |
| 514 | |
|
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515 url = os.path.join('raw', trackData['label'] + '.bam') |
| 3 | 516 trackData.update({ |
|
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517 "urlTemplate": url, |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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518 "type": "JBrowse/View/Track/Alignments2", |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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519 "storeClass": "JBrowse/Store/SeqFeature/BAM", |
| 3 | 520 }) |
| 521 | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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522 # Apollo will only switch to the (prettier) 'bam-read' className if it's not set explicitly in the track config |
|
18be2d72fdee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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523 # So remove the default 'feature' value for these bam tracks |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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524 if 'className' in trackData['style'] and trackData['style']['className'] == 'feature': |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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525 del trackData['style']['className'] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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526 |
| 3 | 527 self._add_track_json(trackData) |
| 528 | |
| 529 if bamOpts.get('auto_snp', 'false') == 'true': | |
| 530 trackData2 = copy.copy(trackData) | |
| 531 trackData2.update({ | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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diff
changeset
|
532 "type": "JBrowse/View/Track/SNPCoverage", |
| 3 | 533 "key": trackData['key'] + " - SNPs/Coverage", |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff
changeset
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534 "label": trackData['label'] + "_autosnp", |
| 3 | 535 }) |
| 536 self._add_track_json(trackData2) | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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diff
changeset
|
537 |
| 3 | 538 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs): |
| 539 dest = os.path.join('data', 'raw', trackData['label'] + '.vcf') | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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diff
changeset
|
540 # ln? |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
541 cmd = ['ln', '-s', data, dest] |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
542 self.subprocess_check_call(cmd) |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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diff
changeset
|
543 cmd = ['bgzip', dest] |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
544 self.subprocess_check_call(cmd) |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
545 cmd = ['tabix', '-p', 'vcf', dest + '.gz'] |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
546 self.subprocess_check_call(cmd) |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
547 |
|
12
db5fe5a3176a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents:
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diff
changeset
|
548 url = os.path.join('raw', trackData['label'] + '.vcf') |
| 3 | 549 trackData.update({ |
|
12
db5fe5a3176a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
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diff
changeset
|
550 "urlTemplate": url, |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
551 "type": "JBrowse/View/Track/HTMLVariants", |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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changeset
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552 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix", |
| 3 | 553 }) |
| 554 self._add_track_json(trackData) | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
555 |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
|
556 def add_features(self, data, format, trackData, gffOpts, metadata=None, **kwargs): |
| 3 | 557 cmd = [ |
| 558 'perl', self._jbrowse_bin('flatfile-to-json.pl'), | |
| 559 self.TN_TABLE.get(format, 'gff'), | |
| 560 data, | |
| 561 '--trackLabel', trackData['label'], | |
| 562 '--key', trackData['key'] | |
| 563 ] | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
564 |
|
13
69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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diff
changeset
|
565 # className in --clientConfig is ignored, it needs to be set with --className |
|
69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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diff
changeset
|
566 if 'className' in trackData['style']: |
|
69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
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diff
changeset
|
567 cmd += ['--className', trackData['style']['className']] |
|
69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents:
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diff
changeset
|
568 |
| 3 | 569 config = copy.copy(trackData) |
| 570 clientConfig = trackData['style'] | |
| 571 del config['style'] | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
572 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff
changeset
|
573 if 'match' in gffOpts: |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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diff
changeset
|
574 config['glyph'] = 'JBrowse/View/FeatureGlyph/Segments' |
| 3 | 575 cmd += ['--type', gffOpts['match']] |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
576 |
| 3 | 577 cmd += ['--clientConfig', json.dumps(clientConfig), |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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diff
changeset
|
578 ] |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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diff
changeset
|
579 |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
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diff
changeset
|
580 trackType = 'JBrowse/View/Track/CanvasFeatures' |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
581 if 'trackType' in gffOpts: |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
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diff
changeset
|
582 trackType = gffOpts['trackType'] |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
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diff
changeset
|
583 |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
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diff
changeset
|
584 if trackType == 'JBrowse/View/Track/CanvasFeatures': |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
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diff
changeset
|
585 if 'transcriptType' in gffOpts and gffOpts['transcriptType']: |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
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diff
changeset
|
586 config['transcriptType'] = gffOpts['transcriptType'] |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
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diff
changeset
|
587 if 'subParts' in gffOpts and gffOpts['subParts']: |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
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diff
changeset
|
588 config['subParts'] = gffOpts['subParts'] |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
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diff
changeset
|
589 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']: |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
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diff
changeset
|
590 config['impliedUTRs'] = gffOpts['impliedUTRs'] |
|
13
69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents:
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diff
changeset
|
591 elif trackType == 'JBrowse/View/Track/HTMLFeatures': |
|
69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents:
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diff
changeset
|
592 if 'transcriptType' in gffOpts and gffOpts['transcriptType']: |
|
69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents:
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diff
changeset
|
593 cmd += ['--type', gffOpts['transcriptType']] |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
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diff
changeset
|
594 |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
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diff
changeset
|
595 cmd += [ |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
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diff
changeset
|
596 '--trackType', gffOpts['trackType'] |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
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diff
changeset
|
597 ] |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
598 |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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diff
changeset
|
599 if metadata: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
|
600 config.update({'metadata': metadata}) |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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diff
changeset
|
601 cmd.extend(['--config', json.dumps(config)]) |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
602 |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
603 self.subprocess_check_call(cmd) |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
604 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
605 if gffOpts.get('index', 'false') == 'true': |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
606 self.tracksToIndex.append("%s" % trackData['label']) |
| 3 | 607 |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
|
608 def add_rest(self, url, trackData): |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
|
609 data = { |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
|
610 "label": trackData['label'], |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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diff
changeset
|
611 "key": trackData['key'], |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
|
612 "category": trackData['category'], |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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diff
changeset
|
613 "type": "JBrowse/View/Track/HTMLFeatures", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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diff
changeset
|
614 "storeClass": "JBrowse/Store/SeqFeature/REST", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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diff
changeset
|
615 "baseUrl": url, |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
|
616 "query": { |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
|
617 "organism": "tyrannosaurus" |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
|
618 } |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
619 } |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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diff
changeset
|
620 self._add_track_json(data) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
621 |
| 3 | 622 def process_annotations(self, track): |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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diff
changeset
|
623 category = track['category'].replace('__pd__date__pd__', TODAY) |
| 3 | 624 outputTrackConfig = { |
| 625 'style': { | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
626 'label': track['style'].get('label', 'description'), |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
627 'className': track['style'].get('className', 'feature'), |
| 3 | 628 'description': track['style'].get('description', ''), |
| 629 }, | |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
630 'overridePlugins': track['style'].get('overridePlugins', False) == 'True', |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
631 'overrideDraggable': track['style'].get('overrideDraggable', False) == 'True', |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
632 'maxHeight': track['style'].get('maxHeight', '600'), |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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633 'category': category, |
| 3 | 634 } |
| 635 | |
|
16
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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636 mapped_chars = { |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
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637 '>': '__gt__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
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638 '<': '__lt__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
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639 "'": '__sq__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
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640 '"': '__dq__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
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641 '[': '__ob__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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642 ']': '__cb__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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643 '{': '__oc__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
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644 '}': '__cc__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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645 '@': '__at__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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646 '#': '__pd__' |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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647 } |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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|
648 |
|
17
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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649 for i, (dataset_path, dataset_ext, track_human_label, extra_metadata) in enumerate(track['trackfiles']): |
|
16
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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650 # Unsanitize labels (element_identifiers are always sanitized by Galaxy) |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
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651 for key, value in mapped_chars.items(): |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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652 track_human_label = track_human_label.replace(value, key) |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
|
653 |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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654 log.info('Processing %s / %s', category, track_human_label) |
| 3 | 655 outputTrackConfig['key'] = track_human_label |
|
17
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
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656 # We add extra data to hash for the case of REST + SPARQL. |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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657 try: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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658 rest_url = track['conf']['options']['url'] |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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659 except KeyError: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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660 rest_url = '' |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
|
661 |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
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662 # I chose to use track['category'] instead of 'category' here. This |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
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663 # is intentional. This way re-running the tool on a different date |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
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664 # will not generate different hashes and make comparison of outputs |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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665 # much simpler. |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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666 hashData = [dataset_path, track_human_label, track['category'], rest_url] |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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667 hashData = '|'.join(hashData).encode('utf-8') |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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668 outputTrackConfig['label'] = hashlib.md5(hashData).hexdigest() + '_%s' % i |
| 3 | 669 |
| 670 # Colour parsing is complex due to different track types having | |
| 671 # different colour options. | |
| 672 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path) | |
| 673 # This used to be done with a dict.update() call, however that wiped out any previous style settings... | |
| 674 for key in colourOptions: | |
| 675 if key == 'style': | |
| 676 for subkey in colourOptions['style']: | |
| 677 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey] | |
| 678 else: | |
| 679 outputTrackConfig[key] = colourOptions[key] | |
| 680 | |
|
12
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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681 if 'menus' in track['conf']['options']: |
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db5fe5a3176a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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682 menus = self.cs.parse_menus(track['conf']['options']) |
|
db5fe5a3176a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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683 outputTrackConfig.update(menus) |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff
changeset
|
684 |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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685 # import pprint; pprint.pprint(track) |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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|
686 # import sys; sys.exit() |
| 3 | 687 if dataset_ext in ('gff', 'gff3', 'bed'): |
| 688 self.add_features(dataset_path, dataset_ext, outputTrackConfig, | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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689 track['conf']['options']['gff'], metadata=extra_metadata) |
| 3 | 690 elif dataset_ext == 'bigwig': |
| 691 self.add_bigwig(dataset_path, outputTrackConfig, | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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692 track['conf']['options']['wiggle'], metadata=extra_metadata) |
| 3 | 693 elif dataset_ext == 'bam': |
| 694 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index'] | |
| 695 if not isinstance(real_indexes, list): | |
| 696 # <bam_indices> | |
| 697 # <bam_index>/path/to/a.bam.bai</bam_index> | |
| 698 # </bam_indices> | |
| 699 # | |
| 700 # The above will result in the 'bam_index' key containing a | |
| 701 # string. If there are two or more indices, the container | |
| 702 # becomes a list. Fun! | |
| 703 real_indexes = [real_indexes] | |
| 704 | |
| 705 self.add_bam(dataset_path, outputTrackConfig, | |
| 706 track['conf']['options']['pileup'], | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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|
707 bam_index=real_indexes[i], metadata=extra_metadata) |
| 3 | 708 elif dataset_ext == 'blastxml': |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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|
709 self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'], metadata=extra_metadata) |
| 3 | 710 elif dataset_ext == 'vcf': |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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|
711 self.add_vcf(dataset_path, outputTrackConfig, metadata=extra_metadata) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
|
712 elif dataset_ext == 'rest': |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
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|
713 self.add_rest(track['conf']['options']['url'], outputTrackConfig, metadata=extra_metadata) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents:
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diff
changeset
|
714 else: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents:
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diff
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|
715 log.warn('Do not know how to handle %s', dataset_ext) |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
716 |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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changeset
|
717 # Return non-human label for use in other fields |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
718 yield outputTrackConfig['label'] |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
719 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
720 def add_final_data(self, data): |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
721 viz_data = {} |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
722 if len(data['visibility']['default_on']) > 0: |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
723 viz_data['defaultTracks'] = ','.join(data['visibility']['default_on']) |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
724 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
725 if len(data['visibility']['always']) > 0: |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
726 viz_data['alwaysOnTracks'] = ','.join(data['visibility']['always']) |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
727 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
728 if len(data['visibility']['force']) > 0: |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
729 viz_data['forceTracks'] = ','.join(data['visibility']['force']) |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
730 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
731 generalData = {} |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
732 if data['general']['aboutDescription'] is not None: |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
733 generalData['aboutThisBrowser'] = {'description': data['general']['aboutDescription'].strip()} |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
734 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
735 generalData['view'] = { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
736 'trackPadding': data['general']['trackPadding'] |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
737 } |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
738 generalData['shareLink'] = (data['general']['shareLink'] == 'true') |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
739 generalData['show_tracklist'] = (data['general']['show_tracklist'] == 'true') |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
740 generalData['show_nav'] = (data['general']['show_nav'] == 'true') |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
741 generalData['show_overview'] = (data['general']['show_overview'] == 'true') |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
742 generalData['show_menu'] = (data['general']['show_menu'] == 'true') |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
743 generalData['hideGenomeOptions'] = (data['general']['hideGenomeOptions'] == 'true') |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
744 generalData['plugins'] = data['plugins'] |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
745 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
746 viz_data.update(generalData) |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
747 self._add_json(viz_data) |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
748 |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
749 if 'GCContent' in data['plugins_python']: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
750 self._add_track_json({ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
751 "storeClass": "JBrowse/Store/SeqFeature/SequenceChunks", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
752 "type": "GCContent/View/Track/GCContentXY", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
753 "label": "GCContentXY", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
754 "urlTemplate": "seq/{refseq_dirpath}/{refseq}-", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
755 "bicolor_pivot": 0.5 |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
756 # TODO: Expose params for everyone. |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
757 }) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
758 |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
759 if 'ComboTrackSelector' in data['plugins_python']: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
760 with open(os.path.join(self.outdir, 'data', 'trackList.json'), 'r') as handle: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
761 trackListJson = json.load(handle) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
762 trackListJson.update({ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
763 "trackSelector": { |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
764 "renameFacets": { |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
765 "tool_tool": "Tool ID", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
766 "tool_tool_id": "Tool ID", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
767 "tool_tool_version": "Tool Version", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
768 "dataset_edam_format": "EDAM", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
769 "dataset_size": "Size", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
770 "history_display_name": "History Name", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
771 "history_user_email": "Owner", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
772 "metadata_dbkey": "Dbkey", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
773 }, |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
774 "displayColumns": [ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
775 "key", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
776 "tool_tool", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
777 "tool_tool_version", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
778 "dataset_edam_format", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
779 "dataset_size", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
780 "history_display_name", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
781 "history_user_email", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
782 "metadata_dbkey", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
783 ], |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
784 "type": "Faceted", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
785 "title": ["Galaxy Metadata"], |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
786 "escapeHTMLInData": False |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
787 }, |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
788 "trackMetadata": { |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
789 "indexFacets": [ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
790 "category", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
791 "key", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
792 "tool_tool_id", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
793 "tool_tool_version", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
794 "dataset_edam_format", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
795 "history_user_email", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
796 "history_display_name" |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
797 ] |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
798 } |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
799 }) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
800 with open(os.path.join(self.outdir, 'data', 'trackList2.json'), 'w') as handle: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
801 json.dump(trackListJson, handle) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
802 |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
803 def clone_jbrowse(self, jbrowse_dir, destination): |
| 3 | 804 """Clone a JBrowse directory into a destination directory. |
| 805 """ | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
806 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
807 # unlike copytree |
| 3 | 808 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination] |
| 809 log.debug(' '.join(cmd)) | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
810 subprocess.check_call(cmd) |
| 3 | 811 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')] |
| 812 log.debug(' '.join(cmd)) | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
813 subprocess.check_call(cmd) |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
814 |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
815 # http://unix.stackexchange.com/a/38691/22785 |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
816 # JBrowse releases come with some broken symlinks |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
817 cmd = ['find', destination, '-type', 'l', '-xtype', 'l'] |
| 3 | 818 log.debug(' '.join(cmd)) |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
819 symlinks = subprocess.check_output(cmd) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
820 for i in symlinks: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
821 try: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
822 os.unlink(i) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
823 except OSError: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
824 pass |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
825 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
826 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
827 if __name__ == '__main__': |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
828 parser = argparse.ArgumentParser(description="", epilog="") |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
829 parser.add_argument('xml', type=argparse.FileType('r'), help='Track Configuration') |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
830 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
831 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release') |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
832 parser.add_argument('--outdir', help='Output directory', default='out') |
| 3 | 833 parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true') |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
834 parser.add_argument('--version', '-V', action='version', version="%(prog)s 0.7.0") |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
835 args = parser.parse_args() |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
836 |
| 3 | 837 tree = ET.parse(args.xml.name) |
| 838 root = tree.getroot() | |
| 839 | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
840 jc = JbrowseConnector( |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
841 jbrowse=args.jbrowse, |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
842 outdir=args.outdir, |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
843 genomes=[ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
844 { |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
845 'path': os.path.realpath(x.attrib['path']), |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
846 'meta': metadata_from_node(x.find('metadata')) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
847 } |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
848 for x in root.findall('metadata/genomes/genome') |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
849 ], |
| 3 | 850 standalone=args.standalone, |
| 851 gencode=root.find('metadata/gencode').text | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
852 ) |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
853 |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
854 extra_data = { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
855 'visibility': { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
856 'default_on': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
857 'default_off': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
858 'force': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
859 'always': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
860 }, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
861 'general': { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
862 'defaultLocation': root.find('metadata/general/defaultLocation').text, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
863 'trackPadding': int(root.find('metadata/general/trackPadding').text), |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
864 'shareLink': root.find('metadata/general/shareLink').text, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
865 'aboutDescription': root.find('metadata/general/aboutDescription').text, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
866 'show_tracklist': root.find('metadata/general/show_tracklist').text, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
867 'show_nav': root.find('metadata/general/show_nav').text, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
868 'show_overview': root.find('metadata/general/show_overview').text, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
869 'show_menu': root.find('metadata/general/show_menu').text, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
870 'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text, |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
871 }, |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
872 'plugins': [{ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
873 'location': 'https://cdn.rawgit.com/TAMU-CPT/blastview/97572a21b7f011c2b4d9a0b5af40e292d694cbef/', |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
874 'name': 'BlastView' |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
875 }], |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
876 'plugins_python': ['BlastView'], |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
877 } |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
878 |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
879 plugins = root.find('plugins').attrib |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
880 if plugins['GCContent'] == 'True': |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
881 extra_data['plugins_python'].append('GCContent') |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
882 extra_data['plugins'].append({ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
883 'location': 'https://cdn.rawgit.com/elsiklab/gccontent/5c8b0582ecebf9edf684c76af8075fb3d30ec3fa/', |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
884 'name': 'GCContent' |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
885 }) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
886 |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
887 if plugins['Bookmarks'] == 'True': |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
888 extra_data['plugins'].append({ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
889 'location': 'https://cdn.rawgit.com/TAMU-CPT/bookmarks-jbrowse/5242694120274c86e1ccd5cb0e5e943e78f82393/', |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
890 'name': 'Bookmarks' |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
891 }) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
892 |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
893 if plugins['ComboTrackSelector'] == 'True': |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
894 extra_data['plugins_python'].append('ComboTrackSelector') |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
895 extra_data['plugins'].append({ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
896 'location': 'https://cdn.rawgit.com/Arabidopsis-Information-Portal/ComboTrackSelector/52403928d5ccbe2e3a86b0fa5eb8e61c0f2e2f57', |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
897 'icon': 'https://galaxyproject.org/images/logos/galaxy-icon-square.png', |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
898 'name': 'ComboTrackSelector' |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
899 }) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
900 |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
901 if plugins['theme'] == 'Minimalist': |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
902 extra_data['plugins'].append({ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
903 'location': 'https://cdn.rawgit.com/erasche/jbrowse-minimalist-theme/d698718442da306cf87f033c72ddb745f3077775/', |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
904 'name': 'MinimalistTheme' |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
905 }) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
906 elif plugins['theme'] == 'Dark': |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
907 extra_data['plugins'].append({ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
908 'location': 'https://cdn.rawgit.com/erasche/jbrowse-dark-theme/689eceb7e33bbc1b9b15518d45a5a79b2e5d0a26/', |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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909 'name': 'DarkTheme' |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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910 }) |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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911 |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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912 GALAXY_INFRASTRUCTURE_URL = root.find('metadata/galaxyUrl').text |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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913 # Sometimes this comes as `localhost` without a protocol |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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914 if not GALAXY_INFRASTRUCTURE_URL.startswith('http'): |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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915 # so we'll prepend `http://` and hope for the best. Requests *should* |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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916 # be GET and not POST so it should redirect OK |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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917 GALAXY_INFRASTRUCTURE_URL = 'http://' + GALAXY_INFRASTRUCTURE_URL |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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918 |
| 3 | 919 for track in root.findall('tracks/track'): |
| 920 track_conf = {} | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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921 track_conf['trackfiles'] = [] |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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922 |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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923 for x in track.findall('files/trackFile'): |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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924 metadata = metadata_from_node(x.find('metadata')) |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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925 |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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926 track_conf['trackfiles'].append(( |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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927 os.path.realpath(x.attrib['path']), |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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928 x.attrib['ext'], |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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929 x.attrib['label'], |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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930 metadata |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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931 )) |
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1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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932 |
| 3 | 933 track_conf['category'] = track.attrib['cat'] |
| 934 track_conf['format'] = track.attrib['format'] | |
| 935 try: | |
| 936 # Only pertains to gff3 + blastxml. TODO? | |
| 937 track_conf['style'] = {t.tag: t.text for t in track.find('options/style')} | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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938 except TypeError as te: |
| 3 | 939 track_conf['style'] = {} |
| 940 pass | |
| 941 track_conf['conf'] = etree_to_dict(track.find('options')) | |
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5
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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942 keys = jc.process_annotations(track_conf) |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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943 |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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944 for key in keys: |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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945 extra_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key) |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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946 |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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947 jc.add_final_data(extra_data) |
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20
558d652cd681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75a0a1c7b26cac156f76e8266a0e2e3d81be7f02
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948 jc.generate_names() |